Index (Simbrain API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

ABSOLUTE - Static variable in class org.simbrain.network.neuron_update_rules.DecayRule: Absolute.
absoluteMovementType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
AbstractConnectionPanel - Class in org.simbrain.network.gui.dialogs.connect: AbstractConnectionPanel is the abstract panel for all specific panels for setting connection properties.
AbstractConnectionPanel() - Constructor for class org.simbrain.network.gui.dialogs.connect.AbstractConnectionPanel: Default constructor for connection panels.
AbstractEffectorPanel - Class in org.simbrain.world.odorworld.dialogs: Super class for effector panels.
AbstractEffectorPanel() - Constructor for class org.simbrain.world.odorworld.dialogs.AbstractEffectorPanel
AbstractFilter - Class in org.simbrain.network.gui.filters: Abstract filter, implements both PNodeFilter and Predicate interfaces.
AbstractFilter() - Constructor for class org.simbrain.network.gui.filters.AbstractFilter
AbstractLayoutPanel - Class in org.simbrain.network.gui.dialogs.layout: AbstractLayoutPanel.
AbstractLayoutPanel() - Constructor for class org.simbrain.network.gui.dialogs.layout.AbstractLayoutPanel
AbstractNeuronRulePanel - Class in org.simbrain.network.gui.dialogs.neuron: AbstractNeuronPanel is the parent class for all panels used to set parameters of specific neuron rule types.
AbstractNeuronRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: This method is the default constructor.
AbstractPixelMatrixNode - Class in org.simbrain.world.visionworld.node: Abstract pixel matrix node.
AbstractPixelMatrixNode(PixelMatrix) - Constructor for class org.simbrain.world.visionworld.node.AbstractPixelMatrixNode: Create a new abstract pixel matrix node with the specified pixel matrix.
AbstractSensorMatrix - Class in org.simbrain.world.visionworld.sensormatrix: Abstract sensor matrix.
AbstractSensorMatrix(int, int, Filter) - Constructor for class org.simbrain.world.visionworld.sensormatrix.AbstractSensorMatrix: Create a new abstract sensor matrix with the specified receptive field width and height and specified filter.
AbstractSensorMatrixNode - Class in org.simbrain.world.visionworld.node: Abstract sensor matrix node.
AbstractSensorMatrixNode(SensorMatrix) - Constructor for class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Create a new abstract sensor matrix node with the specified sensor matrix.
AbstractSensorNode - Class in org.simbrain.world.visionworld.node: Abstract sensor node.
AbstractSensorNode(VisionWorld, Sensor) - Constructor for class org.simbrain.world.visionworld.node.AbstractSensorNode: Create a new abstract sensor node with the specified sensor.
AbstractSensorPanel - Class in org.simbrain.world.odorworld.dialogs: Super class for sensor panels.
AbstractSensorPanel() - Constructor for class org.simbrain.world.odorworld.dialogs.AbstractSensorPanel
AbstractSigmoidalRule - Class in org.simbrain.network.neuron_update_rules: An abstract superclass for discrete and continuous time sigmoial squashing function based update rules containing methods and variables common to both.
AbstractSigmoidalRule() - Constructor for class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
AbstractSigmoidalRule(SquashingFunction) - Constructor for class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
AbstractSigmoidalRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: A rule panel containing all the variables and methods which would be shared between rules panels for discrete and continuous time sigmoidal rule panels.
AbstractSigmoidalRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel
AbstractSpikeResponsePanel - Class in org.simbrain.network.gui.dialogs.synapse: AbstractSpikeResponsePanel.
AbstractSpikeResponsePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: This method is the default constructor.
AbstractSynapseRulePanel - Class in org.simbrain.network.gui.dialogs.synapse: AbstractSynapsePanel is the parent class for all panels used to set parameters of specific synapse update rules.
AbstractSynapseRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: This method is the default constructor.
AbstractVisionWorldModel - Class in org.simbrain.world.visionworld: Abstract implementation of VisionWorldModel which provides VisionWorldModelListener management.
AbstractVisionWorldModel() - Constructor for class org.simbrain.world.visionworld.AbstractVisionWorldModel: Create a new abstract vision world model.
accept(PNode) - Method in class org.simbrain.network.gui.filters.AbstractFilter
acceptChildrenOf(PNode) - Method in class org.simbrain.network.gui.filters.AbstractFilter
actionAdded(NetworkUpdateAction) - Method in interface org.simbrain.network.core.NetworkUpdateManager.UpdateManagerListener: An action was added.
actionAdded(UpdateAction) - Method in interface org.simbrain.workspace.updater.UpdateActionManager.UpdateManagerListener: An action was added.
actionListener - Variable in class org.simbrain.util.StandardDialog: Action listener.
actionManager - Variable in class org.simbrain.network.gui.NetworkPanel: Action manager.
actionOrderChanged() - Method in interface org.simbrain.network.core.NetworkUpdateManager.UpdateManagerListener: The action order was changed.
actionOrderChanged() - Method in interface org.simbrain.workspace.updater.UpdateActionManager.UpdateManagerListener: The action order was changed.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.desktop.NetworkScriptMenu.ScriptAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.desktop.RunScriptAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.ApplyLayoutAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.connection.ApplyConnectionAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.connection.ClearSourceNeurons
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.connection.ConnectNeuronsSimpleAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.connection.SetSourceNeurons
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.AlignHorizontalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.AlignVerticalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.CopyAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.CutAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.DeleteAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.EditModeAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.EditRandomizerPropertiesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.PasteAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.RandomizeObjectsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.SetAutoZoomAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.SpaceHorizontalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.SpaceVerticalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.ZeroSelectedObjectsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.edit.ZoomToFitPageAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.GroupAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.modelgroups.AddGroupAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.modelgroups.NewNeuronGroupAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.network.IterateNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.network.RunNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.network.ShowNetworkHierarchyPanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.network.ShowNetworkPreferencesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.network.ShowNetworkUpdaterDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.network.StopNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.neuron.AddNeuronsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.neuron.ClampNeuronsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.neuron.LoadNeuronScriptAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.neuron.NewNeuronAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.neuron.SetNeuronPropertiesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.neuron.ShowPrioritiesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.selection.SelectAllAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.selection.SelectAllNeuronsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.selection.SelectAllWeightsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.selection.SelectIncomingWeightsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.selection.SelectOutgoingWeightsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.SetTextPropertiesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.ShowDebugAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.ShowLayoutDialogAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.ShowTrainerAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.synapse.AddSynapseGroupAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.synapse.ClampWeightsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.synapse.SetSynapsePropertiesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.synapse.ShowAdjustConnectivityDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.synapse.ShowAdjustSynapsesDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.synapse.ShowWeightMatrixAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.synapse.ShowWeightsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.TestInputAction: Initialize and display the test input panel.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.toolbar.ShowClampToolBarAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.toolbar.ShowEditToolBarAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.toolbar.ShowMainToolBarAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.toolbar.ShowRunToolBarAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.actions.UngroupAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.dialogs.text.TextDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.NeuronGroupSelectionPanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.gui.TextEventHandler
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.actions.OpenPlotAction
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.actions.SavePlotAction
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.actions.SavePlotAsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.barchart.BarChartGui
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.piechart.PieChartGui
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.projection.DataPointColoringDialog: Reinitialize current coloring panel.
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.scatterplot.ScatterPlotDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.plot.scatterplot.ScatterPlotGui
actionPerformed(ActionEvent) - Method in class org.simbrain.util.environment.SmellSourcePanel: Acton Listener.
actionPerformed(ActionEvent) - Method in class org.simbrain.util.widgets.ShowHelpAction
actionPerformed(ActionEvent) - Method in class org.simbrain.util.widgets.StopLight
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.chart.NewBarChartAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.chart.NewHistogramAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.chart.NewPieChartAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.chart.NewProjectionPlotAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.chart.NewRasterPlotAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.chart.NewScatterPlotAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.chart.NewTimeSeriesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.ClearWorkspaceAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.GlobalRunAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.GlobalStopAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.GlobalUpdateAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewConsoleAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewDataWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewDisplayWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewDocViewerAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewGameWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewMidiWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewOdorWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewOscWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewReaderWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewThreeDeeWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.NewVisionWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.OpenCouplingListAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.OpenCouplingManagerAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.OpenDataWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.OpenNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.OpenOdorWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.OpenWorkspaceAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.OpenWorkspaceComponentListAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.PropertyTabAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.QuitWorkspaceAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.SaveWorkspaceAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.SaveWorkspaceAsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.ScriptEditorAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.ShowPropertyDialogAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.actions.ShowWorkspaceUpdaterDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.component_actions.CloseAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.component_actions.OpenAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.component_actions.SaveAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.component_actions.SaveAsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.gui.couplingmanager.DesktopCouplingManager
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.gui.WorkspaceActionManager.ScriptAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.AddAgentAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.AddEntityAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.AddSmellSourceAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.AddTileSensorsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.DeleteEntityAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.EditSmellSourceAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.ShowEntityDialogAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.actions.ShowWorldPrefsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.dialogs.AddEffectorDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.dialogs.AddSensorDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.dialogs.EntityDialog: Respond to button pressing events.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.dialogs.OdorWorldDialog: Performs an appropriate action on the given event.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.CreatePixelMatrixAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.CreateSensorMatrixAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.EditSensorsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.IsometricViewAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.NormalViewAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.OpenVisionWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.PaintViewAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.SaveVisionWorldAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.SaveVisionWorldAsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.SelectAllAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.SelectNoneAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.SideBySideViewAction
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.action.StackedViewAction
actionRemoved(NetworkUpdateAction) - Method in interface org.simbrain.network.core.NetworkUpdateManager.UpdateManagerListener: An action was removed.
actionRemoved(UpdateAction) - Method in interface org.simbrain.workspace.updater.UpdateActionManager.UpdateManagerListener: An action was removed.
ActivityGenerator - Interface in org.simbrain.network.neuron_update_rules.interfaces
add(ArrayList) - Static method in class org.simbrain.network.gui.Clipboard: Add objects to the clipboard.
add(Object) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Add the specified element to the selection.
add(DataPoint) - Method in class org.simbrain.util.projection.NTree: Adds a point to the set.
add(Sensor) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Add the specified sensor to this sensor selection model.
addAction(NetworkUpdateAction) - Method in class org.simbrain.network.core.NetworkUpdateManager: Add an action to the list.
addAction(UpdateAction) - Method in class org.simbrain.workspace.updater.UpdateActionManager: Add an action to the list.
addActionListener(ActionListener) - Method in class org.simbrain.util.widgets.ApplyPanel: Allows outside parties to add other listeners to the apply panel's apply button.
addAddDeleteButtons() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel: Add buttons for adding and deleting sources.
addAddDeleteButtons() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Add buttons for adding and deleting sources.
addAfferent(Synapse) - Method in class org.simbrain.network.core.Neuron: Adds an afferent synapse to this neuron, i.e.
addAgent(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Adds an agent and by default adds several sensors and effectors to it.
AddAgentAction - Class in org.simbrain.world.odorworld.actions: Add agent action.
AddAgentAction(OdorWorldPanel) - Constructor for class org.simbrain.world.odorworld.actions.AddAgentAction: Create an add agent action.
addAll(Collection) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Add all of the specified elements to the selection.
addAll(NTree) - Method in class org.simbrain.util.projection.NTree: adds all the elements from the given tree to this tree
addAll(Collection<Sensor>) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Add all of the specified collection of sensors to this sensor selection model.
addAndLabelSynapseGroup(SynapseGroup) - Method in class org.simbrain.network.groups.Subnetwork: Adds an already constructed synapse group to the subnetwork and provides it with an appropriate label.
addApplyActionListener(ActionListener) - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel: Adds an additional listener to the apply button so that other panels can perform other actions if the button is pressed.
addApplyListenerEx(ActionListener) - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel: Add a special action to the "apply" action for editing excitatory synapses.
addApplyListenerIn(ActionListener) - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel: Add a special action to the "apply" action for editing inhibitory synapses
addAttributeListener(AttributeListener) - Method in class org.simbrain.workspace.WorkspaceComponent: Adds a AttributeListener to this component.
addBindings(NetworkPanel) - Static method in class org.simbrain.network.gui.KeyBindings: Add key bindings.
addBottomText(String) - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Override to add custom notes or other text to bottom of panel.
addBottomText(String) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Add notes or other text to bottom of panel.
addBottomText(String) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Add notes or other text to bottom of panel.
addBrowsePanel() - Method in class org.simbrain.workspace.gui.WorkspaceChangedDialog
addButton(JButton) - Method in class org.simbrain.util.StandardDialog: Adds a new button to the panel.
addChartSettingsListener(ChartSettingsListener) - Method in class org.simbrain.plot.ChartModel: Add a ChartSettings listener.
addClearGraphDataButton() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel: Add button for clearing graph data.
addClearGraphDataButton() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Add button for clearing graph data.
addClipboardListener(ClipboardListener) - Static method in class org.simbrain.network.gui.Clipboard: Add the specified clipboard listener.
addColumn(int) - Method in class org.simbrain.plot.barchart.BarChartModel: Adds a new column to the dataset.
addColumn() - Method in class org.simbrain.plot.barchart.BarChartModel: Adds a bar to the bar chart dataset.
addColumn(T) - Method in class org.simbrain.util.table.MutableTable: Add a new column at the far right of the table.
addColumns(int, T) - Method in class org.simbrain.util.table.MutableTable: Adds a specified number of columns to the right of the table.
addColumns(int) - Method in class org.simbrain.util.table.MutableTable: Adds a specified number of columns to the right of the table.
addComponent(WorkspaceComponent) - Method in class org.simbrain.workspace.ArchiveContents: Adds a new workspace Component to the archive.
addComponentListener(ComponentUpdateListener) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Adds a component listener to this instance.
addConsumerType(AttributeType) - Method in class org.simbrain.workspace.WorkspaceComponent: Add a new type of consumer.
addCoupling(Coupling<?>) - Method in class org.simbrain.workspace.ArchiveContents: Adds a coupling to the archive.
addCoupling(Coupling<?>) - Method in class org.simbrain.workspace.CouplingManager: Adds a coupling to this instance.
addCoupling(Coupling<?>) - Method in class org.simbrain.workspace.Workspace: Adds a coupling to the CouplingManager.
addCouplingListener(CouplingListener) - Method in class org.simbrain.workspace.CouplingManager: Adds a new listener to be updated when changes are made.
addCustomAction - Variable in class org.simbrain.network.gui.NetworkUpdateManagerPanel: Action which allows for creation of custom action.
addCustomAction - Variable in class org.simbrain.workspace.gui.WorkspaceUpdateManagerPanel: Action which allows for creation of custom action.
addCustomMenuItem(JMenuItem) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Add a custom menu item to the list.
addData(double[], Integer) - Method in class org.simbrain.plot.histogram.HistogramModel: Add double array data to a specified data series.
addData(int, double, double) - Method in class org.simbrain.plot.rasterchart.RasterModel: Add data to this model.
addData(int, double, double) - Method in class org.simbrain.plot.timeseries.TimeSeriesModel: Add data to this model.
addDatapoint(DataPointColored) - Method in class org.simbrain.util.projection.Projector: Add a new point to the dataset, using the currently selected add method.
addDataSource() - Method in class org.simbrain.plot.histogram.HistogramModel: Adds a data source to the chart.
addDataSource() - Method in class org.simbrain.plot.piechart.PieChartModel: Adds a data source to the plot.
addDataSource() - Method in class org.simbrain.plot.rasterchart.RasterModel: Adds a data source to the chart.
addDataSource() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel: Adds a data source.
addDataSource() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel: Adds a data source to the chart.
addDataSources(int) - Method in class org.simbrain.plot.barchart.BarChartModel: Create specified number of set of data sources.
addDataSources(int) - Method in class org.simbrain.plot.histogram.HistogramModel: Create specified number of set of data sources.
addDataSources(int) - Method in class org.simbrain.plot.piechart.PieChartModel: Create specified number of set of data sources.
addDataSources(int) - Method in class org.simbrain.plot.rasterchart.RasterModel: Create specified number of set of data sources.
addDataSources(int) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel: Create specified number of set of data sources.
addDataSources(int) - Method in class org.simbrain.plot.timeseries.TimeSeriesModel: Create specified number of set of data sources.
addDesktopComponent(GuiComponent<?>) - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent: Adds a desktop component to this component entry.
addDesktopComponent(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Add a new SimbrainComponent.
addEffector(Effector) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Add an effector.
AddEffectorDialog - Class in org.simbrain.world.odorworld.dialogs: EffectorDialog is a dialog box for adding effectors to Odor World.
AddEffectorDialog(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.AddEffectorDialog: Effector Dialog add effector constructor.
addEfferent(Synapse) - Method in class org.simbrain.network.core.Neuron: Adds an efferent synapse to this neuron, i.e.
addEntity(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Add an Odor World Entity.
AddEntityAction - Class in org.simbrain.world.odorworld.actions: Add entity action.
AddEntityAction(OdorWorldPanel) - Constructor for class org.simbrain.world.odorworld.actions.AddEntityAction: Create a new add entity action.
addErrorListener() - Method in class org.simbrain.network.gui.trainer.IterativeControlsPanel: Add an error listener.
addErrorListener(ErrorListener) - Method in class org.simbrain.network.trainers.IterableTrainer: Add an error listener.
addExcitatorySynapseUnsafe(Synapse) - Method in class org.simbrain.network.groups.SynapseGroup: See: SynapseGroup.addSynapseUnsafe(Synapse).
addExtension(String, String) - Method in class org.simbrain.util.SFileChooser: Adds an extension with the provided description to the filenamefilter.
addExtension(String) - Method in class org.simbrain.util.SFileChooser: Adds an extension with the default description to the filenamefilter.
addFocusListenerToFields(FocusListener) - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
addFocusListenerToFields(FocusListener) - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
addFrame(Image, long) - Method in class org.simbrain.world.odorworld.entities.Animation: Adds an image to the animation with the specified duration (time to display the image).
addGroup(Group) - Method in class org.simbrain.network.core.Network: Add a group to the network.
AddGroupAction - Class in org.simbrain.network.gui.actions.modelgroups: Create a new group using the specified dialog.
AddGroupAction(NetworkPanel, Class<? extends StandardDialog>, String) - Constructor for class org.simbrain.network.gui.actions.modelgroups.AddGroupAction: Create a new add group properties action with the specified network panel.
addGroupListener(GroupListener) - Method in class org.simbrain.network.core.Network: Register a group listener.
addIncomingSg(SynapseGroup) - Method in class org.simbrain.network.groups.NeuronGroup
addInhibitorySynapseUnsafe(Synapse) - Method in class org.simbrain.network.groups.SynapseGroup: See: SynapseGroup.addSynapseUnsafe(Synapse).
addInMessage(String) - Method in class org.simbrain.world.oscworld.OscWorldComponent: Add a new OSC in message with the specified address.
addInputRowAction - Variable in class org.simbrain.network.gui.nodes.SubnetworkNode: Action for adding the current pattern in the network to the training data
addInternalFrame(JInternalFrame) - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Add internal frame.
addInternalMenuBar() - Method in class org.simbrain.network.gui.NetworkPanel: Adds an internal menu bar; used in applets.
addItem(String, JComponent) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Adds an item.
addItem(String, JComponent) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Adds an item.
addItem(String, JComponent) - Method in class org.simbrain.util.LabelledItemPanel: Add a labeled item to the panel.
addItem(JLabel, JComponent, int) - Method in class org.simbrain.util.LabelledItemPanel: Provides support for multi-column labeled item panels.
addItem(String, JComponent, int) - Method in class org.simbrain.util.LabelledItemPanel: Adds a labeled item to the panel on the current myNextItemRow, at the specified column.
addItem(JComponent, int) - Method in class org.simbrain.util.LabelledItemPanel: A function which adds an item without a label.
addItem(String, JComponent) - Method in class org.simbrain.util.propertyeditor.gui.LabelledItemPanel: This method adds a labelled item to the panel.
addItemLabel(JLabel, JComponent) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Adds an item label.
addItemLabel(JLabel, JComponent) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Add item label.
addItemLabel(JLabel, JComponent) - Method in class org.simbrain.util.LabelledItemPanel: Modification of addItem which takes a label, rather than text, as an argument.
addItemLabel(JLabel, JComponent) - Method in class org.simbrain.util.propertyeditor.gui.LabelledItemPanel: Modification of addItem which takes a label, rather than text, as an argument.
AdditiveRule - Class in org.simbrain.network.neuron_update_rules: AdditiveNeuron See Haykin (2002), section 14.5.
AdditiveRule() - Constructor for class org.simbrain.network.neuron_update_rules.AdditiveRule
AdditiveRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: AdditiveNeuronPanel.
AdditiveRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.AdditiveRulePanel: Creates an instance of this panel.
addListener(NetworkUpdateManager.UpdateManagerListener) - Method in class org.simbrain.network.core.NetworkUpdateManager: Listen for updates to the update manager.
addListener(TrainerListener) - Method in class org.simbrain.network.trainers.Trainer: Add a trainer listener.
addListener(ChartListener) - Method in class org.simbrain.plot.ChartModel: Add a chart listener.
addListener(ProjectorListener) - Method in class org.simbrain.util.projection.Projector: Add a projector listener.
addListener(UpdateActionManager.UpdateManagerListener) - Method in class org.simbrain.workspace.updater.UpdateActionManager: Listen for updates to the update manager.
addListener(WorkspaceListener) - Method in class org.simbrain.workspace.Workspace: Adds a listener to the workspace.
addListener(TicTacToeGui.Listener) - Method in class org.simbrain.world.game.tictactoe.TicTacToeGui: Adds a listener to the gui.
addListener(TicTacToeModel.Listener) - Method in class org.simbrain.world.game.tictactoe.TicTacToeModel
addListener(WorldListener) - Method in class org.simbrain.world.odorworld.OdorWorld: Add a world listener.
addListener(TextListener) - Method in class org.simbrain.world.textworld.TextWorld: Add a listener.
addMenuBar(SimbrainJTable) - Method in class org.simbrain.world.dataworld.DataWorldDesktopComponent: Creates the Menu Bar and adds it to the frame.
addMenuToSynapseGroupNode(SynapseGroupNode) - Method in class org.simbrain.network.gui.NetworkPanel: Overriden by NetworkPanelDesktop to adorn node with coupling menus.
addModelListener(VisionWorldModelListener) - Method in interface org.simbrain.world.visionworld.VisionWorldModel: Add the specified vision world model listener.
addModelListener(VisionWorldModelListener) - Method in class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Add the specified vision world model listener.
addMouseListener(MouseListener) - Method in class org.simbrain.util.widgets.DropDownTriangle
addMouseListenerToTriangle(MouseAdapter) - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel
addNetworkListener(NetworkListener) - Method in class org.simbrain.network.core.Network: Register a network listener.
addNeuron(Neuron) - Method in class org.simbrain.network.core.Network: Adds a new neuron.
addNeuron(Neuron, boolean) - Method in class org.simbrain.network.groups.NeuronGroup: Add a neuron to group.
addNeuron(Neuron) - Method in class org.simbrain.network.groups.NeuronGroup: Add neuron to group.
addNeuron() - Method in class org.simbrain.network.gui.NetworkPanel: Use the GUI to add a new neuron to the underlying network model.
addNeuronGroup(NeuronGroup) - Method in class org.simbrain.network.groups.Subnetwork: Add a neuron group.
addNeuronGroup(NeuronGroup) - Method in class org.simbrain.network.subnetworks.FeedForward
addNeuronList(ArrayList<Neuron>) - Method in class org.simbrain.network.core.Network: Add an array of neurons and set their parents to this.
addNeuronListener(NeuronListener) - Method in class org.simbrain.network.core.Network: Register a neuron listener.
addNeuronNode(NeuronNode) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Add a neuron node to the group node.
AddNeuronsAction - Class in org.simbrain.network.gui.actions.neuron: Creates a group of neurons.
AddNeuronsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.neuron.AddNeuronsAction: Create a new neuron action with the specified network panel.
AddNeuronsDialog - Class in org.simbrain.network.gui.dialogs.neuron: A dialog for adding multiple neurons to the network.
addNeuronsToPanel(List<Neuron>, Layout) - Method in class org.simbrain.network.gui.NetworkPanel: Using the GUI to add a set of neurons to the underlying network panel.
addNewExcitatorySynapse(Synapse) - Method in class org.simbrain.network.groups.SynapseGroup
addNewInhibitorySynapse(Synapse) - Method in class org.simbrain.network.groups.SynapseGroup
addNewSynapse(Synapse) - Method in class org.simbrain.network.groups.SynapseGroup: Adds a new synapse (one which is "blank") to the synapse group.
addNode(PNode) - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Add a node (neuron or synapse group to the subnetwork's outline) and move synapsegroup nodes to the back.
addNoise - Variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Adds noise to neuron.
addNoise(double[], double) - Static method in class org.simbrain.util.math.SimbrainMath: Add noise to a vector.
addObjects(List<?>) - Method in class org.simbrain.network.core.Network: Adds a list of network elements to this network.
addOutgoingSg(SynapseGroup) - Method in class org.simbrain.network.groups.NeuronGroup
addOutMessage(String) - Method in class org.simbrain.world.oscworld.OscWorldComponent: Add a new OSC out message with the specified address.
addPoint(double[]) - Method in class org.simbrain.plot.projection.ProjectionComponent: Add a new point to the projection dataset using an array.
addPoint(double, double) - Method in class org.simbrain.plot.projection.ProjectionModel: Convenience method for adding points to dataset.
addPoint(DataPoint, double) - Method in class org.simbrain.util.projection.Dataset: Add a new datapoint to the dataset.
addPoint(DataPoint) - Method in class org.simbrain.util.projection.Dataset: Add datapoint without checking whether it is unique or not.
addPreferencesButton() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel: Add button for showing preferences.
addPreferencesButton() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Add button for showing preferences.
addPresetAction - Variable in class org.simbrain.network.gui.NetworkUpdateManagerPanel: Add a preset action.
addPresetAction - Variable in class org.simbrain.workspace.gui.WorkspaceUpdateManagerPanel: Add a preset action.
addProducerType(AttributeType) - Method in class org.simbrain.workspace.WorkspaceComponent: Add a new type of producer.
addPropertyChangeListener(PropertyChangeListener) - Method in interface org.simbrain.world.visionworld.PixelMatrix: Add the specified property change listener.
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface org.simbrain.world.visionworld.PixelMatrix: Add the specified property change listener for the specified property.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Add the specified property change listener.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Add the specified property change listener for the specified property.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Add the specified property change listener.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Add the specified property change listener for the specified property.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.simbrain.world.visionworld.Sensor: Add the specified property change listener.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.simbrain.world.visionworld.Sensor: Add the specified property change listener for the specified property.
addPropertyChangeListenerToFields(PropertyChangeListener) - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
addPropertyChangeListenerToFields(PropertyChangeListener) - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
addRow(double[]) - Method in class org.simbrain.network.trainers.TrainingSet: Add a row of values to the input data table.
addRow(T) - Method in class org.simbrain.util.table.MutableTable: Add a new row.
addRow(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel: Add a new component to the list.
addRow(AttributeType) - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
addRow(Effector) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel: Add a row
addRow(Sensor) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel: Add a row.
addRows(int, T) - Method in class org.simbrain.util.table.MutableTable: Add a specified number of rows to the bottom of the table.
addRows(int) - Method in class org.simbrain.util.table.MutableTable: Add a specified number of rows to the bottom of the table.
addRowToTrainingSet() - Method in class org.simbrain.network.groups.Subnetwork: If this subnetwork is trainable, then add the current activation of the "input" neuron group to the input data of the training set.
addScalarDimension(int) - Method in class org.simbrain.plot.projection.ProjectionComponent: Add a dimension object.
addSelection(Object) - Method in class org.simbrain.network.gui.NetworkPanel: Add objects to the current selection.
addSelectionHandleTo(PNode) - Static method in class org.simbrain.network.gui.nodes.SelectionHandle: Add a selection handle to the specified node, if one does not exist already.
addSelectionListener(NetworkSelectionListener) - Method in class org.simbrain.network.gui.NetworkPanel: Add the specified Network selection listener.
addSelectionListener(NetworkSelectionListener) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Add the specified network selection listener.
addSensor(Sensor) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Add a sensor.
AddSensorDialog - Class in org.simbrain.world.odorworld.dialogs: SensorDialog is a dialog box for adding Sensors to Odor World.
AddSensorDialog(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.AddSensorDialog: Sensor Dialog add sensor constructor.
addSensorSelectionListener(SensorSelectionListener) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Add the specified sensor selection listener.
addSeries(String, double[], int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Adds a series to the dataset.
addSetter(int) - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent: Add a setter with the specified index.
addSliderApplyActionListener(ActionListener) - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel: Adds an additional action listener to the apply button associated with the slider, so that external panels can perform some action.
AddSmellSourceAction - Class in org.simbrain.world.odorworld.actions: Add a new smell source to this entity.
AddSmellSourceAction(OdorWorldPanel, OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.actions.AddSmellSourceAction: Create a new open plot action.
addSourceHandleTo(PNode) - Static method in class org.simbrain.network.gui.nodes.SourceHandle: Add a selection handle to the specified node, if one does not exist already.
addSprite(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.TileMap: Adds a OdorWorldEntity object to this map.
addSynapse(Synapse) - Method in class org.simbrain.network.core.Network: Adds a weight to the neuron network, where that weight already has designated source and target neurons.
addSynapseGroup(SynapseGroup) - Method in class org.simbrain.network.groups.Subnetwork: Add a synapse group.
AddSynapseGroupAction - Class in org.simbrain.network.gui.actions.synapse: Creates a synapse group connecting two neuron groups.
AddSynapseGroupAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.synapse.AddSynapseGroupAction: Create a new neuron action with the specified network panel.
addSynapseListener(SynapseListener) - Method in class org.simbrain.network.core.Network: Register a synapse listener.
addSynapseNode(SynapseNode) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeVisible: Add a synapse node to the group node.
addSynapseUnsafe(Synapse) - Method in class org.simbrain.network.groups.SynapseGroup: Add a synapse to this synapse group adding it to the appropriate synapse set (excitatory or inhibitory if it's weight is above or below zero respecively).
addTab(String, Component) - Method in class org.simbrain.network.gui.dialogs.network.SupervisedTrainingDialog: Add a tab to the dialog.
addTableModelListener(TableModelListener) - Method in class org.simbrain.util.table.SimbrainDataTable
addText(NetworkTextObject) - Method in class org.simbrain.network.core.Network: Add a network text object.
addText(String) - Method in class org.simbrain.world.textworld.TextWorld: Add a text to the end of the underling text object.
addTextIfAboveThreshold(double, String) - Method in class org.simbrain.world.textworld.DisplayWorld: Add the provided text, if the provided value is above threshold.
addTextListener(TextListener) - Method in class org.simbrain.network.core.Network: Register a text listener.
addTileSensors(int, int) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Add a grid of tile sensors.
addTileSensors(int, int, int) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Add a grid of tile sensors, offset by some fraction of a tile's length.
AddTileSensorsAction - Class in org.simbrain.world.odorworld.actions: Action for adding tile sensors.
AddTileSensorsAction(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.actions.AddTileSensorsAction: Construct the action.
addTokenVectorPair(String, double[]) - Method in class org.simbrain.world.textworld.ReaderWorld: Add an entry to the token-vector dictionary.
addToSparsity(double) - Method in class org.simbrain.network.connections.Sparse
addTrainerListeners() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel: Add trainer listeners.
addUndoableAction(UndoManager.UndoableAction) - Method in class org.simbrain.network.gui.UndoManager: Add a new undoable action.
addUpdateAction(NetworkUpdateAction) - Method in class org.simbrain.network.core.Network: Add an update action to the network' action list (the sequence of actions invoked on each iteration of the network).
addUpdateAction(UpdateAction) - Method in class org.simbrain.workspace.ArchiveContents: Adds an update action the archive.
addUpdateAction(UpdateAction) - Method in class org.simbrain.workspace.Workspace: Convenience method for adding an update action to the workspace's action list (the sequence of actions invoked on each iteration of the workspace).
addUpdaterListener(WorkspaceUpdaterListener) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Adds an updater listener to this instance.
addVector(double[], double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Add these vectors.
addVectorTokenPair(String, double[]) - Method in class org.simbrain.world.textworld.DisplayWorld: Add an entry to the vector-token dictionary.
addWordToTokenDictionary(String) - Method in class org.simbrain.world.textworld.TextWorld: Add a word to the dictionary.
addWorkspaceComponent(WorkspaceComponent) - Method in class org.simbrain.workspace.Workspace: Adds a workspace component to the workspace.
addWorkspaceComponentListener(WorkspaceComponentListener) - Method in class org.simbrain.workspace.WorkspaceComponent: Adds a WorkspaceComponentListener to this component.
AdExIFRule - Class in org.simbrain.network.neuron_update_rules: An implementation of adaptive exponential integrate and fire.
AdExIFRule() - Constructor for class org.simbrain.network.neuron_update_rules.AdExIFRule
AdExIFRulePanel - Class in org.simbrain.network.gui.dialogs.neuron
AdExIFRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.AdExIFRulePanel: Creates an instance of this panel.
alignHorizontal() - Method in class org.simbrain.network.gui.NetworkPanel: Aligns neurons horizontally.
AlignHorizontalAction - Class in org.simbrain.network.gui.actions.edit: Aligns horizontal.
AlignHorizontalAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.AlignHorizontalAction: Create a new align horizontal action with the specified network panel.
alignVertical() - Method in class org.simbrain.network.gui.NetworkPanel: Aligns neurons vertically.
AlignVerticalAction - Class in org.simbrain.network.gui.actions.edit: Aligns vertical.
AlignVerticalAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.AlignVerticalAction: Create a new align vertical action with the specified network panel.
AllToAll - Class in org.simbrain.network.connections: Connect every source neuron to every target neuron.
AllToAll() - Constructor for class org.simbrain.network.connections.AllToAll: Construct to all to all connector.
AllToAll(boolean) - Constructor for class org.simbrain.network.connections.AllToAll: Construct all to all connection object.
AllToAllPanel - Class in org.simbrain.network.gui.dialogs.connect.connector_panels: The AllToAllPanel is panel for editing all to all connections.
AllToAllPanel(AllToAll, NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.connect.connector_panels.AllToAllPanel: Construct a new all to all panel.
Animation - Class in org.simbrain.world.odorworld.entities: The Animation class manages a series of images (frames) and the amount of time to display each frame.
Animation(String[], long) - Constructor for class org.simbrain.world.odorworld.entities.Animation: Creates an animation from a list of images, specified in terms of their file locations.
Animation(String) - Constructor for class org.simbrain.world.odorworld.entities.Animation: An animation with a single image; equivalent to a static image.
apply() - Method in class org.simbrain.network.trainers.BackpropTrainer
apply() - Method in class org.simbrain.network.trainers.BPTTTrainer
apply() - Method in class org.simbrain.network.trainers.CompetitiveTrainer
apply() - Method in class org.simbrain.network.trainers.HopfieldTrainer
apply() - Method in class org.simbrain.network.trainers.LMSIterative
apply() - Method in class org.simbrain.network.trainers.LMSOffline
apply() - Method in class org.simbrain.network.trainers.SOMTrainer
apply() - Method in class org.simbrain.network.trainers.Trainer: Apply the algorithm.
apply(int) - Method in interface org.simbrain.world.odorworld.behaviors.Behavior: Apply the rule associated with the behavior.
apply(int) - Method in class org.simbrain.world.odorworld.behaviors.NewtonianBouncer
apply(int) - Method in class org.simbrain.world.odorworld.behaviors.StationaryBehavior
applyConnection(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.connect.AbstractConnectionPanel: Apply this connection panel's connection to the provided source and target neurons.
applyConnection(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.AllToAllPanel
applyConnection(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.OneToOnePanel: Apply this connection panel's connection to the provided source and target neurons.
applyConnection(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.RadialPanel
applyConnection(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel: Apply this connection panel's connection to the provided source and target neurons.
ApplyConnectionAction - Class in org.simbrain.network.gui.actions.connection: Apply specified connection either from selected neurons to themselves ("self connect") or from source to target.
ApplyConnectionAction(NetworkPanel, ConnectNeurons, String) - Constructor for class org.simbrain.network.gui.actions.connection.ApplyConnectionAction: Construct the action.
applyCurrentConnection(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.connections.QuickConnectionManager: Apply the current connection object to indicated source and target neurons.
applyEffectors() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Apply impact of all effectors.
applyInputs() - Method in class org.simbrain.network.groups.NeuronGroup: Apply any input values to the activations of the neurons in this group.
applyLayout() - Method in class org.simbrain.network.groups.NeuronGroup: Apply this group's layout to its neurons.
applyLayout(Point2D) - Method in class org.simbrain.network.groups.NeuronGroup: Apply this group's layout to its neurons based on a specified initial position.
ApplyLayoutAction - Class in org.simbrain.network.gui.actions: Apply specified layout to selected neurons.
ApplyLayoutAction(NetworkPanel, Layout, String) - Constructor for class org.simbrain.network.gui.actions.ApplyLayoutAction: Construct the action.
applyLearningRules(SynapseUpdateRule, SynapseUpdateRule, List<Synapse>) - Static method in class org.simbrain.network.connections.ConnectionUtilities
ApplyPanel - Class in org.simbrain.util.widgets: A widget that contains an apply button, for cases when it should be possible to immediately apply changes in an editing panel (as opposed to waiting to press ok in the parent dialog).
applyUserPrefsToNetwork() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Push settings from user preferences to Simbrain objects.
ArchiveContents - Class in org.simbrain.workspace: Instances of this class are used for building and reading the TOC of an archive.
ArchiveContents(Workspace, WorkspaceComponentSerializer) - Constructor for class org.simbrain.workspace.ArchiveContents: The component serializer for this archive.
ArchiveContents.ArchivedAttribute - Class in org.simbrain.workspace: The class used to represent an attribute in the archive.
ArchiveContents.ArchivedComponent - Class in org.simbrain.workspace: Represents the data used to store components in the archive.
ArchiveContents.ArchivedComponent.ArchivedDesktopComponent - Class in org.simbrain.workspace: Class used to represent a desktop component in the archive.
ArchiveContents.ArchivedCoupling - Class in org.simbrain.workspace: Class used to represent a coupling in the archive.
ArchiveContents.ArchivedUpdateAction - Class in org.simbrain.workspace: A persistable form of update action that can be used to recreate the action.
ArchivedAttribute(ArchiveContents, Attribute) - Constructor for class org.simbrain.workspace.ArchiveContents.ArchivedAttribute: Creates a new instance.
ArchivedCoupling(ArchiveContents, Coupling<?>) - Constructor for class org.simbrain.workspace.ArchiveContents.ArchivedCoupling: Creates a new instance.
asArrayList() - Method in class org.simbrain.util.projection.NTree: returns the tree as an arraylist.
asByteArray(double) - Method in enum org.simbrain.network.util.io_utilities.GroupSerializer.Precision
asByteArray(long) - Method in enum org.simbrain.network.util.io_utilities.GroupSerializer.Precision
asDoubleArray() - Method in class org.simbrain.util.table.NumericTable: Returns a double array representation of the table.
asFlatList() - Method in class org.simbrain.util.table.SimbrainDataTable: Returns the contents of the table as a flat list.
asStringArray() - Method in class org.simbrain.util.table.SimbrainDataTable: Returns a string array representation of the table.
atan(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: The arctan function given an upper and lower limit and slope for a particular value.
Attribute - Interface in org.simbrain.workspace: Defines the base API for consumers and producers.
AttributeList<E> - Class in org.simbrain.workspace: Utility class for creating and maintaining a list of "getterSetters", which are objects which are simple objects that call get or set for some property.
AttributeList(int) - Constructor for class org.simbrain.workspace.AttributeList: Construct the list.
AttributeList.GetterSetter<E> - Class in org.simbrain.workspace: Helper object for use with couplings.
AttributeListener - Interface in org.simbrain.workspace: Listener for attribute related events, broadly (this includes potential attributes and attribute types).
AttributeManager - Class in org.simbrain.workspace: The main usage of this class by API users is to create potential attributes (PotentialConsumer and PotentialProducer), which are in turn used to create couplings.
AttributeManager(WorkspaceComponent) - Constructor for class org.simbrain.workspace.AttributeManager
attributeObjectRemoved(Object) - Method in interface org.simbrain.workspace.AttributeListener: The base object of an attribute has been removed.
AttributeType - Class in org.simbrain.workspace: Encapsulates type information about potential attribute.
AttributeType(WorkspaceComponent, String, String, Class<?>, boolean) - Constructor for class org.simbrain.workspace.AttributeType: Construct an attribute type object.
AttributeType(WorkspaceComponent, String, Class<?>, boolean) - Constructor for class org.simbrain.workspace.AttributeType: Construct an attribute type object with no method name.
AttributeTypeModel() - Constructor for class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
AttributeTypePanel - Class in org.simbrain.workspace.gui.couplingmanager: Displays a list of attribute types.
AttributeTypePanel(WorkspaceComponent, PotentialAttributePanel.ProducerOrConsumer) - Constructor for class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel: Workspace component list panel constructor.
AttributeTypePanel.AttributeTypeModel - Class in org.simbrain.workspace.gui.couplingmanager: Table model which represents workspace components.
attributeTypeVisibilityChanged(AttributeType) - Method in interface org.simbrain.workspace.AttributeListener: The visibility of an attribute type changed.
await() - Method in class org.simbrain.workspace.updater.LatchCompletionSignal: Calls await on the underlying latch.

B

BackpropCreationDialog - Class in org.simbrain.network.gui.dialogs.network: BackpropDialog is a dialog box for creating a Backprop network.
BackpropCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.BackpropCreationDialog: Construct the dialog.
BackpropEditorDialog - Class in org.simbrain.network.gui.dialogs.network: BackpropDialog is a dialog box for editing a Backprop network.
BackpropEditorDialog(NetworkPanel, BackpropNetwork) - Constructor for class org.simbrain.network.gui.dialogs.network.BackpropEditorDialog: Default constructor.
BackpropNetwork - Class in org.simbrain.network.subnetworks: Backprop network.
BackpropNetwork(Network, int[], Point2D) - Constructor for class org.simbrain.network.subnetworks.BackpropNetwork: Construct a new backprop network.
BackpropNetworkNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of a group of a backprop network.
BackpropNetworkNode(NetworkPanel, BackpropNetwork) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.BackpropNetworkNode: Create a layered network.
BackpropTrainer - Class in org.simbrain.network.trainers: Backprop trainer.
BackpropTrainer(Trainable, List<List<Neuron>>) - Constructor for class org.simbrain.network.trainers.BackpropTrainer: Construct the backprop trainer.
BarChartComponent - Class in org.simbrain.plot.barchart: Data for a JFreeChart bar chart.
BarChartComponent(String) - Constructor for class org.simbrain.plot.barchart.BarChartComponent: Create new BarChart Component.
BarChartComponent(String, BarChartModel) - Constructor for class org.simbrain.plot.barchart.BarChartComponent: Create new BarChart Component from a specified model.
BarChartComponent(String, int) - Constructor for class org.simbrain.plot.barchart.BarChartComponent: Initializes a jfreechart with specific number of data sources.
BarChartComponent.BarChartSetter - Class in org.simbrain.plot.barchart: Object which sets a value of one bar in a bar chart.
BarChartGui - Class in org.simbrain.plot.barchart: Display a PieChart.
BarChartGui(GenericFrame, BarChartComponent) - Constructor for class org.simbrain.plot.barchart.BarChartGui: Construct the GUI Bar Chart.
BarChartModel - Class in org.simbrain.plot.barchart: Data for a JFreeChart pie chart.
BarChartModel() - Constructor for class org.simbrain.plot.barchart.BarChartModel: Bar chart model constructor.
BarChartSetter(int) - Constructor for class org.simbrain.plot.barchart.BarChartComponent.BarChartSetter: Construct a setter object.
BasicEntity - Class in org.simbrain.world.odorworld.entities: BasicEntity represents a static entity in the Odor World environment, with a static image file.
BasicEntity(Animation, OdorWorld) - Constructor for class org.simbrain.world.odorworld.entities.BasicEntity: Construct a basic entity with a specified animation.
BasicEntity(OdorWorld) - Constructor for class org.simbrain.world.odorworld.entities.BasicEntity: Construct a default entity.
BasicEntity(String, OdorWorld) - Constructor for class org.simbrain.world.odorworld.entities.BasicEntity: Construct a basic entity with a single image location.
beginTraining() - Method in interface org.simbrain.network.trainers.TrainerListener: Called when training begins.
Behavior - Interface in org.simbrain.world.odorworld.behaviors: Represents a type of behavior for an OdorWorldEntity.
behavior - Variable in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Behavior.
bias - Variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Bias.
BiasedUpdateRule - Interface in org.simbrain.network.neuron_update_rules.interfaces: Biased Neuron is for neuron's with a bias, e.g.
BinaryRule - Class in org.simbrain.network.neuron_update_rules: BinaryNeuron takes one of two values.
BinaryRule() - Constructor for class org.simbrain.network.neuron_update_rules.BinaryRule
BinaryRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: BinaryNeuronPanel creates a dialog for setting preferences of binary neurons.
BinaryRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.BinaryRulePanel: Creates binary neuron preferences panel.
bipolar(double) - Static method in class org.simbrain.network.subnetworks.Hopfield: Convenience method to convert binary values (1,0) to bipolar values(1,-1).
bite() - Method in class org.simbrain.world.odorworld.LifeCycle: Take one step closer to death.
blue - Variable in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: The blue threshold.
board - Variable in class org.simbrain.world.game.tictactoe.TicTacToeModel: The state of the board.
BoundedUpdateRule - Interface in org.simbrain.network.neuron_update_rules.interfaces: An interface for updates rules that make use of an upper and lower bound, either for clipping or for setting intrinsic bounds.
boxable - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
BPTTCreationDialog - Class in org.simbrain.network.gui.dialogs.network: Creates a GUI dialog to set the parameters for and then build a BPTT Network.
BPTTCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.BPTTCreationDialog: Constructs a labeled item panel dialog for the creation of a simple recurrent network.
BPTTNetwork - Class in org.simbrain.network.subnetworks: Implements a network to be trained using backprop through time.
BPTTNetwork(Network, int, int, int, Point2D) - Constructor for class org.simbrain.network.subnetworks.BPTTNetwork: Constructor specifying root network, and number of nodes in each layer.
BPTTNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of a group of a BPTT network.
BPTTNode(NetworkPanel, BPTTNetwork) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.BPTTNode: Create a layered network.
BPTTTrainer - Class in org.simbrain.network.trainers: Trainer for backprop through time Networks.
BPTTTrainer(BPTTNetwork) - Constructor for class org.simbrain.network.trainers.BPTTTrainer: Construct the SRN trainer.
buffer - Variable in class org.simbrain.workspace.Coupling: Value of buffer.
BUFFERED_IMAGE - Static variable in class org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditors: Buffered image pixel matrix editor.
BufferedImagePixelMatrix - Class in org.simbrain.world.visionworld.pixelmatrix: BufferedImage pixel matrix.
BufferedImagePixelMatrix() - Constructor for class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Create a new BufferedImage pixel matrix with an empty image the default dimensions.
BufferedImagePixelMatrix(int, int) - Constructor for class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Create a new BufferedImage pixel matrix with an empty image the specified dimensions.
BufferedImagePixelMatrix(BufferedImage) - Constructor for class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Create a new BufferedImage pixel matrix with the specified image.
BufferedImagePixelMatrixEditor - Class in org.simbrain.world.visionworld.pixelmatrix.editor: Buffered image pixel matrix editor.
BufferedImagePixelMatrixEditor() - Constructor for class org.simbrain.world.visionworld.pixelmatrix.editor.BufferedImagePixelMatrixEditor: Create a new buffered image pixel matrix editor.
BufferedUpdate - Class in org.simbrain.network.update_actions: Buffered update of loose items (neurons and synapses), i.e.
BufferedUpdate(Network) - Constructor for class org.simbrain.network.update_actions.BufferedUpdate
bufferedUpdateAllNeurons() - Method in class org.simbrain.network.core.Network: Calls Neuron.update() for each neuron.
BufferedUpdateTask - Class in org.simbrain.network.update_actions.concurrency_tools
BufferedUpdateTask(Neuron[]) - Constructor for class org.simbrain.network.update_actions.concurrency_tools.BufferedUpdateTask
buildNetwork() - Method in class org.simbrain.network.util.CascadingNetworkBuilder: Create the cascading network.
buildPopupMenu() - Method in class org.simbrain.util.table.SimbrainJTable: Build the context menu for the table.
buildPopupMenu() - Method in class org.simbrain.world.dataworld.DesktopJTable: Build the context menu for the table.
buildPopupMenu(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorldPanel: Create a popup menu based on location of mouse click.
BumpSensor - Class in org.simbrain.world.odorworld.sensors: Very simple bump sensor.
BumpSensor(OdorWorldEntity, double) - Constructor for class org.simbrain.world.odorworld.sensors.BumpSensor: Construct bump sensor.

C

calcCenter(Point2D, Point2D) - Method in class org.simbrain.network.gui.nodes.SynapseNode: Calculates the position of the synapse circle based on the positions of the source and target NeuronNodes.
calcPSR() - Method in class org.simbrain.network.core.Synapse: For spiking source neurons, returns the spike-responder's value times the synapse strength.
calcStats() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
calculateExcitatoryRatio() - Method in class org.simbrain.network.groups.SynapseGroup: If a randomize operation changes the ratio of excitatory to inhibitory synapses, this method can be called to change the excitatoryRatio to reflect this value.
calcWeightedSum() - Method in class org.simbrain.network.core.Synapse: For non-spiking neurons returns the weighted sum, i.e.
CanvasHelper - Class in org.simbrain.world.threedee: Helper class that creates a jME canvas and sets it up with.
CanvasHelper() - Constructor for class org.simbrain.world.threedee.CanvasHelper
capture() - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Capture a new screen shot.
CascadingNetworkBuilder - Class in org.simbrain.network.util: Creates a cascading network.
CascadingNetworkBuilder(Network, int, int) - Constructor for class org.simbrain.network.util.CascadingNetworkBuilder: Create a cascading network builder with a specific number of layers and branches per neuron.
CascadingNetworkBuilder(Network) - Constructor for class org.simbrain.network.util.CascadingNetworkBuilder: Create a cascading network builder using default values.
cbImplementation - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: Implementation combo box.
CellIndex(int, int) - Constructor for class org.simbrain.util.table.SimbrainJTable.CellIndex: Construct the cell index.
centerDialog() - Method in class org.simbrain.util.StandardDialog: Center the dialog on the screen.
changedUpdateController() - Method in class org.simbrain.workspace.gui.ComponentPanel
changedUpdateController() - Method in interface org.simbrain.workspace.updater.WorkspaceUpdaterListener: Called when the update controller is changed.
changeNumThreads() - Method in class org.simbrain.workspace.gui.ComponentPanel
changeNumThreads() - Method in interface org.simbrain.workspace.updater.WorkspaceUpdaterListener: Called when the number of threads on an update controller is changed.
changeRowsColumns(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for changing the number of rows and columns in the table.
changesExist() - Method in class org.simbrain.workspace.Workspace: Check whether there have been changes in the workspace or its components.
changeState() - Method in class org.simbrain.util.widgets.DropDownTriangle: Changes the state of the triangle: if called when pointing "up" (left/right) the triangle changes to point down and vice versa.
changeState() - Method in class org.simbrain.util.widgets.LinkIcon: Changes the lock icon's image to whatever it currently is not.
chartInitialized(int) - Method in interface org.simbrain.plot.ChartListener: The chart has been reinitialized to a new number of data sources.
ChartListener - Interface in org.simbrain.plot: Listen for changes in a chart model object.
ChartModel - Class in org.simbrain.plot: Base class for chart model classes.
ChartModel() - Constructor for class org.simbrain.plot.ChartModel
ChartSettingsListener - Interface in org.simbrain.plot: Listener for changes in a chart model's settings.
chartSettingsUpdated() - Method in interface org.simbrain.plot.ChartSettingsListener: The chart settings have been updated.
checkBounds() - Method in class org.simbrain.network.core.Synapse: If weight value is above or below its bounds set it to those bounds.
checkBounds() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel: Enable or disable the upper and lower bounds fields depending on state of rounding button.
checkCoordinates() - Method in class org.simbrain.util.projection.ProjectCoordinate: If the current coordinate axes are outside acceptable bounds, set them to acceptable values (currently 0 and 1).
checkData(boolean, boolean, Object[][]) - Method in class org.simbrain.util.table.MutableTable: Check the integrity of the data.
checkParamsNonNegative() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer: Checks to make sure that there are no negative parameters.
checkSynapses(ConnectionUtilities.SynapseParameterGetter<T>, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup: A generic method which takes in a functional interface and a polarity.
ClampNeuronsAction - Class in org.simbrain.network.gui.actions.neuron: Clamps neurons action.
ClampNeuronsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.neuron.ClampNeuronsAction: Create a new clamp neurons action with the specified network panel.
clampNeuronsAction - Variable in class org.simbrain.network.gui.nodes.NeuronGroupNode: Action for clamping neurons
ClampWeightsAction - Class in org.simbrain.network.gui.actions.synapse: Clamps weights action.
ClampWeightsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.synapse.ClampWeightsAction: Create a new clamp weights action with the specified network panel.
clear() - Method in class org.simbrain.network.core.NetworkUpdateManager: Remove all actions completely.
clear() - Method in class org.simbrain.network.core.Neuron: Forward to updaterule's clearing method.
clear(Neuron) - Method in class org.simbrain.network.core.NeuronUpdateRule: Set activation to 0; override for other "clearing" behavior (e.g.
clear(Neuron) - Method in class org.simbrain.network.core.SpikingNeuronUpdateRule
clear(Synapse) - Method in class org.simbrain.network.core.SynapseUpdateRule: Set activation to 0; override for other "clearing" behavior (e.g.
clear() - Method in class org.simbrain.network.groups.SynapseGroup: Removes all synapses from this synapse group and the network.
clear() - Static method in class org.simbrain.network.gui.Clipboard: Clear the clipboard.
clear() - Method in class org.simbrain.network.gui.NetworkSelectionModel: Clear the selection.
clear(Neuron) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
clear(Neuron) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
clear(Neuron) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
clear() - Method in class org.simbrain.util.projection.Dataset: Clear all data.
clear() - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel: Clear the component list.
clear() - Method in class org.simbrain.workspace.updater.UpdateActionManager: Remove all actions completely.
clear() - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Clear this sensor selection model.
clearActivations() - Method in class org.simbrain.network.core.Network: Set the activation level of all neurons to zero.
clearActivations() - Method in class org.simbrain.network.groups.NeuronGroup: Set all activations to 0.
clearActivations() - Method in class org.simbrain.network.groups.Subnetwork: Set all activations to 0.
clearBiases() - Method in class org.simbrain.network.core.Network: Set biases on all neurons with a bias to 0.
clearChart() - Method in class org.simbrain.plot.piechart.PieChartModel: Clears data from the chart.
clearChart() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel: Clears the chart of plotted data.
clearClipboard() - Static method in class org.simbrain.world.odorworld.WorldClipboard: Clear all items from clipboard.
clearCouplings() - Method in class org.simbrain.workspace.CouplingManager: Clear all couplings.
clearCurrentTask(ComponentUpdatePart) - Method in class org.simbrain.workspace.updater.UpdateThread: Clears the current component update.
clearData() - Method in class org.simbrain.plot.projection.ProjectionComponent: Clear the dataset.
clearData() - Method in class org.simbrain.plot.rasterchart.RasterModel: Clears the plot.
clearData() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel: Clears the plot.
clearDesktop() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Clear desktop of all components.
clearInputs() - Method in class org.simbrain.network.core.Network: Clears out input values of network nodes, which otherwise linger and cause problems.
clearNeuronList() - Method in class org.simbrain.network.groups.NeuronGroup: Clear the neuron list.
clearPanel() - Method in class org.simbrain.network.gui.NetworkPanel: Remove all nodes from panel.
clearSelection() - Method in class org.simbrain.network.gui.NetworkPanel: Clear the selection.
clearSourceElements() - Method in class org.simbrain.network.gui.NetworkPanel: Clear all source elements.
ClearSourceNeurons - Class in org.simbrain.network.gui.actions.connection: Clear source neurons action.
ClearSourceNeurons(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.connection.ClearSourceNeurons: Construct action.
clearWorkspace() - Method in class org.simbrain.workspace.gui.ComponentPanel
clearWorkspace() - Method in class org.simbrain.workspace.gui.CouplingMenuComponent
clearWorkspace() - Method in class org.simbrain.workspace.Workspace: Remove all components (networks, worlds, etc.) from this workspace.
ClearWorkspaceAction - Class in org.simbrain.workspace.actions: Clear the current workspace.
ClearWorkspaceAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.ClearWorkspaceAction: Create a clear workspace action with the specified workspace.
clip(double) - Method in class org.simbrain.network.core.Synapse: Utility function for use in learning rules.
clip(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
clip(double) - Method in class org.simbrain.network.neuron_update_rules.DecayRule: Clip the current activation.
clip(double) - Method in class org.simbrain.network.neuron_update_rules.IACRule: Clip the current activation.
clip(double) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.ClippableUpdateRule: Clip the current activation.
clip(double) - Method in class org.simbrain.network.neuron_update_rules.LinearRule: Clip the current activation.
clip(double) - Method in enum org.simbrain.util.SimbrainConstants.Polarity: Clips any value appropriately, e.g.
Clipboard - Class in org.simbrain.network.gui: Buffer which holds network objects for cutting and pasting.
Clipboard() - Constructor for class org.simbrain.network.gui.Clipboard
clipboardChanged() - Method in interface org.simbrain.network.gui.ClipboardListener: Notify of clipboard changed.
ClipboardEvent - Class in org.simbrain.network.gui: An event object representing a change in clipboard content.
ClipboardEvent() - Constructor for class org.simbrain.network.gui.ClipboardEvent: Create a new clipboard event with the specified source.
ClipboardListener - Interface in org.simbrain.network.gui: Model listener.
ClippableUpdateRule - Interface in org.simbrain.network.neuron_update_rules.interfaces: Interface for update rules which can clip their values above and below upper and lower bounds (clipping can be turned on or off).
clipped - Variable in class org.simbrain.network.synapse_update_rules.StaticSynapseRule: Clipped.
clipping - Variable in class org.simbrain.util.randomizer.Randomizer: Whether the Gaussian distribution should be clipped at upper / lower bound values.
clone() - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns a clone of the dataset.
close() - Method in class org.simbrain.workspace.gui.GuiComponent: Closes this view.
close() - Method in class org.simbrain.workspace.WorkspaceComponent: Closes the WorkspaceComponent.
close() - Method in class org.simbrain.world.threedee.sensors.Sight
CloseAction - Class in org.simbrain.workspace.component_actions: Close component action.
CloseAction(WorkspaceComponent) - Constructor for class org.simbrain.workspace.component_actions.CloseAction: Create a new close network action with the specified.
closeDialogCancel() - Method in class org.simbrain.network.gui.dialogs.neuron.AddNeuronsDialog: Overriden to perform specific clean up when dialog closed.
closeDialogCancel() - Method in class org.simbrain.plot.scatterplot.ScatterPlotDialog
closeDialogCancel() - Method in class org.simbrain.util.StandardDialog: Overriden to perform specific clean up when dialog closed.
closeDialogCancel() - Method in class org.simbrain.world.odorworld.dialogs.EntityDialog
closeDialogOk() - Method in class org.simbrain.network.desktop.DesktopNetworkDialog: Commit changes to the network (in superclass) and set all defaults.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.connect.QuickConnectPreferencesPanel.QuickConnectDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.group.NeuronGroupCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.group.SynapseGroupDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.layout.LayoutDialog: Overrideen to perform specific clean up when dialog closed.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.BackpropCreationDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.BPTTCreationDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.CompetitiveGroupCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.CompetitiveNetworkCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.CompetitiveTrainingDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog: Overrideen to perform specific clean up when dialog closed.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.ESNTrainingDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.FeedForwardCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldEditTrainDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.KwtaCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.KwtaPropertiesDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.LMSCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.SOMGroupCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.SOMNetworkCreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.SOMTrainingDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.SRNCreationDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.SupervisedTrainingDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.network.WTACreationDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.NetworkDialog
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.neuron.AddNeuronsDialog: Overrideen to perform specific clean up when dialog closed.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronDialog: Overrideen to perform specific clean up when dialog closed.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog: Overrideen to perform specific clean up when dialog closed.
closeDialogOk() - Method in class org.simbrain.network.gui.dialogs.text.TextDialog
closeDialogOk() - Method in class org.simbrain.plot.projection.DataPointColoringDialog
closeDialogOk() - Method in class org.simbrain.plot.projection.ProjectionPreferencesDialog
closeDialogOk() - Method in class org.simbrain.plot.scatterplot.ScatterPlotDialog
closeDialogOk() - Method in class org.simbrain.util.StandardDialog: Overrideen to perform specific clean up when dialog closed.
closeDialogOk() - Method in class org.simbrain.world.odorworld.dialogs.AddEffectorDialog
closeDialogOk() - Method in class org.simbrain.world.odorworld.dialogs.AddSensorDialog
closeDialogOk() - Method in class org.simbrain.world.odorworld.dialogs.EntityDialog
closeDialogOk() - Method in class org.simbrain.world.textworld.dictionary.DictionarySelector
closeNetwork() - Method in class org.simbrain.network.gui.NetworkPanel: Close model Network.
closing() - Method in class org.simbrain.console.ConsoleComponent
closing() - Method in class org.simbrain.console.ConsoleDesktopComponent
closing() - Method in class org.simbrain.docviewer.DocViewerComponent
closing() - Method in class org.simbrain.docviewer.DocViewerDesktopComponent
closing() - Method in class org.simbrain.network.desktop.NetworkDesktopComponent
closing() - Method in class org.simbrain.network.NetworkComponent
closing() - Method in class org.simbrain.plot.barchart.BarChartComponent
closing() - Method in class org.simbrain.plot.barchart.BarChartGui
closing() - Method in class org.simbrain.plot.histogram.HistogramComponent
closing() - Method in class org.simbrain.plot.histogram.HistogramGui
closing() - Method in class org.simbrain.plot.piechart.PieChartComponent
closing() - Method in class org.simbrain.plot.piechart.PieChartGui
closing() - Method in class org.simbrain.plot.projection.ProjectionComponent
closing() - Method in class org.simbrain.plot.projection.ProjectionGui
closing() - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent
closing() - Method in class org.simbrain.plot.rasterchart.RasterPlotGui
closing() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
closing() - Method in class org.simbrain.plot.scatterplot.ScatterPlotGui
closing() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent
closing() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotGui
closing() - Method in class org.simbrain.workspace.gui.GuiComponent: Perform cleanup after closing.
closing() - Method in class org.simbrain.workspace.WorkspaceComponent: Perform cleanup after closing.
closing() - Method in class org.simbrain.world.dataworld.DataWorldComponent
closing() - Method in class org.simbrain.world.dataworld.DataWorldDesktopComponent
closing() - Method in class org.simbrain.world.game.GameComponent: Called when the component is closed.
closing() - Method in class org.simbrain.world.game.GameDesktopComponent: Called when the desktop component is closing.
closing() - Method in class org.simbrain.world.odorworld.OdorWorldComponent
closing() - Method in class org.simbrain.world.odorworld.OdorWorldDesktopComponent
closing() - Method in class org.simbrain.world.oscworld.OscWorldComponent: Perform cleanup after closing.
closing() - Method in class org.simbrain.world.oscworld.OscWorldDesktopComponent: Perform cleanup after closing.
closing() - Method in class org.simbrain.world.textworld.DisplayComponent
closing() - Method in class org.simbrain.world.textworld.DisplayComponentDesktopGui
closing() - Method in class org.simbrain.world.textworld.ReaderComponent
closing() - Method in class org.simbrain.world.textworld.ReaderComponentDesktopGui
closing() - Method in class org.simbrain.world.visionworld.VisionWorldComponent
closing() - Method in class org.simbrain.world.visionworld.VisionWorldDesktopComponent
col - Variable in class org.simbrain.util.table.SimbrainJTable.CellIndex: Column Index.
collideHorizontal() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Called before update() if the creature collided with a tile horizontally.
collideVertical() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Called before update() if the creature collided with a tile vertically.
collisionX() - Method in interface org.simbrain.world.odorworld.behaviors.Behavior: Register a collision in the x direction.
collisionX() - Method in class org.simbrain.world.odorworld.behaviors.NewtonianBouncer
collisionX() - Method in class org.simbrain.world.odorworld.behaviors.StationaryBehavior
collissionY() - Method in interface org.simbrain.world.odorworld.behaviors.Behavior: Register a collision in the y direction.
collissionY() - Method in class org.simbrain.world.odorworld.behaviors.NewtonianBouncer
collissionY() - Method in class org.simbrain.world.odorworld.behaviors.StationaryBehavior
color - Variable in class org.simbrain.plot.histogram.OverwritableHistogramDataset.ColoredDataSeries: The color of a given data series.
ColoredDataSeries(HistogramBin[]) - Constructor for class org.simbrain.plot.histogram.OverwritableHistogramDataset.ColoredDataSeries: Create the data series.
colorToFloat(Color) - Static method in class org.simbrain.util.Utils: Returns the Hue associated with a Color.
ColumnAttribute(int) - Constructor for class org.simbrain.world.dataworld.DataWorldComponent.ColumnAttribute: Construct a column attribute object.
columnNames - Variable in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel: Column names.
columnNames - Variable in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel: Column names.
columnNames - Variable in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel: Column names.
columnNames - Variable in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel: Column names.
columns - Variable in class org.simbrain.util.JMultiLineToolTip
columns() - Method in interface org.simbrain.world.visionworld.SensorMatrix: Return the number of columns of this sensor matrix.
columns() - Method in class org.simbrain.world.visionworld.sensormatrix.DenseSensorMatrix: Return the number of columns of this sensor matrix.
columns() - Method in class org.simbrain.world.visionworld.sensormatrix.SparseSensorMatrix: Return the number of columns of this sensor matrix.
ComboBoxRenderer - Class in org.simbrain.util: ComboBoxRenderer formats and inserts images into combo boxes.
ComboBoxRenderer() - Constructor for class org.simbrain.util.ComboBoxRenderer: Combo box renderer.
ComboBoxWrapper - Interface in org.simbrain.util.propertyeditor: Wrapper for any object to be represented by a combo box in a ReflectivePropertyEditor.
CommandLineReader - Class in org.simbrain.console: This is a quick hack to turn empty lines entered interactively on the command line into ';\n' empty lines for the interpreter.
CommandLineReader(Reader) - Constructor for class org.simbrain.console.CommandLineReader
commit(NetworkPanel, String) - Method in class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel: Create the layered network.
commit() - Method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Commit the changes in the panel to the object being edited.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.AbstractConnectionPanel: Commit any changes made in the panel to the connection object being represented.
commitChanges(SynapseGroup) - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionPanel: Use the state of the gui to set the connection object of the synapse group being created.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.AllToAllPanel
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.OneToOnePanel: Commit any changes made in the panel to the connection object being represented.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.RadialPanel: Commit any changes made in the panel to the connection object being represented.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel: Commit any changes made in the panel to the connection object being represented.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.QuickConnectPreferencesPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(SynapseGroup) - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel: Commits changes to a synapse group.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel: For loose neurons just commits changes to the randomizer panels.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel: Applies the settings in the randomizer panel to the randomizer given to or created by this panel if the display triangle displays "Enabled".
commitChanges() - Method in class org.simbrain.network.gui.dialogs.ConnectivityAdjustmentPanel
commitChanges() - Method in class org.simbrain.network.gui.dialogs.group.NeuronGroupPanel
commitChanges() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.group.SynapseGroupDialog: Commit changes.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.layout.AbstractLayoutPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.layout.GridLayoutPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.layout.HexagonalGridLayoutPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.layout.LayoutDialog
commitChanges() - Method in class org.simbrain.network.gui.dialogs.layout.LineLayoutPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Called externally to change values in the layout reflecting changes in the dialog.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog: Create an ESN from the data entered in this panel.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.network.WTAPropertiesPanel
commitChanges() - Method in class org.simbrain.network.gui.dialogs.NetworkPropertiesPanel: Commits changes when ok is pressed in parent dialog.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.AdExIFRulePanel
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.AdExIFRulePanel
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.LogisticGeneratorPanel
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.LogisticGeneratorPanel
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.RandomGeneratorPanel
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.RandomGeneratorPanel
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.SinusoidalGeneratorPanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.SinusoidalGeneratorPanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.StochasticGeneratorPanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.StochasticGeneratorPanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronDialog: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended: Specifically: Uses the values from text fields to alter corresponding values in the neuron(s) being edited.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AdditiveRulePanel
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AdditiveRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.BinaryRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.BinaryRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ContinuousSigmoidalRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ContinuousSigmoidalRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.HodgkinHuxleyRulePanel
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.HodgkinHuxleyRulePanel
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IACRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IACRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IntegrateAndFireRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IntegrateAndFireRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IzhikevichRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IzhikevichRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.LinearRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.LinearRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.PointNeuronRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.PointNeuronRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.RunningAverageRulePanel
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.RunningAverageRulePanel
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SigmoidalRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SigmoidalRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SpikingThresholdRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SpikingThresholdRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges(Neuron) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ThreeValueRulePanel: Called to commit changes to a single neuron.
commitChanges(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ThreeValueRulePanel: Called externally when the dialog is closed, to commit any changes made to many neurons simultaneously.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel: Commit changes to the panel to the synapse update rule of a template synapse.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel: Commit changes to the panel to the synapse update rules of the synapses being edited.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Synapse) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel: Commit changes to the panel.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel
commitChanges(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesExtended: Uses the values from text fields to alter corresponding values in the synapse(s) being edited.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple
commitChanges() - Method in class org.simbrain.network.gui.trainer.DataPanel: Called externally when the data in the visible table can be converted to a double array and applied to the data holder.
commitChanges() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineTrainingPanel
commitChanges() - Method in class org.simbrain.network.gui.trainer.TrainingSetPanel
commitChanges() - Method in class org.simbrain.util.environment.SmellSourcePanel: Set values based on fields.
commitChanges() - Method in class org.simbrain.util.widgets.ApplyPanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in interface org.simbrain.util.widgets.EditablePanel: Uses the data in the fields of the panel which implements this to alter the data of an appropriate model object accordingly.
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.AbstractEffectorPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.AbstractSensorPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.AddEffectorDialog: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.AddSensorDialog: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.EntityDialog: Commits changes to the entity that are shown in the dialog.
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.HearingSensorPanel
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.SmellSensorPanel
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.SpeechEffectorPanel
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.StraightEffectorPanel
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.TileSensorPanel
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.TileSetPanel
commitChanges() - Method in class org.simbrain.world.odorworld.dialogs.TurningEffectorPanel
commitChanges() - Method in class org.simbrain.world.textworld.dictionary.TokenDictionaryPanel
commitChanges() - Method in class org.simbrain.world.textworld.dictionary.TokenToVectorPanel
commitChanges() - Method in class org.simbrain.world.textworld.dictionary.VectorToTokenPanel
commitRandom(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronNoiseGenPanel: Commits the randomizer for the list of neurons being edited.
commitRandom(Randomizer) - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel: Called externally when dialog is being closed.
commitRandom(Randomizer) - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel: Called externally when dialog is being closed.
compare(Neuron, Neuron) - Method in class org.simbrain.network.core.Network.PriorityComparator
compare(Neuron, Neuron) - Method in class org.simbrain.network.gui.NeuronComparator
compare(Neuron, Neuron) - Method in class org.simbrain.network.subnetworks.KWTA.PointNeuronComparator
compare(Neuron, Neuron) - Method in enum org.simbrain.network.util.OrientationComparator
compareDatasets() - Method in class org.simbrain.util.projection.Projector: Check the integrity of the two datasets by checking: (1) That the low-d set is at least 2 dimensions (2) That the low d space is lower dimensional than the hi d space (3) That both datasets have the same number of points.
CompetitiveGroup - Class in org.simbrain.network.subnetworks: Competitive implements a simple competitive network.
CompetitiveGroup(Network, int) - Constructor for class org.simbrain.network.subnetworks.CompetitiveGroup: Constructs a competitive network with specified number of neurons.
CompetitiveGroup(Network, CompetitiveGroup) - Constructor for class org.simbrain.network.subnetworks.CompetitiveGroup: Copy constructor.
CompetitiveGroup.UpdateMethod - Enum in org.simbrain.network.subnetworks: Specific implementation of competitive learning.
CompetitiveGroupCreationDialog - Class in org.simbrain.network.gui.dialogs.network: CompetitiveDialog.
CompetitiveGroupCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.CompetitiveGroupCreationDialog: This method is the default constructor.
CompetitiveGroupNode - Class in org.simbrain.network.gui.nodes.neuronGroupNodes: PNode representation of Competitive network.
CompetitiveGroupNode(NetworkPanel, CompetitiveGroup) - Constructor for class org.simbrain.network.gui.nodes.neuronGroupNodes.CompetitiveGroupNode: Create a Competitive Network PNode.
CompetitiveNetwork - Class in org.simbrain.network.subnetworks: CompetitiveNetwork is a small network encompassing a Competitive group.
CompetitiveNetwork(Network, int, int, Point2D) - Constructor for class org.simbrain.network.subnetworks.CompetitiveNetwork: Construct an SOM Network.
CompetitiveNetworkCreationDialog - Class in org.simbrain.network.gui.dialogs.network: CompetitiveDialog is used as an assistant to create Competitive networks.
CompetitiveNetworkCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.CompetitiveNetworkCreationDialog: This method is the default constructor.
CompetitiveNetworkNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of competitive network.
CompetitiveNetworkNode(NetworkPanel, CompetitiveNetwork) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.CompetitiveNetworkNode: Create a competitive Network PNode.
CompetitivePropertiesPanel - Class in org.simbrain.network.gui.dialogs.network: CompetitivePropertiesDialog is a panel box for setting the properties of a competitive network.
CompetitivePropertiesPanel.CompetitivePropsPanelType - Enum in org.simbrain.network.gui.dialogs.network: Whether the panel is for creating a competitive group, network, or editing a competitive group.
CompetitiveTrainer - Class in org.simbrain.network.trainers: A trainer for SOM Networks.
CompetitiveTrainer(CompetitiveNetwork) - Constructor for class org.simbrain.network.trainers.CompetitiveTrainer: Construct the competitive network trainer.
CompetitiveTrainerControlsPanel - Class in org.simbrain.network.gui.trainer.subnetworkTrainingPanels: Training panel for Competitive Network.
CompetitiveTrainerControlsPanel(NetworkPanel, CompetitiveTrainer, CompetitiveNetwork) - Constructor for class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.CompetitiveTrainerControlsPanel: Construct the Competitive Training Controls Panel.
CompetitiveTrainingDialog - Class in org.simbrain.network.gui.dialogs.network: Dialog for training a Competitive network.
CompetitiveTrainingDialog(NetworkPanel, CompetitiveNetwork) - Constructor for class org.simbrain.network.gui.dialogs.network.CompetitiveTrainingDialog: Construct the dialog.
CompletionSignal - Interface in org.simbrain.workspace.updater: Simple interface for calling back when completed.
component - Variable in class org.simbrain.network.desktop.NetworkPanelDesktop: Reference to Desktop Component.
component - Variable in class org.simbrain.world.dataworld.DesktopJTable: Parent component.
componentAdded(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.ComponentPanel: Called when a component is added.
componentAdded(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.CouplingMenuComponent: Called when a component is added.
componentAdded(WorkspaceComponent) - Method in interface org.simbrain.workspace.WorkspaceListener: Called when a component is added.
componentMap - Variable in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Associate property names with JComponents that are used to set those values.
componentOnOffToggled() - Method in interface org.simbrain.workspace.WorkspaceComponentListener: Called when the component is turned on or off.
ComponentPanel - Class in org.simbrain.workspace.gui: Displays a list of all currently open workspace components.
ComponentPanel(SimbrainDesktop) - Constructor for class org.simbrain.workspace.gui.ComponentPanel: Workspace component list panel constructor.
ComponentPanel.ComponentTableModel - Class in org.simbrain.workspace.gui: Table model which represents workspace components.
componentRemoved(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.ComponentPanel: Called when a component is removed.
componentRemoved(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.CouplingMenuComponent: Called when a component is removed.
componentRemoved(WorkspaceComponent) - Method in interface org.simbrain.workspace.WorkspaceListener: Called when a component is removed.
components - Variable in class org.simbrain.world.threedee.sensors.Sight
ComponentTableModel() - Constructor for class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
componentUpdated() - Method in class org.simbrain.network.gui.NetworkPanel
componentUpdated() - Method in interface org.simbrain.workspace.WorkspaceComponentListener: Called when the workspace component is updated.
ComponentUpdateListener - Interface in org.simbrain.workspace.updater: The listener interface for observers interested in events related to component update activities.
ComponentUpdatePart - Class in org.simbrain.workspace.updater: Represents a single part of a component update.
ComponentUpdatePart(WorkspaceComponent, Runnable, String, Object) - Constructor for class org.simbrain.workspace.updater.ComponentUpdatePart: Creates a new instance with the given parent, runnable, description and lock.
ComponentUpdatePart(WorkspaceComponent, Runnable, String) - Constructor for class org.simbrain.workspace.updater.ComponentUpdatePart: Creates a new instance with the given parent, runnable, description using this object as the lock.
computeFullBounds(PBounds) - Method in class org.simbrain.network.gui.nodes.OutlinedObjects: Change the full bounds computation to take into account that we are expanding the children's bounds Do this instead of overriding getBoundsReference() since the node is not volatile.
concatenate(T[], T[]) - Static method in class org.simbrain.util.Utils: Concatenate two arrays A, B to produce a third array A + B.
ConcurrentBufferedUpdate - Class in org.simbrain.network.update_actions
ConcurrentBufferedUpdate.CyclicTaskQueue - Class in org.simbrain.network.update_actions: A memory saving version of a BlockingQueue specifically set up to prevent memory leaks in the form of LinkedList nodes and with the express purpose of making synchronization points easier to implement.
CondensedConnectionPanel - Class in org.simbrain.network.gui.dialogs.connect: A panel that combines a DensityBasedConnectionPanel (Sparse) with a SynapsePolarityAndRandomizerPanel with the ability to create a synapse group with the given properties given a source and target neuron group.
CondensedConnectionPanel(NetworkPanel, Window, int) - Constructor for class org.simbrain.network.gui.dialogs.connect.CondensedConnectionPanel: Creates a CondensedConnectionPanel.
ConditionallyEnabledAction - Class in org.simbrain.network.gui.actions: Subclass this class if an action should be enabled or not depending on whether neurons, synapses or both are selected in the network panel.
ConditionallyEnabledAction(NetworkPanel, String, ConditionallyEnabledAction.EnablingCondition) - Constructor for class org.simbrain.network.gui.actions.ConditionallyEnabledAction: Construct the update action.
ConditionallyEnabledAction.EnablingCondition - Enum in org.simbrain.network.gui.actions: Possible conditions under which to enable the action: NEURONS: if at least one neuron is selected SYNAPSES: if at least one synapse is selected ALLITEMS: if at least one synapse or neuron is selected SOURCE_NEURONS: if at least one neuron is designated as source neuron SOURCE_AND_TARGET_NEURONS: if at least one neuron is designated as source and one neuron is designated as target. SOURCE_AND_TARGET_NEURON_GROUPS: if at least one neuron group is designated as source and one neuron group is designated as target.
confirmOverwrite(File) - Method in class org.simbrain.util.SFileChooser: Ask user whether to overwrite the give existing file.
conformToTemplates(Collection<Synapse>, Synapse, Synapse) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Makes the synapses in the given collection conform to the parameters of the given template synapses, which are essentially information ferries.
connectAllToAll(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.connections.AllToAll: Connect all to all using underlying connection object to store parameters.
connectAllToAll(List<Neuron>, List<Neuron>, boolean, boolean, boolean) - Static method in class org.simbrain.network.connections.AllToAll: Connects every source neuron to every target neuron.
connectionDensity - Variable in class org.simbrain.network.connections.Sparse: Generally speaking the connectionDensity parameter represents a probability reflecting how many possible connections between a given source neuron and all available target neurons will actually be made.
ConnectionDialog - Class in org.simbrain.network.gui.dialogs.connect: Dialog wrapper for all connection panels.
ConnectionPanel - Class in org.simbrain.network.gui.dialogs.connect: Panel for editing connection objects when creating new synapse groups.
ConnectionSynapsePropertiesPanel - Class in org.simbrain.network.gui.dialogs.connect: A panel allowing synapse learning rules to be set and random weights to be activated/adjusted, designed with segregation of inhibitory and excitatory weights in mind.
ConnectionUtilities - Class in org.simbrain.network.connections: A set of static utility functions/interfaces/etc for manipulating synapses.
ConnectionUtilities() - Constructor for class org.simbrain.network.connections.ConnectionUtilities
ConnectionUtilities.SynapseParameterGetter<T> - Interface in org.simbrain.network.connections: A functional interface that is intended to check/return the value of some parameter(s) of a(some) synapse(s).
ConnectionUtilities.SynapseParameterSetter<T> - Interface in org.simbrain.network.connections: A functional interface that is intended to be used to set some parameter of the synapse to the specified value.
ConnectivityAdjustmentPanel - Class in org.simbrain.network.gui.dialogs: Panel for adjusting the connectivity between a source and target set of neurons.
ConnectivityAdjustmentPanel(Sparse, NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.ConnectivityAdjustmentPanel
connectLayers(Sparse, Sparse, Sparse) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Connects all the layers of the network based on 3 connection objects each with their own connection parameters.
connectNeuronGroups(NeuronGroup, NeuronGroup, ConnectNeurons) - Method in class org.simbrain.network.core.Network: Connect a source neuron group to a target neuron group using a connection object.
connectNeuronGroups(NeuronGroup, NeuronGroup) - Method in class org.simbrain.network.groups.Subnetwork: Connects one group of neurons to another group of neurons using an All to All connection.
connectNeuronGroups(NeuronGroup, NeuronGroup, ConnectNeurons) - Method in class org.simbrain.network.groups.Subnetwork: Connects two groups of neurons according to some connection style.
connectNeuronGroups(NeuronGroup, NeuronGroup, String, String, ConnectNeurons) - Method in class org.simbrain.network.groups.Subnetwork: Connects two groups of neurons according to some connection style, and allows for custom labels of the neuron groups within the weights label.
connectNeurons(SynapseGroup) - Method in class org.simbrain.network.connections.AllToAll: Connects neurons such that every source neuron is connected to every target neuron.
ConnectNeurons - Interface in org.simbrain.network.connections: Implementing classes create connections (collections of synapses) between groups of neurons.
connectNeurons(SynapseGroup) - Method in interface org.simbrain.network.connections.ConnectNeurons: Apply connection to a synapse group using specified parameters.
connectNeurons(SynapseGroup) - Method in class org.simbrain.network.connections.OneToOne: Apply connection to a synapse group using specified parameters.
connectNeurons(SynapseGroup) - Method in class org.simbrain.network.connections.Radial: Apply connection to a synapse group using specified parameters.
connectNeurons(boolean) - Method in class org.simbrain.network.connections.RadialSimple: Make the connections.
connectNeurons(SynapseGroup) - Method in class org.simbrain.network.connections.RadialSimple
connectNeurons(SynapseGroup) - Method in class org.simbrain.network.connections.RadialSimpleConstrainedKIn
connectNeurons(SynapseGroup) - Method in class org.simbrain.network.connections.Sparse
ConnectNeuronsSimpleAction - Class in org.simbrain.network.gui.actions.connection: Connect neurons action.
ConnectNeuronsSimpleAction(NetworkPanel, Collection<NeuronNode>, NeuronNode) - Constructor for class org.simbrain.network.gui.actions.connection.ConnectNeuronsSimpleAction: Create a new connect neurons action.
connectOneToOne(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.connections.OneToOne: Use this connection object to make connections.
connectOneToOne(List<Neuron>, List<Neuron>, boolean, boolean) - Static method in class org.simbrain.network.connections.OneToOne
connectRadialNoPolarity(List<Neuron>, List<Neuron>, double, double, boolean) - Static method in class org.simbrain.network.connections.Radial
connectRadialPolarized(List<Neuron>, List<Neuron>, double, double, double, double, double, double, boolean) - Static method in class org.simbrain.network.connections.Radial
connectSparse(List<Neuron>, List<Neuron>) - Method in class org.simbrain.network.connections.Sparse: Connect source to target neurons using this instance of the sparse object's properties to set all parameters of the connections.
connectSparse(List<Neuron>, List<Neuron>, double, boolean, boolean, boolean) - Static method in class org.simbrain.network.connections.Sparse: Connects two lists of neurons with synapses assigning connections between source and target neurons randomly in such a way that results in "sparsity" percentage of possible connections being created.
ConsoleComponent - Class in org.simbrain.console: Workspace component corresponding to a beanshell window.
ConsoleComponent(String) - Constructor for class org.simbrain.console.ConsoleComponent: Constructor.
ConsoleDesktopComponent - Class in org.simbrain.console: Desktop graphical component displaying a beanshell interpreter.
ConsoleDesktopComponent(GenericFrame, ConsoleComponent) - Constructor for class org.simbrain.console.ConsoleDesktopComponent: Constructor.
Consumer - Class in org.simbrain.network.update_actions.concurrency_tools: The underlying runnable consumer assigned to a thread, which consumes network update tasks i.e.
Consumer(ConcurrentBufferedUpdate.CyclicTaskQueue, int) - Constructor for class org.simbrain.network.update_actions.concurrency_tools.Consumer
Consumer<E> - Interface in org.simbrain.workspace: A wrapper for a public setter in a Simbrain object.
consumer - Variable in class org.simbrain.workspace.gui.CouplingMenuConsumer: The base attribute for this menu.
container - Variable in class org.simbrain.network.gui.dialogs.text.TextDialog: Main container.
containsAsIncoming(SynapseGroup) - Method in class org.simbrain.network.groups.NeuronGroup
containsAsOutgoing(SynapseGroup) - Method in class org.simbrain.network.groups.NeuronGroup
containseEquivalentCoupling(Coupling<?>) - Method in class org.simbrain.workspace.CouplingManager: Returns whether the coupling is referenced by this manager.
containsEntity(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Does the world contain this entity?
containsNeuron(Neuron) - Method in class org.simbrain.network.groups.NeuronGroup: True if the group contains the specified neuron.
ContextMenuEventHandler - Class in org.simbrain.network.gui: Context menu event handler.
ContextMenuEventHandler(NetworkPanel) - Constructor for class org.simbrain.network.gui.ContextMenuEventHandler: Construct with a network panel.
contextualDecrement(Neuron) - Method in class org.simbrain.network.core.NeuronUpdateRule: Decrement a neuron by increment, respecting neuron specific constraints.
contextualDecrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
contextualDecrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Decrement a neuron by increment, respecting neuron specific constraints.
contextualDecrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.DecayRule: Decrement a neuron by increment, respecting neuron specific constraints.
contextualDecrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.IACRule: Decrement a neuron by increment, respecting neuron specific constraints.
contextualDecrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.LinearRule: Decrement a neuron by increment, respecting neuron specific constraints.
contextualDecrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.SigmoidalRule
contextualDecrementSelectedObjects() - Method in class org.simbrain.network.gui.NetworkPanel: Invoke contextual decrement (which respects neuron specific rules) on selected objects.
contextualIncrement(Neuron) - Method in class org.simbrain.network.core.NeuronUpdateRule: Increment a neuron by increment, respecting neuron specific constraints.
contextualIncrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
contextualIncrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Increment a neuron by increment, respecting neuron specific constraints.
contextualIncrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.DecayRule: Increment a neuron by increment, respecting neuron specific constraints.
contextualIncrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.IACRule: Increment a neuron by increment, respecting neuron specific constraints.
contextualIncrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.LinearRule: Increment a neuron by increment, respecting neuron specific constraints.
contextualIncrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
contextualIncrement(Neuron) - Method in class org.simbrain.network.neuron_update_rules.SigmoidalRule
contextualIncrementSelectedObjects() - Method in class org.simbrain.network.gui.NetworkPanel: Invoke contextual increment (which respects neuron specific rules) on selected objects.
ContinuousSigmoidalRule - Class in org.simbrain.network.neuron_update_rules: Continuous Sigmoidal Rule provides various squashing function ouputs for a neuron whose activation is numerically integrated continuously over time.
ContinuousSigmoidalRule() - Constructor for class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Default sigmoidal.
ContinuousSigmoidalRule(SquashingFunction) - Constructor for class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Construct a sigmoid update with a specified implementation.
ContinuousSigmoidalRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels
convertV(float) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule: Converts a voltage from the modern convention to the convention used by the program.
ConvolvedJumpAndDecay - Class in org.simbrain.network.synapse_update_rules.spikeresponders
ConvolvedJumpAndDecay() - Constructor for class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
ConvolvedJumpAndDecayPanel - Class in org.simbrain.network.gui.dialogs.synapse.spike_responders: A panel for setting the values of a convolved jump and decay spike responder.
ConvolvedJumpAndDecayPanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel: This method is the default constructor.
copy() - Method in class org.simbrain.network.gui.NetworkPanel: Copy to the clipboard.
CopyableGroup<T extends Group> - Interface in org.simbrain.network.groups: An interface so that subclasses of groups can be copied accurately.
CopyAction - Class in org.simbrain.network.gui.actions.edit: Copy action.
CopyAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.CopyAction: Create a new copy action with the specified network panel.
copyActivations(NeuronGroup) - Method in class org.simbrain.network.groups.NeuronGroup: Copy activations from one neuron group to this one.
copyEntity(BasicEntity) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Copy an entity from a world.
copyItem(OdorWorldEntity) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Copy an abstract entity from a world.
CopyPaste - Class in org.simbrain.network.util: CopyPaste provides utilities for creating copies of arbitrary collections of network objects (neurons, synapses, groups, text objects, etc.).
CopyPaste() - Constructor for class org.simbrain.network.util.CopyPaste
copyTemplateSynapse(Synapse) - Static method in class org.simbrain.network.core.Synapse: Makes a deep copy of a template synapse (one with no source or target).
coupleOneToMany(List<PotentialProducer>, List<PotentialConsumer>) - Method in class org.simbrain.workspace.Workspace: Couple each source attribute to all target attributes.
coupleOneToOne(List<PotentialProducer>, List<PotentialConsumer>) - Method in class org.simbrain.workspace.Workspace: Couple each source attribute to one target attribute, as long as there are target attributes to couple to.
Coupling<E> - Class in org.simbrain.workspace: A coupling is an object that allows different objects in the Simbrain workspace to communicate with each other.
Coupling(Consumer<E>) - Constructor for class org.simbrain.workspace.Coupling: Create a coupling between a specified consuming attribute, without yet specifying the corresponding producing attribute.
Coupling(Producer<E>) - Constructor for class org.simbrain.workspace.Coupling: Create a coupling between a specified producing attribute, without yet specifying the corresponding consuming attribute.
Coupling(Producer<E>, Consumer<E>) - Constructor for class org.simbrain.workspace.Coupling: Create a new coupling between the specified producing attribute and consuming attribute.
Coupling(PotentialProducer, PotentialConsumer) - Constructor for class org.simbrain.workspace.Coupling: Create a new coupling by actualizing a potential producer and a potential consumer.
couplingAdded(Coupling) - Method in class org.simbrain.plot.projection.ProjectionComponent
couplingAdded(Coupling<?>) - Method in interface org.simbrain.workspace.CouplingListener: Called when a coupling is added.
couplingAdded(Coupling) - Method in class org.simbrain.workspace.gui.CouplingListPanel: Called when a coupling is added.
couplingAdded(Coupling<?>) - Method in class org.simbrain.workspace.WorkspaceComponent: Called when a coupling is attached to this component.
CouplingListener - Interface in org.simbrain.workspace: Listener for coupling related events.
CouplingListPanel - Class in org.simbrain.workspace.gui: Displays a list of the current couplings in the network.
CouplingListPanel(SimbrainDesktop, Vector<Coupling<?>>) - Constructor for class org.simbrain.workspace.gui.CouplingListPanel: Creates a new coupling list panel using the applicable desktop and coupling lists.
CouplingManager - Class in org.simbrain.workspace: Manages all the couplings for a Workspace instance.
CouplingManager(Workspace) - Constructor for class org.simbrain.workspace.CouplingManager: Construct a coupling manager.
CouplingMenuComponent - Class in org.simbrain.workspace.gui: A menu for creating a set of couplings from one component to another.
CouplingMenuComponent(String, Workspace, WorkspaceComponent) - Constructor for class org.simbrain.workspace.gui.CouplingMenuComponent
CouplingMenuConsumer - Class in org.simbrain.workspace.gui: Menu for making a single coupling.
CouplingMenuConsumer(String, Workspace, PotentialConsumer) - Constructor for class org.simbrain.workspace.gui.CouplingMenuConsumer: Construct the menu.
CouplingMenuItem - Class in org.simbrain.workspace.gui: A menu item corresponding to a potential coupling.
CouplingMenuItem(Workspace, String, PotentialProducer, PotentialConsumer) - Constructor for class org.simbrain.workspace.gui.CouplingMenuItem: Creates a new instance.
CouplingMenuProducer - Class in org.simbrain.workspace.gui: Menu for making a single coupling.
CouplingMenuProducer(String, Workspace, PotentialProducer) - Constructor for class org.simbrain.workspace.gui.CouplingMenuProducer: Construct the menu.
couplingRemoved(Coupling<?>) - Method in interface org.simbrain.workspace.CouplingListener: Called when a coupling is removed.
couplingRemoved(Coupling) - Method in class org.simbrain.workspace.gui.CouplingListPanel: Called when a coupling is removed.
couplingRemoved(Coupling<?>) - Method in class org.simbrain.workspace.WorkspaceComponent: Called when a coupling attached to this component is removed.
createAddNeuronsDialog(NetworkPanel) - Static method in class org.simbrain.network.gui.dialogs.neuron.AddNeuronsDialog: A factory method that creates an AddNeuronsDialog to prevent references to "this" from escaping during construction.
createAlignMenu() - Method in class org.simbrain.network.gui.NetworkPanel: Return the align sub menu.
createApplyPanel(EditablePanel) - Static method in class org.simbrain.util.widgets.ApplyPanel: A factory method to create an apply panel.
createAttachMenuBar(GenericFrame, ScriptEditor) - Method in class org.simbrain.util.scripteditor.ScriptEditor: Creates the menu bar.
createAttributeSet(String, int, boolean, boolean) - Static method in class org.simbrain.network.gui.nodes.TextNode: Creates an attribute set of the specified kind.
createBasicNeuronInfoPanel(List<Neuron>, Window) - Static method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple: Creates a basic neuron info panel.
createBasicNeuronInfoPanel(List<Neuron>, Window, boolean) - Static method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple: Creates a basic neuron info panel.
createBasicSynapseInfoPanel(Collection<Synapse>, Window) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple: Creates a basic synapse info panel.
createBasicSynapseInfoPanel(Collection<Synapse>, Window, boolean) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple: Creates a basic synapse info panel.
createBidirectionalSynapseGN(NetworkPanel, SynapseGroup, SynapseGroup) - Static method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional: Create a bidirectional simple synapse group PNode.
createBlankSynapseInfoPanel(Collection<Synapse>, Window, boolean) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple
createBlankSynapsePropertiesPanel(Collection<Synapse>, Window, boolean) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
createCombinedNeuronInfoPanel(List<Neuron>, Window) - Static method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel: Creates a combined neuron info panel, which includes the basic neuron info panel and a neuron update settings panel.
createCombinedNeuronInfoPanel(List<Neuron>, Window, boolean) - Static method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel: Creates a combined neuron info panel, which includes the basic neuron info panel and a neuron update settings panel.
createCombinedNeuronInfoPanel(List<Neuron>, Window, boolean, boolean) - Static method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel: Creates a combined neuron info panel, which includes the basic neuron info panel and a neuron update settings panel.
createCompetitivePropertiesPanel(NetworkPanel, CompetitivePropertiesPanel.CompetitivePropsPanelType) - Static method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel: A factory method for creating a competitive properties panel for cases where the panel is being created.
createCompetitivePropertiesPanel(NetworkPanel, CompetitiveGroup) - Static method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel: Creates a competitive properties panel from a CompetitiveGroup allowing that group to be edited.
createConcurrentBufferedUpdate(Network) - Static method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate: A static factory method that creates a concurrent buffered update class for a network.
createConnectionDialog(AbstractConnectionPanel, ConnectNeurons, NetworkPanel) - Static method in class org.simbrain.network.gui.dialogs.connect.ConnectionDialog: Create an instance of a connection dialog.
createConnectionPanel(Window, NetworkPanel) - Static method in class org.simbrain.network.gui.dialogs.connect.ConnectionPanel: Construct a connection panel.
createConsumer(Object, String, Class<?>[], Object[], String) - Method in class org.simbrain.workspace.AttributeManager: Create a consumer.
createConsumer(PotentialAttribute) - Method in class org.simbrain.workspace.AttributeManager: Create an actual consumer from a potential consumer.
createConsumer() - Method in class org.simbrain.workspace.PotentialConsumer: Actualize this potential attribute into a consumer.
createContextMenu() - Method in class org.simbrain.network.gui.nodes.NeuronNode
createContinuousSigmoidalRulePanel() - Static method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ContinuousSigmoidalRulePanel: Creates a fully functional continuous sigmoidal rule panel.
createDataWorld(NumericTable, String) - Static method in class org.simbrain.world.dataworld.DataWorldComponent: Create the data world component.
createDesktopComponent(GenericFrame, WorkspaceComponent) - Static method in class org.simbrain.workspace.gui.SimbrainDesktop: Creates an instance of the proper wrapper class around the provided instance.
createEditMenu() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Create and return a new Edit menu for this Network panel.
createEditToolBar() - Method in class org.simbrain.network.gui.NetworkPanel: Create the edit tool bar.
createESNDialog(NetworkPanel) - Static method in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog: A static initializer.
createFileMenu() - Method in class org.simbrain.network.desktop.NetworkDesktopComponent: Create and return a new File menu for this Network panel.
createFilter() - Method in interface org.simbrain.world.visionworld.filter.editor.FilterEditor: Create a new instance of Filter from the properties of this filter editor.
createFilter() - Method in class org.simbrain.world.visionworld.filter.editor.PixelAccumulatorEditor: Create a new instance of Filter from the properties of this filter editor.
createFilter() - Method in class org.simbrain.world.visionworld.filter.editor.RandomFilterEditor: Create a new instance of Filter from the properties of this filter editor.
createFilter() - Method in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: Create a new instance of Filter from the properties of this filter editor.
createFilter() - Method in class org.simbrain.world.visionworld.filter.editor.UniformFilterEditor: Create a new instance of Filter from the properties of this filter editor.
createHelpMenu() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Create and return a new Help menu for this Network panel.
createHistogram() - Method in class org.simbrain.plot.histogram.HistogramPanel: Create the histogram panel based on the data.
createInsertMenu() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Create and return a new Insert menu for this Network panel.
createMainToolBar() - Method in class org.simbrain.network.gui.NetworkPanel: Create the main tool bar.
createNetworkContextMenu() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: This version adds the script menu.
createNetworkContextMenu() - Method in class org.simbrain.network.gui.NetworkPanel: Create a new context menu for this Network panel.
createNeuronDialog(Collection<NeuronNode>, Frame) - Static method in class org.simbrain.network.gui.dialogs.neuron.NeuronDialog
createNeuronDialog(Collection<NeuronNode>) - Static method in class org.simbrain.network.gui.dialogs.neuron.NeuronDialog: Creates a neuron dialog from a collection of NeuronNodes.
createNeuronGroupPanel(NetworkPanel, Window) - Static method in class org.simbrain.network.gui.dialogs.group.NeuronGroupPanel: Creates a neuron group panel meant for creating neuron groups.
createNeuronGroupPanel(NetworkPanel, NeuronGroup, Window) - Static method in class org.simbrain.network.gui.dialogs.group.NeuronGroupPanel: Creates a neuron group panel meant for editing an existing neuron group.
createNewRow(T) - Method in class org.simbrain.util.table.MutableTable: Create a new row for the table, with a specified value.
createNewRow(T, int) - Method in class org.simbrain.util.table.MutableTable: Create a new row for the table, with a specified value.
createPixelMatrix() - Method in class org.simbrain.world.visionworld.pixelmatrix.editor.BufferedImagePixelMatrixEditor: Create a new instance of PixelMatrix from the properties of this pixel matrix editor.
createPixelMatrix() - Method in interface org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditor: Create a new instance of PixelMatrix from the properties of this pixel matrix editor.
createPixelMatrix() - Method in class org.simbrain.world.visionworld.pixelmatrix.editor.ScreenCapturePixelMatrixEditor: Create a new instance of PixelMatrix from the properties of this pixel matrix editor.
createPixelMatrix() - Method in class org.simbrain.world.visionworld.VisionWorld: Create pixel matrix.
CreatePixelMatrixAction - Class in org.simbrain.world.visionworld.action: Create pixel matrix action.
CreatePixelMatrixAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.CreatePixelMatrixAction: Create a new create pixel matrix action.
CreatePixelMatrixDialog - Class in org.simbrain.world.visionworld.dialog: Create pixel matrix dialog.
CreatePixelMatrixDialog(VisionWorld) - Constructor for class org.simbrain.world.visionworld.dialog.CreatePixelMatrixDialog: Create a new pixel matrix dialog.
createPolarityRatioPanel(Window, SynapsePolarityAndRandomizerPanel.RandBehavior) - Static method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
createPolarityRatioPanel(Window, SynapsePolarityAndRandomizerPanel.RandBehavior, SynapseGroup) - Static method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
createPolarityRatioPanel(Window, PolarizedRandomizer, PolarizedRandomizer, boolean, boolean) - Static method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
createPolarityRatioPanel(Window) - Static method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
createPolarityRatioPanel(Window, SynapseGroup) - Static method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
createPotentialConsumer(Object, String, Class<?>[], Object[]) - Method in class org.simbrain.workspace.AttributeManager: Create a potential consumer using auxiliary arguments.
createPotentialConsumer(Object, String, Class<?>) - Method in class org.simbrain.workspace.AttributeManager: Create a potential consumer without auxiliary arguments.
createPotentialConsumer(Object, AttributeType) - Method in class org.simbrain.workspace.AttributeManager: Create a potential consumer using an attribute type.
createPotentialProducer(Object, String, Class<?>, Class<?>[], Object[]) - Method in class org.simbrain.workspace.AttributeManager: Create a potential producer using auxiliary arguments.
createPotentialProducer(Object, String, Class<?>) - Method in class org.simbrain.workspace.AttributeManager: Create a potential producer (without auxiliary arguments).
createPotentialProducer(Object, AttributeType) - Method in class org.simbrain.workspace.AttributeManager: Create a potential producer using an attribute type.
createProducer(Object, String, Class<?>, Class<?>[], Object[], String) - Method in class org.simbrain.workspace.AttributeManager: Create a producer based on an argument.
createProducer(PotentialAttribute) - Method in class org.simbrain.workspace.AttributeManager: Create an actual producer from a potential producer.
createProducer() - Method in class org.simbrain.workspace.PotentialProducer: Actualize this potential attribute into a producer.
createReaderPanel(ReaderWorld, JToolBar) - Static method in class org.simbrain.world.textworld.ReaderPanel: Factory method for panel (so that listeners are not created in constructor).
createReaderPanel(ReaderWorld) - Static method in class org.simbrain.world.textworld.ReaderPanel: Factory method for panel (so that listeners are not created in constructor).
createReaderWorld() - Static method in class org.simbrain.world.textworld.ReaderWorld: Factory method for Reader world.
createRecurrentSynapseGN(NetworkPanel, SynapseGroup) - Static method in class org.simbrain.network.gui.nodes.SynapseGroupNodeRecurrent
createRow(String, String, JComponent) - Static method in class org.simbrain.network.gui.NetworkUtils: Helper method for creating formatted rows in dialog boxes, which consist of a label, a component, and some tool-tip for the label.
createRunToolBar() - Method in class org.simbrain.network.gui.NetworkPanel: Create the iteration tool bar.
createSelectionMenu() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Create a selection JMenu.
createSensorMatrix(Filter) - Method in class org.simbrain.world.visionworld.sensormatrix.editor.DenseSensorMatrixEditor: Create a new instance of SensorMatrix from the properties of this sensor matrix editor and the specified default filter.
createSensorMatrix(Filter) - Method in interface org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditor: Create a new instance of SensorMatrix from the properties of this sensor matrix editor and the specified default filter.
createSensorMatrix(Filter) - Method in class org.simbrain.world.visionworld.sensormatrix.editor.SparseSensorMatrixEditor: Create a new instance of SensorMatrix from the properties of this sensor matrix editor and the specified default filter.
createSensorMatrix() - Method in class org.simbrain.world.visionworld.VisionWorld: Create sensor matrix.
CreateSensorMatrixAction - Class in org.simbrain.world.visionworld.action: Create sensor matrix action.
CreateSensorMatrixAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.CreateSensorMatrixAction: Create a new create sensor matrix action.
CreateSensorMatrixDialog - Class in org.simbrain.world.visionworld.dialog: Create sensor matrix dialog.
CreateSensorMatrixDialog(VisionWorld) - Constructor for class org.simbrain.world.visionworld.dialog.CreateSensorMatrixDialog: Create a new create sensor matrix dialog.
createSigmoidalRulePanel() - Static method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SigmoidalRulePanel: Creates a fully functional discrete sigmoidal rule panel.
createSpacingMenu() - Method in class org.simbrain.network.gui.NetworkPanel: Return the space sub menu.
createSparsityAdjustmentPanel(Sparse, NetworkPanel) - Static method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel: Create the sparsity based connection panel.
createSynapseAdjustmentPanel(NetworkPanel, List<Synapse>) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel
createSynapseDialog(Collection<SynapseNode>) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog: Creates a synapse dialog from a collection of SynapseNodes.
createSynapseDialog(Collection<SynapseNode>, Frame) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog
createSynapseDialog(List<Synapse>) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog: Creates synapse dialog from a collection of synapses.
createSynapseGroup(NeuronGroup, NeuronGroup) - Static method in class org.simbrain.network.groups.SynapseGroup: Completely creates a synapse group between the two neuron groups with all default parameters.
createSynapseGroup(NeuronGroup, NeuronGroup, double) - Static method in class org.simbrain.network.groups.SynapseGroup: Completely creates a synapse group with the desired parameters.
createSynapseGroup(NeuronGroup, NeuronGroup, ConnectNeurons) - Static method in class org.simbrain.network.groups.SynapseGroup: Completely creates a synapse group with the desired parameters.
createSynapseGroup(NeuronGroup, NeuronGroup, ConnectNeurons, double) - Static method in class org.simbrain.network.groups.SynapseGroup: Completely creates a synapse group with the desired parameters.
createSynapseGroup(NeuronGroup, NeuronGroup, ConnectNeurons, double, PolarizedRandomizer, PolarizedRandomizer) - Static method in class org.simbrain.network.groups.SynapseGroup: Completely creates a synapse group with the desired parameters.
createSynapseGroup(NeuronGroup, NeuronGroup) - Method in class org.simbrain.network.gui.dialogs.connect.CondensedConnectionPanel: Creates a synapse group from the parameters in the panel and between two neuron groups.
createSynapseGroupAdjustmentPanel(Window, SynapseGroup, boolean) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel: Create the synapse group adjustment panel.
createSynapseGroupDialog(NetworkPanel, NeuronGroup, NeuronGroup) - Static method in class org.simbrain.network.gui.dialogs.group.SynapseGroupDialog: Creates a synapse group dialog based on a source and target neuron group.
createSynapseGroupDialog(NetworkPanel, SynapseGroup) - Static method in class org.simbrain.network.gui.dialogs.group.SynapseGroupDialog: Creates a synapse group dialog based on a given synapse group it goes without saying that this means this dialog will be editing the given synapse group.
createSynapseGroupDialog(Frame, NetworkPanel, SynapseGroup) - Static method in class org.simbrain.network.gui.dialogs.group.SynapseGroupDialog
createSynapsePropertiesPanel(Window, SynapseGroup) - Static method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel
createSynapsePropertiesPanel(Window, Collection<Synapse>) - Static method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel
createSynapsePropertiesPanel(Window) - Static method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel
createSynapsePropertiesPanel(Collection<Synapse>, Window) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel: Creates a combined synapse info panel, which includes the basic synapse info panel and a synapse update settings panel.
createSynapsePropertiesPanel(Collection<Synapse>, Window, boolean) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel: Creates a combined synapse info panel, which includes the basic synapse info panel and a synapse update settings panel.
createTable(SimbrainDataTable) - Static method in class org.simbrain.util.table.SimbrainJTable: Creates a new simbrain gui jtable.
createTestInputPanel(NetworkPanel, NeuronGroup) - Static method in class org.simbrain.network.gui.dialogs.TestInputPanel
createTestInputPanel(NetworkPanel, List<Neuron>) - Static method in class org.simbrain.network.gui.dialogs.TestInputPanel: Create panel using a network panel and a list of selected neurons for case where no data holder is provided (currently, applying test inputs to an arbitrary set of loose neurons).
createTestInputPanel(NetworkPanel, List<Neuron>, NumericMatrix) - Static method in class org.simbrain.network.gui.dialogs.TestInputPanel: Create the test input panel.
createToolTip() - Method in class org.simbrain.network.gui.NetworkPanel: Overridden so that multi-line tooltips can be used.
createToolTip() - Method in class org.simbrain.world.visionworld.VisionWorld
createUI(JComponent) - Static method in class org.simbrain.util.MultiLineToolTipUI
createUpdateAction(Workspace, WorkspaceComponentDeserializer, ArchiveContents.ArchivedUpdateAction) - Method in class org.simbrain.workspace.ArchiveContents: Create a "real" update action from an archived update action.
createVectorDictionaryEditor(JPanel, JPanel) - Static method in class org.simbrain.world.textworld.dictionary.DictionarySelector: Factory method to create the editor.
createViewMenu() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Create and return a new View menu for this Network panel.
createVisionWorld() - Method in class org.simbrain.world.threedee.sensors.Sight
cubicBezierMidpoint(Point2D, Point2D, Point2D, Point2D) - Static method in class org.simbrain.util.math.SimbrainMath: Returns the midpoint for a cubic Bezier curve.
CURRENT_CONVERTER - Static variable in class org.simbrain.network.neuron_update_rules.AdExIFRule: A converter from pA to nA, since most other sims in Simbrain use nano Amps.
currentItemChanged(TextWorld.TextItem) - Method in interface org.simbrain.world.textworld.TextListener: The current item has changed.
currentItemChanged(TextWorld.TextItem) - Method in class org.simbrain.world.textworld.TextListener.TextAdapter
CustomToolBar - Class in org.simbrain.network.gui: CustomToolBar is custom tool bar for the Network Panel whose key bindings have been removed so that users may use keyboard shortcuts even while the toolbar is in focus.
CustomToolBar() - Constructor for class org.simbrain.network.gui.CustomToolBar: Private default constructor.
CustomUpdate - Class in org.simbrain.network.update_actions: Update using a custom action saved as a beanshell script.
CustomUpdate(Network, String) - Constructor for class org.simbrain.network.update_actions.CustomUpdate: Create a new custom update action.
CustomUpdate(Network, File) - Constructor for class org.simbrain.network.update_actions.CustomUpdate: Create a new custom update action from a file containing the custom script.
cut() - Method in class org.simbrain.network.gui.NetworkPanel: Cut to the clipboard.
CutAction - Class in org.simbrain.network.gui.actions.edit: Cut action.
CutAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.CutAction: Create a new cut action with the specified network panel.
cutItem(OdorWorldEntity, OdorWorldPanel) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Cuts an object from a world.
CyclicTaskQueue(Collection<Neuron>) - Constructor for class org.simbrain.network.update_actions.ConcurrentBufferedUpdate.CyclicTaskQueue
CyclicTaskQueue(Collection<Neuron>, int) - Constructor for class org.simbrain.network.update_actions.ConcurrentBufferedUpdate.CyclicTaskQueue

D

data - Variable in class org.simbrain.plot.histogram.OverwritableHistogramDataset.ColoredDataSeries: The data in a data series.
DataColoringManager - Class in org.simbrain.util.projection: Manage the coloring of datapoints.
DataColoringManager(Projector) - Constructor for class org.simbrain.util.projection.DataColoringManager: Construct a data coloring manager.
dataHolder - Variable in class org.simbrain.network.gui.trainer.DataPanel: The external object that has the data being edited.
DataNotInitializedException(String) - Constructor for exception org.simbrain.network.trainers.Trainer.DataNotInitializedException
DataPanel - Class in org.simbrain.network.gui.trainer: A data table used to represent input or target data for a group of neurons in a Simbrain neuron.
DataPanel(List<Neuron>, NumericMatrix, int, String) - Constructor for class org.simbrain.network.gui.trainer.DataPanel: Panel which represents input or target data.
DataPoint - Class in org.simbrain.util.projection: Datapoint represents a single datapoint.
DataPoint(double[]) - Constructor for class org.simbrain.util.projection.DataPoint: Initialize a datapoint.
datapointAdded() - Method in interface org.simbrain.util.projection.ProjectorListener: Fired when a new datapoint is added to the projector.
DataPointColored - Class in org.simbrain.util.projection: DataPointColored extends DataPoint adding functions for coloring datapoints.
DataPointColored(double[]) - Constructor for class org.simbrain.util.projection.DataPointColored: Default constructor for adding datasets.
DataPointColoringDialog - Class in org.simbrain.plot.projection: DataPointColoringDialog is a dialog box for making changes to the coloring method in projection plot.
DataPointColoringDialog(ProjectionModel) - Constructor for class org.simbrain.plot.projection.DataPointColoringDialog: Dialog constructor.
Dataset - Class in org.simbrain.util.projection: Dataset represents a set of n-dimensional points.
Dataset(int) - Constructor for class org.simbrain.util.projection.Dataset: Creates and instance of Dataset.
Dataset(int, int) - Constructor for class org.simbrain.util.projection.Dataset: Creates an instance of Dataset.
dataSourceAdded(int) - Method in interface org.simbrain.plot.ChartListener: A data source was added at the specified index.
dataSourceRemoved(int) - Method in interface org.simbrain.plot.ChartListener: A data source was removed at the specified index.
DataWorldComponent - Class in org.simbrain.world.dataworld: DataWorldComponent is a data table which other Simbrain components can use.
DataWorldComponent.ColumnAttribute - Class in org.simbrain.world.dataworld: Object which sets a value of one bar in a bar chart.
DataWorldDesktopComponent - Class in org.simbrain.world.dataworld: DataWorldComponent is a "spreadsheet world" used to send rows of raw data to input nodes.
DataWorldDesktopComponent(GenericFrame, DataWorldComponent) - Constructor for class org.simbrain.world.dataworld.DataWorldDesktopComponent: Default constructor.
debug() - Method in class org.simbrain.network.core.Neuron: Sends relevant information about the network to standard output.
debug() - Method in class org.simbrain.plot.barchart.BarChartModel: Used for debugging model.
debug() - Method in class org.simbrain.plot.projection.ProjectionComponent: Used for debugging model.
debug(Object) - Method in class org.simbrain.util.Logger
debugString() - Method in class org.simbrain.network.gui.NetworkPanel
decay(double) - Method in class org.simbrain.network.core.Synapse: Decay this synapse by the indicated percentage.
DecayRule - Class in org.simbrain.network.neuron_update_rules: DecayNeuron implements various forms of standard decay.
DecayRule() - Constructor for class org.simbrain.network.neuron_update_rules.DecayRule
DecayRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: DecayNeuronPanel.
DecayRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: This method is the default constructor.
decodeNumericByteArray(ByteBuffer) - Method in class org.simbrain.network.core.Synapse
decrementActivation(Neuron) - Method in class org.simbrain.network.core.NeuronUpdateRule: Decrement a neuron by increment.
decrementActivation(double, double) - Method in class org.simbrain.util.projection.DataPointColored: Decrement the activation of this point (for decay trail coloring).
decrementSelectedObjects() - Method in class org.simbrain.network.gui.NetworkPanel: Decreases neuron and synapse activation levels.
decrementWeight() - Method in class org.simbrain.network.core.Synapse: Decrement this weight by increment.
deepCopy() - Method in class org.simbrain.network.core.Neuron: Provides a deep copy of this neuron.
deepCopy() - Method in class org.simbrain.network.core.NeuronUpdateRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.core.SynapseUpdateRule: Returns a deep copy of the update rule.
deepCopy(Network) - Method in interface org.simbrain.network.groups.CopyableGroup: Returns a deep copy of a copyable group using the same root network as the original.
deepCopy(Network) - Method in class org.simbrain.network.groups.NeuronGroup
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel
deepCopy() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.DecayRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.IACRule
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.LinearRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.RunningAverageRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.SigmoidalRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule: Returns a deep copy of the update rule.
deepCopy() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
deepCopy(Network) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup
deepCopy() - Method in class org.simbrain.network.subnetworks.SOMGroup
deepCopy(Network) - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.HebbianRule
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.OjaRule
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.Step
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.UDF: Does not actually copy this UDF object.
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.StaticSynapseRule
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
deepCopy() - Method in class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule
DEFAULT_ACTIVATED - Static variable in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule: Activated.
DEFAULT_ACTIVATION - Static variable in class org.simbrain.util.projection.DataPointColored: Default activation level.
DEFAULT_ACTIVATION - Static variable in class org.simbrain.world.odorworld.sensors.TileSensor: Default Activation Amount.
DEFAULT_ALPHA - Static variable in class org.simbrain.network.subnetworks.SOMGroup: Default alpha.
DEFAULT_ALPHA - Static variable in class org.simbrain.plot.histogram.HistogramPanel: Constant Alpha value governing transparency of histogram colors.
DEFAULT_AMOUNT - Static variable in class org.simbrain.world.odorworld.effectors.Turning: Default amount.
DEFAULT_BASE_LINE_STRENGTH - Static variable in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule: Base line strength.
DEFAULT_BATCH_SIZE - Static variable in class org.simbrain.network.subnetworks.SOMGroup: Default batchSize.
DEFAULT_BIDIRECT_PREF - Static variable in class org.simbrain.network.connections.OneToOne
DEFAULT_BINS - Static variable in class org.simbrain.plot.histogram.HistogramModel: The default number of bins.
DEFAULT_BUMP_RATE - Static variable in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule: Bump rate.
DEFAULT_COLOR - Static variable in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
DEFAULT_CONNECTION_DENSITY - Static variable in class org.simbrain.network.connections.Sparse: The default sparsity (between 0 and 1).
DEFAULT_CONNECTION_MANAGER - Static variable in class org.simbrain.network.groups.SynapseGroup: All to All.
DEFAULT_DECAY_RATE - Static variable in class org.simbrain.network.subnetworks.SOMGroup: The default alphaDecayRate.
DEFAULT_DECAY_RATE - Static variable in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule: Rate at which the synapse will decay.
DEFAULT_DIRECTION - Static variable in class org.simbrain.world.odorworld.effectors.Turning: Default direction.
DEFAULT_DIST_CONST - Static variable in class org.simbrain.network.connections.Radial: For neurons with no polarity.
DEFAULT_DISTRIBUTION - Static variable in class org.simbrain.util.randomizer.Randomizer
DEFAULT_EE_CONST - Static variable in class org.simbrain.network.connections.Radial
DEFAULT_EI_CONST - Static variable in class org.simbrain.network.connections.Radial
DEFAULT_EXCITATORY_RATIO - Static variable in class org.simbrain.network.groups.SynapseGroup: The default ratio (all excitatory) for all synapse groups.
DEFAULT_EXCITATORY_STRENGTH - Static variable in class org.simbrain.network.connections.ConnectionUtilities: The default excitatory strength.
DEFAULT_FF_PREF - Static variable in class org.simbrain.network.connections.Sparse: Sets the default behavior concerning whether or not the number of efferents of each source neurons should be equalized.
DEFAULT_FIRING_THRESHOLD - Static variable in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule: Pseudo spike threshold.
DEFAULT_FLOOR - Static variable in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
DEFAULT_GROUP_SIZE - Static variable in class org.simbrain.network.groups.NeuronGroup: The number of neurons in the group by default.
DEFAULT_H_SPACING - Static variable in class org.simbrain.network.layouts.GridLayout: The default horizontal spacing.
DEFAULT_H_SPACING - Static variable in class org.simbrain.network.layouts.HexagonalGridLayout: The default horizontal spacing.
DEFAULT_HEIGHT - Static variable in class org.simbrain.world.odorworld.sensors.TileSensor: Default height.
DEFAULT_HEIGHT - Static variable in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Default height.
DEFAULT_HEIGHT - Static variable in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Default height.
DEFAULT_IE_CONST - Static variable in class org.simbrain.network.connections.Radial
DEFAULT_II_CONST - Static variable in class org.simbrain.network.connections.Radial
DEFAULT_INCREMENT - Static variable in class org.simbrain.network.core.NeuronUpdateRule: The default increment of a neuron using this rule.
DEFAULT_INHIBITORY_STRENGTH - Static variable in class org.simbrain.network.connections.ConnectionUtilities: The default inhibitory strength.
DEFAULT_INIT_EXTENDED_DISPLAY - Static variable in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple: The default initial display for extended information.
DEFAULT_INIT_NSIZE - Static variable in class org.simbrain.network.subnetworks.SOMGroup: Default initial neighborhood size.
DEFAULT_INITIAL_FUNCTION - Static variable in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog
DEFAULT_INPUT_POPULATION - Static variable in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog
DEFAULT_INPUT_THRESHOLD - Static variable in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule: Input threshold.
DEFAULT_KAPPA - Static variable in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
DEFAULT_LABEL - Static variable in class org.simbrain.world.odorworld.effectors.StraightMovement: Default label.
DEFAULT_LABEL - Static variable in class org.simbrain.world.odorworld.effectors.Turning: Default label.
DEFAULT_LABEL - Static variable in class org.simbrain.world.odorworld.sensors.SmellSensor: Default label.
DEFAULT_LAMBDA - Static variable in class org.simbrain.network.connections.Radial
DEFAULT_LAMBDA - Static variable in class org.simbrain.network.synapse_update_rules.HebbianCPCARule: Default Sigmoidal function.
DEFAULT_LAYOUT - Static variable in class org.simbrain.network.groups.NeuronGroup: Default layout for neuron groups.
DEFAULT_LAYOUT - Static variable in class org.simbrain.network.subnetworks.SOMGroup: Default layout for neuron groups.
DEFAULT_LEAK_CONSTANT - Static variable in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Default leak constant ContinuousSigmoidalRule.leak.
DEFAULT_LEARNING_RATE - Static variable in class org.simbrain.network.synapse_update_rules.HebbianCPCARule: Default Learning rate.
DEFAULT_LEARNING_RATE - Static variable in class org.simbrain.network.synapse_update_rules.HebbianRule: Default learning rate.
DEFAULT_LEARNING_RATE - Static variable in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule: Learning rate.
DEFAULT_LEARNING_RATE - Static variable in class org.simbrain.network.synapse_update_rules.OjaRule: Learning rate.
DEFAULT_LEARNING_RATE - Static variable in class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule: Default learning rate.
DEFAULT_LINE_ORIENTATION - Static variable in class org.simbrain.network.layouts.LineLayout: The default orientation of the line.
DEFAULT_LOWER_BOUND - Static variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: The Default lower bound.
DEFAULT_M - Static variable in class org.simbrain.network.synapse_update_rules.HebbianCPCARule: Default Maximum weight value (see equation 4.19 in O'Reilly and Munakata).
DEFAULT_MANUAL_COLS - Static variable in class org.simbrain.network.layouts.GridLayout: The default allowed state for manual cols.
DEFAULT_MANUAL_COLS - Static variable in class org.simbrain.network.layouts.HexagonalGridLayout: The default allowed state for manual cols.
DEFAULT_NEIGHBORHOOD_DECAY_AMOUNT - Static variable in class org.simbrain.network.subnetworks.SOMGroup: The default neighborhoodDecayAmount.
DEFAULT_NEURON_TYPES - Static variable in class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel: Maps string values to corresponding NeuronUpdateRules for the combo-boxes governing desired Neuron type for a given layer.
DEFAULT_NORMALIZATION_FACTOR - Static variable in class org.simbrain.network.synapse_update_rules.OjaRule: Normalization factor.
DEFAULT_NUM_COLUMNS - Static variable in class org.simbrain.network.layouts.GridLayout: The default number of columns if manual columns are allowed.
DEFAULT_NUM_COLUMNS - Static variable in class org.simbrain.network.layouts.HexagonalGridLayout: The default number of columns if manual columns are allowed.
DEFAULT_NUM_UNITS - Static variable in class org.simbrain.network.subnetworks.Hopfield: Default number of neurons.
DEFAULT_ORIENTATION - Static variable in class org.simbrain.network.connections.OneToOne
DEFAULT_ORIGIN_X - Static variable in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Default origin x.
DEFAULT_ORIGIN_Y - Static variable in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Default origin y.
DEFAULT_OUTPUT_AMOUNT - Static variable in class org.simbrain.world.odorworld.sensors.Hearing: Default output amount.
DEFAULT_OUTPUT_POPULATION - Static variable in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog
DEFAULT_OUTPUT_THRESHOLD - Static variable in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule: Output threshold.
DEFAULT_OUTPUT_THRESHOLD_MOMENTUM - Static variable in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule: Output threshold momentum.
DEFAULT_PANEL_NAME - Static variable in class org.simbrain.network.gui.dialogs.group.SummaryPanel: The default name for this type of panel.
DEFAULT_PHRASE - Static variable in class org.simbrain.world.odorworld.effectors.Speech: Default phrase.
DEFAULT_PHRASE - Static variable in class org.simbrain.world.odorworld.sensors.Hearing: Default phrase.
DEFAULT_PLASTICITY_TYPE - Static variable in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule: Plasticity type.
DEFAULT_POLARITY - Static variable in class org.simbrain.util.randomizer.PolarizedRandomizer
DEFAULT_RADIUS - Static variable in class org.simbrain.world.odorworld.sensors.SmellSensor: Initial length of mouse whisker.
DEFAULT_RANDOM_STREAM - Static variable in enum org.simbrain.util.math.ProbDistribution
DEFAULT_RANDOM_STREAM - Static variable in class org.simbrain.util.math.SimbrainMath: A default random stream that can be used by any calls to SSJ classes/functions.
DEFAULT_RESERVOIR_POPULATION - Static variable in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog
DEFAULT_SCALING_FACTOR - Static variable in class org.simbrain.world.odorworld.effectors.StraightMovement: Default scaling factor.
DEFAULT_SELF_CONNECT_PREF - Static variable in class org.simbrain.network.connections.Sparse: The default preference as to whether or not self connections are allowed.
DEFAULT_SPACING - Static variable in class org.simbrain.network.gui.NetworkPanel: Default spacing for new points.
DEFAULT_SPACING - Static variable in class org.simbrain.network.layouts.LineLayout: The default spacing between neurons when laid out.
DEFAULT_SPECTRAL_RADIUS - Static variable in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog
DEFAULT_SQUASHING_FUNCTION - Static variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: The default squashing function, informs the default upper and lower bounds.
DEFAULT_THETA - Static variable in class org.simbrain.network.synapse_update_rules.HebbianCPCARule: Default Weight offset.
DEFAULT_THETA - Static variable in class org.simbrain.world.odorworld.sensors.SmellSensor: Angle of whisker in radians.
DEFAULT_THRESHOLD - Static variable in class org.simbrain.world.odorworld.effectors.Speech: Default threshold.
DEFAULT_TIME_CONSTANT - Static variable in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Default time constant (ms).
DEFAULT_TIME_TYPE - Static variable in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog
DEFAULT_UPDATE - Static variable in class org.simbrain.network.subnetworks.Hopfield: Default update mechanism.
DEFAULT_UPDATE_RULE - Static variable in class org.simbrain.network.core.Neuron: The default neuron update rule.
DEFAULT_UPPER_BOUND - Static variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: The Default upper bound.
DEFAULT_UPPER_BOUND - Static variable in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: The default activation ceiling.
DEFAULT_USE_SLIDING_OUTPUT_THRESHOLD - Static variable in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule: Use sliding output threshold.
DEFAULT_V_SPACING - Static variable in class org.simbrain.network.layouts.GridLayout: The default vertical spacing.
DEFAULT_V_SPACING - Static variable in class org.simbrain.network.layouts.HexagonalGridLayout: The default vertical spacing.
DEFAULT_WIDTH - Static variable in class org.simbrain.world.odorworld.sensors.TileSensor: Default width.
DEFAULT_WIDTH - Static variable in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Default width.
DEFAULT_WIDTH - Static variable in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Default width.
DEFAULT_X - Static variable in class org.simbrain.world.odorworld.sensors.TileSensor: Default X coordinate of the upper left corner.
DEFAULT_Y - Static variable in class org.simbrain.world.odorworld.sensors.TileSensor: Default Y coordinate of the upper left corner.
defaultInit() - Method in class org.simbrain.plot.barchart.BarChartModel: Default initialization.
defaultInit() - Method in class org.simbrain.plot.piechart.PieChartModel: Default initialization.
defaultInit() - Method in class org.simbrain.plot.rasterchart.RasterModel: Default plot initialization.
defaultInit() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel: Default Initialization.
defaultInit() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel: Default plot initialization.
delete() - Method in class org.simbrain.network.groups.Group: Perform necessary deletion cleanup.
delete() - Method in class org.simbrain.network.groups.NeuronGroup
delete() - Method in class org.simbrain.network.groups.Subnetwork
delete() - Method in class org.simbrain.network.groups.SynapseGroup: Perform necessary deletion cleanup.
DeleteAction - Class in org.simbrain.network.gui.actions.edit: Delete action.
DeleteAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.DeleteAction: Create a new delete action with the specified network panel.
deleteActionsAction - Variable in class org.simbrain.network.gui.NetworkUpdateManagerPanel: Action which deletes selected actions.
deleteActionsAction - Variable in class org.simbrain.workspace.gui.WorkspaceUpdateManagerPanel: Action which deletes selected actions.
deleteAllEntities() - Method in class org.simbrain.world.odorworld.OdorWorld: Delete all entities.
deleteConnectedSynapses() - Method in class org.simbrain.network.core.Neuron: Delete connected synapses and remove them from the network and any other structures.
deleteCouplingsAction - Variable in class org.simbrain.workspace.gui.CouplingListPanel: Action which deletes current couplings.
deleteEntity(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Delete entity.
DeleteEntityAction - Class in org.simbrain.world.odorworld.actions: Delete entity.
DeleteEntityAction(OdorWorldPanel, OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.actions.DeleteEntityAction: Create a delete entity action.
deleteFanIn() - Method in class org.simbrain.network.core.Neuron: Removes all synapses from fanIn and from the network or any intermediate structures.
deleteFanOut() - Method in class org.simbrain.network.core.Neuron: Removes all synapses from fanOut and from the network or any intermediate structures.
deleteSelectedObjects() - Method in class org.simbrain.network.gui.NetworkPanel: Delete selected items.
deleteText(NetworkTextObject) - Method in class org.simbrain.network.core.Network: Delete a network text object.
DENSE - Static variable in class org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditors: Dense sensor matrix editor.
DenseSensorMatrix - Class in org.simbrain.world.visionworld.sensormatrix: Dense sensor matrix.
DenseSensorMatrix(int, int, int, int, Filter) - Constructor for class org.simbrain.world.visionworld.sensormatrix.DenseSensorMatrix: Create a new dense sensor matrix with the specified filter.
DenseSensorMatrixEditor - Class in org.simbrain.world.visionworld.sensormatrix.editor: Dense sensor matrix editor.
DenseSensorMatrixEditor() - Constructor for class org.simbrain.world.visionworld.sensormatrix.editor.DenseSensorMatrixEditor: Create a new dense sensor matrix editor.
DensityEstimator() - Constructor for class org.simbrain.network.connections.Radial.DensityEstimator
derivAtan(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: The derivative of the arc tangent given the original function's upper and lower bounds, and slope for a given value.
derivLogistic(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: The derivative of the logistic function given the original function's upper and lower bounds, and slope for a given value.
derivTanh(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: The derivative of the hyperbolic tangent given the original function's upper and lower bounds, and slope for a given value.
derivVal(double, double, double, double) - Method in enum org.simbrain.util.math.SquashingFunction: Gives the value of the derivative of the given squashing function for some input value, a ceiling, floor, and slope.
deserialize(InputStream) - Method in class org.simbrain.workspace.WorkspaceSerializer: Deserializes all the entries in the provided stream.
deserialize(InputStream, Collection<? extends String>) - Method in class org.simbrain.workspace.WorkspaceSerializer: Creates a workspace from a zip compressed input stream.
deserializeDesktopComponent(String, WorkspaceComponent, InputStream, String) - Method in class org.simbrain.workspace.WorkspaceComponentDeserializer: Deserializes a desktop component given a class, input stream and name.
deserializeWorkspaceComponent(ArchiveContents.ArchivedComponent, InputStream) - Method in class org.simbrain.workspace.WorkspaceComponentDeserializer: Deserializes a workspace component using the information from the provided component and input stream.
deserializeWorkspaceComponent(Class<?>, String, InputStream, String) - Static method in class org.simbrain.workspace.WorkspaceComponentDeserializer: Deserialized a component for the given class, input and input format.
desktop - Variable in class org.simbrain.workspace.actions.DesktopAction
DesktopAction - Class in org.simbrain.workspace.actions
DesktopAction(String, SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.DesktopAction
DesktopCouplingManager - Class in org.simbrain.workspace.gui.couplingmanager: GUI dialog for creating couplings.
DesktopCouplingManager(SimbrainDesktop, GenericJInternalFrame) - Constructor for class org.simbrain.workspace.gui.couplingmanager.DesktopCouplingManager: Creates and displays the coupling manager.
DesktopJTable - Class in org.simbrain.world.dataworld: Extends SimbrainJTable context menu with attribute menus.
DesktopJTable(NumericTable, DataWorldComponent) - Constructor for class org.simbrain.world.dataworld.DesktopJTable: Construct the table.
DesktopNetworkDialog - Class in org.simbrain.network.desktop: Overrides the network dialog box to add features that don't work on applets, but that work in the desktop, in particular anything reliant on user preferences.
DesktopNetworkDialog(NetworkPanel) - Constructor for class org.simbrain.network.desktop.DesktopNetworkDialog: Construct the dialog.
determinant2by2(Point2D, Point2D) - Static method in class org.simbrain.util.math.SimbrainMath: A fast determinant utility to find the determinant of the 2 by 2 matrix made up of the vectors (stored as 2D points) v0 and v1, i.e.
determineProperEndPoints() - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow: Determines what the end points should be depending on what this arrow connects.
determineProperEndPoints() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional: Determines what the end points should be depending on what this arrow connects.
determineProperEndPoints() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
dictionaryChanged() - Method in interface org.simbrain.world.textworld.TextListener: The dictionary has changed.
dictionaryChanged() - Method in class org.simbrain.world.textworld.TextListener.TextAdapter
DictionarySelector - Class in org.simbrain.world.textworld.dictionary: Top level dialog for displaying dictionary editors.
DifferentiableUpdateRule - Interface in org.simbrain.network.neuron_update_rules.interfaces: Indicates that an update rule is differentiable, and has a getDerivative function.
Dimension(int) - Constructor for class org.simbrain.plot.projection.ProjectionComponent.Dimension: Construct a Dimension object.
dimensions - Variable in class org.simbrain.util.projection.NTree: The number of dimensions this structure supports
DirectedCubicArrow - Class in org.simbrain.util.widgets
DirectedCubicArrow() - Constructor for class org.simbrain.util.widgets.DirectedCubicArrow
DirectedCubicArrow(DirectedCubicArrow.BezierTemplate) - Constructor for class org.simbrain.util.widgets.DirectedCubicArrow
DirectedCubicArrow(DirectedCubicArrow.BezierTemplate, Color, float, float) - Constructor for class org.simbrain.util.widgets.DirectedCubicArrow
DirectedCubicArrow.BezierTemplate - Enum in org.simbrain.util.widgets
disable() - Method in class org.simbrain.util.SwitchableActionListener: Sets the active flag to false.
disable() - Method in class org.simbrain.util.SwitchableChangeListener
disable() - Method in class org.simbrain.util.SwitchablePropertyChangeListener
disableOkButton() - Method in class org.simbrain.util.StandardDialog: Disables the Ok button if certain constraints of the dialog have not be fulfilled.
disableSynapsesAction - Variable in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Action for disabling synapses
disableTableModificationMenus() - Method in class org.simbrain.util.table.SimbrainJTable: Disable popup menus that allow table structure to changed.
displayClosestWord(double[]) - Method in class org.simbrain.world.textworld.DisplayWorld: Display the string associated with the closest matching vector in the dictionary.
DisplayComponent - Class in org.simbrain.world.textworld: DisplayComponent is a component which wraps a display world with consumers.
DisplayComponent(String) - Constructor for class org.simbrain.world.textworld.DisplayComponent: Creates a new frame of type TextWorld.
DisplayComponent(String, DisplayWorld) - Constructor for class org.simbrain.world.textworld.DisplayComponent: Construct a component from an existing world; used in deserializing.
DisplayComponentDesktopGui - Class in org.simbrain.world.textworld: DisplayComponentDesktopGui is the container for the display component.
DisplayComponentDesktopGui(GenericFrame, DisplayComponent) - Constructor for class org.simbrain.world.textworld.DisplayComponentDesktopGui: Creates a new frame of type TextWorld.
displayLocalHtmlInBrowser(String) - Static method in class org.simbrain.util.Utils: Launch an .html page using the system's default browser.
displayNeuronGroups() - Method in class org.simbrain.network.groups.Subnetwork
displayNPTriangle - Variable in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: For showing/hiding the neuron panel.
DisplayOrder - Annotation Type in org.simbrain.util.propertyeditor: An annotation that can be used to control the order in which fields are displayed in a reflective property editor.
displayPanel(JPanel, String) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
displayPanel(JPanel, String) - Method in class org.simbrain.network.gui.NetworkPanel: Display a panel in a dialog.
displayPanel(JComponent) - Static method in class org.simbrain.util.SimpleFrame: Show the provided panel in a jframe.
displayPanel(JComponent, String) - Static method in class org.simbrain.util.SimpleFrame: Show the panel in a jframe with the provided title.
DisplayPanel - Class in org.simbrain.world.textworld: Display text data from another source.
DisplayPanel(DisplayWorld, JToolBar) - Constructor for class org.simbrain.world.textworld.DisplayPanel: Construct a reader panel to represent data in a text world.
displayPanelInWindow(JPanel, String) - Method in class org.simbrain.network.gui.NetworkPanel: A copy of displayPanel except returning a subclass of Window.
displaySynapseGroupDialog(NetworkPanel) - Static method in class org.simbrain.network.gui.actions.synapse.AddSynapseGroupAction: Display the add synapse group dialog.
DisplayWorld - Class in org.simbrain.world.textworld: DisplayWorld intuitively models "speaking", though it can also be useful as a diagnostic component.
DisplayWorld() - Constructor for class org.simbrain.world.textworld.DisplayWorld: Constructs an instance of TextWorld.
DisplayWorld.StringDataPoint - Class in org.simbrain.world.textworld: Associates a datapoint object (basically a double vector that can be processed by the ntree) with a string.
dispose() - Method in interface org.simbrain.util.genericframe.GenericFrame
disposeSplash() - Static method in class org.simbrain.workspace.gui.SplashWindow: Closes the splash window.
distance(Point, Point) - Static method in class org.simbrain.util.math.SimbrainMath: Calculates the Euclidean distance between two points.
distance(double[], double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Returns the Euclidean distance between src and target vectors.
distanceToMidpoints(Point2D, Point2D) - Static method in enum org.simbrain.util.widgets.DirectedCubicArrow.BezierTemplate
DocViewerComponent - Class in org.simbrain.docviewer: Component corresponding to a Document Viewer.
DocViewerComponent() - Constructor for class org.simbrain.docviewer.DocViewerComponent: Construct a new document viewer component.
DocViewerComponent(String) - Constructor for class org.simbrain.docviewer.DocViewerComponent: Construct a new document viewer component with a specified title.
DocViewerDesktopComponent - Class in org.simbrain.docviewer: A very simple component which displays html and allows it to be edited.
DocViewerDesktopComponent(GenericFrame, DocViewerComponent) - Constructor for class org.simbrain.docviewer.DocViewerDesktopComponent: Constructor the gui component.
done() - Method in interface org.simbrain.workspace.updater.CompletionSignal: Signals that the event is done.
done() - Method in class org.simbrain.workspace.updater.LatchCompletionSignal: Called when a task is done.
doStopped() - Method in class org.simbrain.workspace.WorkspaceComponent: Called after a global update ends.
doubleArray - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
doubleArrayToString(double[]) - Static method in class org.simbrain.util.Utils: Utility to class to convert arrays of doubles to strings.
doubleArrayToStringArray(double[]) - Static method in class org.simbrain.util.Utils: Converts an array of doubles into an array of Strings of those doubles.
doubleMatrixToString(double[][]) - Static method in class org.simbrain.util.Utils: Convert a 2-d array of doubles to a string.
doubleMatrixToStringMatrix(double[][]) - Static method in class org.simbrain.util.Utils: Converts a matrix of doubles into a matrix of Strings representing those doubles.
doubleParsable(JTextField) - Static method in class org.simbrain.util.Utils: Tests whether the string in a text field is parsable into a double.
doubleParsable(String) - Static method in class org.simbrain.util.Utils: Like Utils.doubleParsable(JTextField) but checks for the formatting of a string rather than a text field.
downstairs - Variable in class org.simbrain.util.projection.Projector: A set of low-d datapoints, each of which is an array of doubles The projection of the upstairs data.
drag(PInputEvent) - Method in class org.simbrain.network.gui.DragEventHandler
drag(PInputEvent) - Method in class org.simbrain.network.gui.WandEventHandler
drag(PInputEvent) - Method in class org.simbrain.world.visionworld.SelectionEventHandler
DragEventHandler - Class in org.simbrain.network.gui: Handle simbrain drag events, which pan the canvas, create lassos for selection.
DragEventHandler(NetworkPanel) - Constructor for class org.simbrain.network.gui.DragEventHandler: Create a new selection event handler.
draw(Graphics2D, OdorWorld, int, int) - Method in class org.simbrain.world.odorworld.OdorWorldRenderer: Draws the odor world.
DropDownTriangle - Class in org.simbrain.util.widgets
DropDownTriangle(DropDownTriangle.UpDirection, boolean, Window) - Constructor for class org.simbrain.util.widgets.DropDownTriangle: Creates an unlabeled drop down triangle pointing either left or right in the "up" state and starting either "up" or down.
DropDownTriangle(DropDownTriangle.UpDirection, boolean, String, String, Window) - Constructor for class org.simbrain.util.widgets.DropDownTriangle: Creates a drop down triangle with a label displayed when it is in the "up" state and a label displayed when it is in the "down" state.
DropDownTriangle.UpDirection - Enum in org.simbrain.util.widgets
dx - Variable in class org.simbrain.world.odorworld.entities.OdorWorldEntity: X Velocity.
dy - Variable in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Y Velocity.

E

EchoStateNetwork - Class in org.simbrain.network.subnetworks: Builds an Echo-State Network with options for all valid weight configurations.
EchoStateNetwork(Network, int, int, int, Point2D) - Constructor for class org.simbrain.network.subnetworks.EchoStateNetwork: Constructor with size of layers specified.
EchoStateNetwork(Network, Point2D) - Constructor for class org.simbrain.network.subnetworks.EchoStateNetwork: Creates an empty ESN where neuron groups and synapse groups must be manually added.
edit() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Edit the sensor for this sensor node.
EditablePanel - Interface in org.simbrain.util.widgets: JPanels that edit the properties of an object can implement this interface to achieve standard behaviors associated with editing properties.
EditableRandomizerPanel(Window, PolarizedRandomizer, boolean) - Constructor for class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel
EditableRandomizerPanel(Window, PolarizedRandomizer) - Constructor for class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel
EditableRandomizerPanel(Window, SimbrainConstants.Polarity) - Constructor for class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel
editAction - Variable in class org.simbrain.network.gui.nodes.SubnetworkNode: Action for invoking the default edit and properties menu.
EditMode - Class in org.simbrain.network.gui: Typesafe enumeration of edit modes.
EditModeAction - Class in org.simbrain.network.gui.actions.edit: Build mode action.
EditModeAction(String, NetworkPanel, EditMode) - Constructor for class org.simbrain.network.gui.actions.edit.EditModeAction: Create a new edit mode action with the specified name, network panel, and edit mode.
EditRandomizerPropertiesAction - Class in org.simbrain.network.gui.actions.edit: Edit properties of randomizer object for network.
EditRandomizerPropertiesAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.EditRandomizerPropertiesAction: Construct the action.
EditSensorDialog - Class in org.simbrain.world.visionworld.dialog: Edit sensor dialog.
EditSensorDialog(Sensor) - Constructor for class org.simbrain.world.visionworld.dialog.EditSensorDialog: Create a new edit sensor dialog.
editSensors() - Method in class org.simbrain.world.visionworld.VisionWorld: Edit the selected sensors, if any.
EditSensorsAction - Class in org.simbrain.world.visionworld.action: Edit sensors action.
EditSensorsAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.EditSensorsAction: Create a new edit sensors action.
EditSensorsDialog - Class in org.simbrain.world.visionworld.dialog: Edit sensors dialog.
EditSensorsDialog(Collection<Sensor>) - Constructor for class org.simbrain.world.visionworld.dialog.EditSensorsDialog: Create a new edit sensor dialog.
EditSmellSourceAction - Class in org.simbrain.world.odorworld.actions: Action for showing a dialog to edit a smell source.
EditSmellSourceAction(OdorWorldPanel, OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.actions.EditSmellSourceAction: Create a new open plot action.
Effector - Class in org.simbrain.world.odorworld.effectors: Abstract class for Odor World effectors.
Effector(OdorWorldEntity, String) - Constructor for class org.simbrain.world.odorworld.effectors.Effector: Construct the effector.
effectorAdded(Effector) - Method in interface org.simbrain.world.odorworld.WorldListener: An effector was added.
effectorAdded(Effector) - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
EffectorModel() - Constructor for class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
EffectorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel showing an agent's effectors.
EffectorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.EffectorPanel: Construct the effector panel.
EffectorPanel.EffectorModel - Class in org.simbrain.world.odorworld.dialogs: Table model which represents effectors.
effectorRemoved(Effector) - Method in interface org.simbrain.world.odorworld.WorldListener: An effector was added.
effectorRemoved(Effector) - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
EMPTY_PIXEL_MATRIX - Static variable in class org.simbrain.world.visionworld.MutableVisionWorldModel: Empty pixel matrix.
enable() - Method in class org.simbrain.util.SwitchableActionListener: Sets the active flag to true.
enable() - Method in class org.simbrain.util.SwitchableChangeListener
enable() - Method in class org.simbrain.util.SwitchablePropertyChangeListener
enableOkButton() - Method in class org.simbrain.util.StandardDialog: Enables the Ok button.
enableStatusTriangle - Variable in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel: A DropDownTriangle used to show or hide SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel.randomizerPanel.
enableSynapsesAction - Variable in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Action for enabling synapses
endDrag(PInputEvent) - Method in class org.simbrain.network.gui.DragEventHandler
endDrag(PInputEvent) - Method in class org.simbrain.network.gui.WandEventHandler
endDrag(PInputEvent) - Method in class org.simbrain.world.visionworld.SelectionEventHandler
endTraining() - Method in interface org.simbrain.network.trainers.TrainerListener: Called when training ends.
entityAdded(OdorWorldEntity) - Method in interface org.simbrain.world.odorworld.WorldListener: An entity was added to the world.
entityAdded(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
entityChanged(OdorWorldEntity) - Method in interface org.simbrain.world.odorworld.WorldListener: An entity was changed.
entityChanged(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
EntityDialog - Class in org.simbrain.world.odorworld.dialogs: DialogWorldEntity displays the dialog box for settable values of creatures and entities within a world environment.
EntityDialog(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.EntityDialog: Create and show the world entity dialog box.
entityRemoved(OdorWorldEntity) - Method in interface org.simbrain.world.odorworld.WorldListener: An entity was removed to the world.
entityRemoved(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
equals(Object) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Tests this dataset for equality with an arbitrary object.
equals(Object) - Method in class org.simbrain.workspace.Coupling
ErrorListener - Interface in org.simbrain.network.trainers: Classes which implement this interface fire events indicating changes in the error associated with an iterable trainer.
ErrorPlotPanel - Class in org.simbrain.network.gui.trainer: Component for representing error in a trainer.
ErrorPlotPanel(IterableTrainer) - Constructor for class org.simbrain.network.gui.trainer.ErrorPlotPanel: Construct a trainer panel around a trainer object.
errorUpdated() - Method in interface org.simbrain.network.trainers.ErrorListener: Called when the error value is updated.
ESNCreationDialog - Class in org.simbrain.network.gui.dialogs.network: A panel for creating and setting the parameters of an arbitrary Echo-State Network.
ESNCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.ESNCreationDialog: Creates an dialog for creating and setting the parameters of an Echo State Network in a given networkPanel.
ESNNetworkNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of an Echo State Network.
ESNNetworkNode(NetworkPanel, EchoStateNetwork) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.ESNNetworkNode: Create an ESN network.
ESNOfflineTrainingPanel - Class in org.simbrain.network.gui.trainer.subnetworkTrainingPanels: Panel for training ESN's.
ESNOfflineTrainingPanel(NetworkPanel, EchoStateNetwork, Window) - Constructor for class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.ESNOfflineTrainingPanel: Construct an ESN Training Panel.
ESNTrainingDialog - Class in org.simbrain.network.gui.dialogs.network: Dialog for training an ESN network.
ESNTrainingDialog(NetworkPanel, EchoStateNetwork) - Constructor for class org.simbrain.network.gui.dialogs.network.ESNTrainingDialog: Construct the dialog.
evaluate(Object) - Method in class org.simbrain.network.gui.filters.AbstractFilter
evaluate(Object) - Method in interface org.simbrain.util.Predicate: Does the object have the relevant property?
exp_sum(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: An exponential sum of an array.
exportToCSV(File) - Method in class org.simbrain.util.projection.Dataset: Save the current datast to a stored file.
exRandomizerEnabled() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel

F

FeedForward - Class in org.simbrain.network.subnetworks: A standard feed-forward network, where a succession of neuron groups and synapse groups are organized into layers.
FeedForward(Network, int[], Point2D, Neuron) - Constructor for class org.simbrain.network.subnetworks.FeedForward: Construct a feed-forward network.
FeedForward(Network, int[], Point2D) - Constructor for class org.simbrain.network.subnetworks.FeedForward: Add the layered network to the specified network, with a specified number of layers and nodes in each layer.
FeedForwardCreationDialog - Class in org.simbrain.network.gui.dialogs.network: FeedForwardCreationDialog is a dialog box for creating a generic layered network.
FeedForwardCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.FeedForwardCreationDialog: This method is the default constructor.
fill(List<SimbrainJTable.CellIndex>, double) - Method in class org.simbrain.util.table.NumericTable: Fill the table at selected indices with the indicated value.
fill(T) - Method in class org.simbrain.util.table.SimbrainDataTable: Fills the table with the given value.
fill(double) - Method in class org.simbrain.util.table.SimbrainJTable: Fills the table with the given value.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel: Fills the fields based on certain default values.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.AdExIFRulePanel
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.LogisticGeneratorPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.RandomGeneratorPanel: Fill field values to default values for random neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.SinusoidalGeneratorPanel: Populates the fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.StochasticGeneratorPanel: Populates the fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AdditiveRulePanel: Fill field values to default values for additive neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.BinaryRulePanel: Fill field values to default values for binary neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ContinuousSigmoidalRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: Fill field values to default values for additive neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.HodgkinHuxleyRulePanel: Fill field values to default values for binary neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IACRulePanel: Fill field values to default values for binary neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IntegrateAndFireRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IzhikevichRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.LinearRulePanel: Fill field values to default values for linear neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.PointNeuronRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.RunningAverageRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SigmoidalRulePanel: Fill field values to default values for sigmoidal neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SpikingThresholdRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ThreeValueRulePanel: Fill field values to default values for binary neuron.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel: Fills fields with default values.
fillDefaultValues() - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel: Fills fields with default values.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.connect.AbstractConnectionPanel: Populates fields with data from a connect neurons object.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel: Does nothing.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.AllToAllPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.OneToOnePanel: Populates fields with data from a connect neurons object.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.RadialPanel: Populates fields with data from a connect neurons object.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
fillFieldValues(SynapseGroup) - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel: Fills the field values for this sub-panel based on the values of an already existing connection object.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.ConnectivityAdjustmentPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.group.NeuronGroupPanel
fillFieldValues(NeuronGroup) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
fillFieldValues(SynapseGroup) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.group.SynapseGroupDialog: Set the initial values of dialog components.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.layout.AbstractLayoutPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.layout.GridLayoutPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.layout.HexagonalGridLayoutPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.layout.LineLayoutPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel: Initialize the panel with field values.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.network.KwtaPropertiesDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.network.SRNCreationDialog: Fills the fields with default values.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.network.WTAPropertiesPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.NetworkPropertiesPanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.AdExIFRulePanel
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.LogisticGeneratorPanel
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.RandomGeneratorPanel
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.SinusoidalGeneratorPanel: Populates the field with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.StochasticGeneratorPanel: Populates the fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AdditiveRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.BinaryRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ContinuousSigmoidalRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.HodgkinHuxleyRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IACRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IntegrateAndFireRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IzhikevichRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.LinearRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.PointNeuronRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.RunningAverageRulePanel
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SigmoidalRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SpikingThresholdRulePanel: Populate fields with current data.
fillFieldValues(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ThreeValueRulePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel
fillFieldValues(List<SpikeResponder>) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel: Populate fields with current data.
fillFieldValues(List<SynapseUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel
fillFieldValues(List<SpikeResponder>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel: Populate fields with current data.
fillFieldValues(List<SpikeResponder>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: Populate fields with current data.
fillFieldValues(List<SpikeResponder>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: Populate fields with current data.
fillFieldValues(List<SpikeResponder>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: Populate fields with current data.
fillFieldValues(List<SpikeResponder>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel: Populate fields with current data.
fillFieldValues(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesExtended: Fills the values of the text fields based on the corresponding values of the synapses to be edited.
fillFieldValues(SynapseGroup, SimbrainConstants.Polarity) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesExtended
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
fillFieldValues(SynapseGroup, SimbrainConstants.Polarity) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
fillFieldValues() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple
fillFieldValues(SynapseGroup, SimbrainConstants.Polarity) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple: Fills field values based on a given synapse group's values and which synapse polarity it should use to get those values.
fillFieldValues() - Method in class org.simbrain.network.gui.trainer.DataPanel
fillFieldValues() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineTrainingPanel
fillFieldValues() - Method in class org.simbrain.network.gui.trainer.TrainingSetPanel
fillFieldValues(ArrayList<Randomizer>) - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel: Populates the fields with current values.
fillFieldValues(Randomizer) - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel: Fills fields with values from a Random Source.
fillFieldValues(ArrayList<Randomizer>) - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel: Populates the fields with current values.
fillFieldValues(Randomizer) - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel: Fills fields with values from a Random Source.
fillFieldValues() - Method in class org.simbrain.util.widgets.ApplyPanel
fillFieldValues() - Method in interface org.simbrain.util.widgets.EditablePanel: Initialize the panel with field values.
fillFieldValues() - Method in class org.simbrain.world.odorworld.dialogs.OdorWorldDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.world.textworld.dictionary.TokenDictionaryPanel
fillFieldValues() - Method in class org.simbrain.world.textworld.dictionary.TokenToVectorPanel
fillFieldValues() - Method in class org.simbrain.world.textworld.dictionary.VectorToTokenPanel
fillFrame() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionDialog: Fills the standard dialog with the connection panel and a help button.
Filter - Interface in org.simbrain.world.visionworld: Filter.
filter(BufferedImage) - Method in interface org.simbrain.world.visionworld.Filter: Reduce the specified image to a single value.
filter(BufferedImage) - Method in class org.simbrain.world.visionworld.filter.PixelAccumulator: Reduce the specified image to a single value.
filter(BufferedImage) - Method in class org.simbrain.world.visionworld.filter.RandomFilter: Reduce the specified image to a single value.
filter(BufferedImage) - Method in class org.simbrain.world.visionworld.filter.RgbFilter: Reduce the specified image to a single value.
filter(BufferedImage) - Method in class org.simbrain.world.visionworld.filter.UniformFilter: Reduce the specified image to a single value.
FilterEditor - Interface in org.simbrain.world.visionworld.filter.editor: Filter editor.
FilterEditorException - Exception in org.simbrain.world.visionworld.filter.editor: Filter editor exception.
FilterEditorException() - Constructor for exception org.simbrain.world.visionworld.filter.editor.FilterEditorException: Create a new filter editor exception.
FilterEditorException(String) - Constructor for exception org.simbrain.world.visionworld.filter.editor.FilterEditorException: Create a new filter editor exception with the specified message.
FilterEditorException(Throwable) - Constructor for exception org.simbrain.world.visionworld.filter.editor.FilterEditorException: Create a new filter editor exception with the specified cause.
FilterEditorException(String, Throwable) - Constructor for exception org.simbrain.world.visionworld.filter.editor.FilterEditorException: Create a new filter editor exception with the specified message and cause.
FilterEditors - Class in org.simbrain.world.visionworld.filter.editor: Filter editors.
FilterEditors() - Constructor for class org.simbrain.world.visionworld.filter.editor.FilterEditors
Filters - Class in org.simbrain.network.gui.filters: Filters.
findMaxEig(double[][]) - Static method in class org.simbrain.network.util.SimnetUtils: Find the largest eigenvalue for the provided matrix.
findMaxX(List<Neuron>) - Static method in enum org.simbrain.network.util.OrientationComparator
findMaxY(List<Neuron>) - Static method in enum org.simbrain.network.util.OrientationComparator
findMidpointX(List<Neuron>) - Static method in enum org.simbrain.network.util.OrientationComparator
findMidpointY(List<Neuron>) - Static method in enum org.simbrain.network.util.OrientationComparator
findMinX(List<Neuron>) - Static method in enum org.simbrain.network.util.OrientationComparator
findMinY(List<Neuron>) - Static method in enum org.simbrain.network.util.OrientationComparator
FindReplaceDialog - Class in org.simbrain.util.scripteditor: A find / replace dialog for RSyntaxTextArea (by Robert Futrell).
FindReplaceDialog(JFrame, ScriptEditor) - Constructor for class org.simbrain.util.scripteditor.FindReplaceDialog: Construct the panel.
finishedComponentUpdate(WorkspaceComponent, int, int) - Method in interface org.simbrain.workspace.updater.ComponentUpdateListener: Called when a component update ends.
fireAttributeObjectRemoved(Object) - Method in class org.simbrain.workspace.WorkspaceComponent: Fire attribute object removed event (when the base object of an attribute is removed).
fireAttributeTypeVisibilityChanged(AttributeType) - Method in class org.simbrain.workspace.WorkspaceComponent: Fire attribute type visibility changed event.
fireChartInitialized(int) - Method in class org.simbrain.plot.ChartModel: Fire chart initialized.
fireClipboardChanged() - Static method in class org.simbrain.network.gui.Clipboard: Fire a clipboard changed event to all registered model listeners.
fireComponentToggleEvent() - Method in class org.simbrain.workspace.WorkspaceComponent: Notify all workspaceComponentListeners of a component has been turned on or off.
fireCurrentItemChanged(TextWorld.TextItem) - Method in class org.simbrain.world.textworld.TextWorld: Notify listeners that the caret position has changed.
fireDataPointAdded() - Method in class org.simbrain.util.projection.Projector: Notify listeners that a new datapoint has been added to the projector.
fireDataSourceAdded(int) - Method in class org.simbrain.plot.ChartModel: Fire data source added event.
fireDataSourceRemoved(int) - Method in class org.simbrain.plot.ChartModel: Fire data source removed event.
fireDictionaryChangedEvent() - Method in class org.simbrain.world.textworld.TextWorld: Notify listeners that the dictionary has changed.
fireEffectorAdded(Effector) - Method in class org.simbrain.world.odorworld.OdorWorld: Fire effector added event.
fireEffectorRemoved(Effector) - Method in class org.simbrain.world.odorworld.OdorWorld: Fire effector removed event.
fireEntityAdded(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Fire entity added event.
fireEntityChanged(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Fire entity changed event.
fireEntityRemoved(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Fire entity removed event.
fireErrorUpdated() - Method in class org.simbrain.network.trainers.IterableTrainer: Notify listeners that the error value has been updated.
fireErrorUpdated() - Method in class org.simbrain.util.projection.IterableProjectionMethod: Notify listeners that the error value has been updated.
fireGroupAdded(Group) - Method in class org.simbrain.network.core.Network: Fire a group added event to all registered model listeners.
fireGroupChanged(Group, Group, String) - Method in class org.simbrain.network.core.Network: Fire a group changed event to all registered model listeners.
fireGroupChanged(NetworkEvent<Group>, String) - Method in class org.simbrain.network.core.Network: This version of fireGroupChanged fires a pre-set event, which may have an auxiliary object set.
fireGroupChanged(Group, String) - Method in class org.simbrain.network.core.Network
fireGroupParametersChanged(Group) - Method in class org.simbrain.network.core.Network: Fire a group parameters changed event.
fireGroupRemoved(Group) - Method in class org.simbrain.network.core.Network: Fire a group deleted event to all registered model listeners.
fireGroupUpdated(Group) - Method in class org.simbrain.network.core.Network: Fire a group update event event.
fireGuiToggleEvent() - Method in class org.simbrain.workspace.WorkspaceComponent: Notify all workspaceComponentListeners that the gui has been turned on or off.
fireNeuronAdded(Neuron) - Method in class org.simbrain.network.core.Network: Fire a neuron added event to all registered model listeners.
fireNeuronChanged(Neuron) - Method in class org.simbrain.network.core.Network: Fire a neuron changed event to all registered model listeners.
fireNeuronLabelChanged(Neuron) - Method in class org.simbrain.network.core.Network: Fire a label changed event to all registered model listeners.
fireNeuronMoved(Neuron) - Method in class org.simbrain.network.core.Network: Fire a network changed event to all registered model listeners.
fireNeuronRemoved(Neuron) - Method in class org.simbrain.network.core.Network: Fire a neuron deleted event to all registered model listeners.
fireNeuronsUpdated() - Method in class org.simbrain.network.core.Network: Fire this event when the visible state of a neuron (e.g.
fireNeuronsUpdated(Collection<Neuron>) - Method in class org.simbrain.network.core.Network: Fire this event when the visible state of a specified list of neuron (e.g.
fireNeuronTypeChanged(NeuronUpdateRule, NeuronUpdateRule) - Method in class org.simbrain.network.core.Network: Fire a neuron type changed event to all registered model listeners.
firePixelMatrixChanged(PixelMatrix, PixelMatrix) - Method in class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Fire a pixel matrix changed event to all registered vision world model listeners.
firePositionChangedEvent() - Method in class org.simbrain.world.textworld.TextWorld: Notify listeners that the caret position has changed.
firePotentialAttributesChanged() - Method in class org.simbrain.workspace.WorkspaceComponent: Fire potential attributes changed event.
firePrefsChangedEvent() - Method in class org.simbrain.world.textworld.TextWorld: Notify listeners that preferences have changed.
fireProgressUpdate(String, int) - Method in class org.simbrain.network.trainers.Trainer: Notify listeners of an update in training progress.
fireProjectionMethodChanged() - Method in class org.simbrain.util.projection.Projector: Notify listeners that the projection method has been changed.
fireProjectorColorsChanged() - Method in class org.simbrain.util.projection.Projector: Notify listeners that the colors of some datapoints have changed but nothing else.
fireProjectorDataChanged() - Method in class org.simbrain.util.projection.Projector: Notify listeners that data (in particular the underlying points) have been changed.
firePropertyChangedEvent() - Method in class org.simbrain.world.odorworld.OdorWorld: Fire a property changed event.
fireSelectionChanged(Set, Set) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Fire a wholesale selection model changed event to all registered selection listeners.
fireSelectionChanged() - Method in class org.simbrain.network.gui.NetworkSelectionModel: A hack to broadcast a selection changed event.
fireSelectionChanged(Set<Sensor>, Set<Sensor>) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Fire a selection changed event.
fireSensorAdded(Sensor) - Method in class org.simbrain.world.odorworld.OdorWorld: Fire sensor added event.
fireSensorMatrixChanged(SensorMatrix, SensorMatrix) - Method in class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Fire a sensor matrix changed event to all registered vision world model listeners.
fireSensorRemoved(Sensor) - Method in class org.simbrain.world.odorworld.OdorWorld: Fire sensor removed event.
fireSettingsChanged() - Method in class org.simbrain.plot.ChartModel: Fire settings updated event.
fireSynapseAdded(Synapse) - Method in class org.simbrain.network.core.Network: Fire a synapse added event to all registered model listeners.
fireSynapseChanged(Synapse) - Method in class org.simbrain.network.core.Network: Fire a synapse changed event to all registered model listeners.
fireSynapseRemoved(Synapse) - Method in class org.simbrain.network.core.Network: Fire a synapse deleted event to all registered model listeners.
fireSynapsesUpdated() - Method in class org.simbrain.network.core.Network: Fire this event when the visible state of a synapse (e.g.
fireSynapsesUpdated(Collection<Synapse>) - Method in class org.simbrain.network.core.Network: Fire this event when the visible state of a specified list of synapses (e.g.
fireSynapseTypeChanged(SynapseUpdateRule, SynapseUpdateRule) - Method in class org.simbrain.network.core.Network: Fire a synapse type changed event to all registered model listeners.
fireTextAdded(NetworkTextObject) - Method in class org.simbrain.network.core.Network: Fire a text added event to all registered model listeners.
fireTextChanged(NetworkTextObject) - Method in class org.simbrain.network.core.Network: Fire a text changed event to all registered model listeners.
fireTextChangedEvent() - Method in class org.simbrain.world.textworld.TextWorld: Notify listeners that the text has changed.
fireTextRemoved(NetworkTextObject) - Method in class org.simbrain.network.core.Network: Fire a text deleted event to all registered model listeners.
fireTrainingBegin() - Method in class org.simbrain.network.trainers.Trainer: Notify listeners that training has begin.
fireTrainingEnd() - Method in class org.simbrain.network.trainers.Trainer: Notify listeners that training has ended.
fireUpdateEvent() - Method in class org.simbrain.workspace.WorkspaceComponent: Notify all workspaceComponentListeners of a componentUpdated event.
fireUpdateEvent() - Method in class org.simbrain.world.odorworld.OdorWorld: Fire an update event.
FitzhughNagumo - Class in org.simbrain.network.neuron_update_rules
FitzhughNagumo() - Constructor for class org.simbrain.network.neuron_update_rules.FitzhughNagumo
fixedwidth - Variable in class org.simbrain.util.JMultiLineToolTip
flip() - Method in class org.simbrain.util.widgets.StopLight: Quick method which flips the state of the stoplight to green if the current state is red and red if the current state is green.
floatToHue(float) - Static method in class org.simbrain.util.Utils: Converts a floating point value into a color in HSB, with Saturation and Brightness 1.
FLUSH_FREQUENCY - Static variable in class org.simbrain.network.groups.NeuronGroup: The default for how often NeuronGroup.writeActsToFile() should flush the output stream when writing to a file.
forceSetActivation(double) - Method in class org.simbrain.network.core.Neuron: Sets the activation of the neuron regardless of the state of the neuron.
forceSetActivationLevels(double) - Method in class org.simbrain.network.groups.NeuronGroup: Force set all activations to a specified value.
forceSetActivations(double[]) - Method in class org.simbrain.network.groups.NeuronGroup: Force set activations of neurons using an array of doubles.
forceSetStrength(double) - Method in class org.simbrain.network.core.Synapse
freezeSynapses(boolean) - Method in class org.simbrain.network.core.Network: Freeze or unfreeze all synapses in the network.
freezeSynapsesAction - Variable in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Action for freezing synapses
fullUpdate() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel: Updates the entire panel by changing the histogram to reflect and the statistics panel to reflect the current values.

G

GameAttributes - Class in org.simbrain.world.game: A consumer and producer that delegates to a game model.
GameAttributes(WorkspaceComponent, GameModel) - Constructor for class org.simbrain.world.game.GameAttributes: Creates a new instance with the given parent and model.
GameComponent - Class in org.simbrain.world.game: Component type for board games.
GameComponent() - Constructor for class org.simbrain.world.game.GameComponent: Creates a new game component.
GameDesktopComponent - Class in org.simbrain.world.game: Desktop Component for board games.
GameDesktopComponent(GenericFrame, GameComponent) - Constructor for class org.simbrain.world.game.GameDesktopComponent: Creates a new desktop component.
GameModel - Class in org.simbrain.world.game: base class for a simple square board game.
GameModel(String, int) - Constructor for class org.simbrain.world.game.GameModel: Creates a new instance with the given name and size.
generateTerminaMappings(Set<SynapseGroupArrow>) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
GENERATOR_MAP - Static variable in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Associations between names of activity generators and panels for editing them.
GenericFrame - Interface in org.simbrain.util.genericframe: Abstraction which is neutral between JFrames, JInternalFrames, and JDialogs.
GenericJDialog - Class in org.simbrain.util.genericframe: JDialog which implements Generic Frame.
GenericJDialog(Frame, String) - Constructor for class org.simbrain.util.genericframe.GenericJDialog
GenericJDialog() - Constructor for class org.simbrain.util.genericframe.GenericJDialog
GenericJFrame - Class in org.simbrain.util.genericframe: JFrame which implements Generic Frame.
GenericJFrame() - Constructor for class org.simbrain.util.genericframe.GenericJFrame
GenericJInternalFrame - Class in org.simbrain.util.genericframe: JInternalFrame which implements Generic Frame
GenericJInternalFrame() - Constructor for class org.simbrain.util.genericframe.GenericJInternalFrame
GenericListModel<E> - Class in org.simbrain.workspace.gui.couplingmanager: A list of items viewed by a JList.
GenericListModel(List<? extends E>) - Constructor for class org.simbrain.workspace.gui.couplingmanager.GenericListModel: Constructs a list of consumers.
GenericListModel(Collection<? extends E>) - Constructor for class org.simbrain.workspace.gui.couplingmanager.GenericListModel: Constructs a list of consumers.
get(int) - Method in class org.simbrain.util.projection.DataPoint: Get the value at a specified location in this vector.
get(int) - Method in class org.simbrain.util.projection.NTree
get(int, int) - Method in class org.simbrain.world.game.GameModel: Returns the value of the cell at the given coordinates.
get(int, int) - Method in class org.simbrain.world.game.tictactoe.TicTacToeModel: Returns the value of the cell at the given coordinates.
get_k_current() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
get_m3h() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
get_n4() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
get_na_current() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
get_vClampValue() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getA() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getA() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getActionList() - Method in class org.simbrain.network.core.NetworkUpdateManager
getActionList() - Method in class org.simbrain.workspace.updater.UpdateActionManager
getActionManager() - Method in class org.simbrain.network.gui.NetworkPanel
getActivation() - Method in class org.simbrain.network.core.Neuron
getActivationAmount() - Method in class org.simbrain.world.odorworld.sensors.TileSensor
getActivationProbability() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder
getActivations() - Method in class org.simbrain.network.groups.NeuronGroup: Return activations as a double array.
getActivationVector(List<Neuron>) - Static method in class org.simbrain.network.core.Network: Get the activations associated with a list of neurons.
getAdaptationParameter() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Return the adaptation parameter.
getAdaptationTimeConstant() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getAddAgentItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getAddColumnsAction(MutableTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for adding columns to a jtable.
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getAddNoise() - Method in interface org.simbrain.network.neuron_update_rules.interfaces.NoisyUpdateRule: Return true if add noise is turned on.
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getAddNoise() - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
getAddRowsAction(MutableTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for adding rows to a table.
getAddSourceAction(RasterPlotPanel) - Static method in class org.simbrain.plot.rasterchart.RasterPlotActions: Add a data source.
getAddSourceAction(TimeSeriesPlotPanel) - Static method in class org.simbrain.plot.timeseries.TimeSeriesPlotActions: Add a data source.
getAddSynapseGroupAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getAlignHorizontalAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the align horizontal action.
getAlignVerticalAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the align vertical action.
getAllSynapses() - Method in class org.simbrain.network.groups.SynapseGroup
getAllToAll() - Method in class org.simbrain.network.connections.QuickConnectionManager
getAlpha() - Method in class org.simbrain.network.subnetworks.SOMGroup: get Alpha.
getAlpha() - Method in class org.simbrain.network.trainers.LMSOffline
getAlphaDecayRate() - Method in class org.simbrain.network.subnetworks.SOMGroup: Get alphaDecayRate.
getAmount() - Method in class org.simbrain.world.odorworld.effectors.Speech
getAmount() - Method in class org.simbrain.world.odorworld.effectors.StraightMovement
getAmount() - Method in class org.simbrain.world.odorworld.effectors.Turning
getAnimation() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
getAppletMenuBar(NetworkPanel) - Static method in class org.simbrain.network.gui.NetworkMenuBar
getApplicableTypes() - Method in class org.simbrain.world.odorworld.effectors.Effector: Return a list of entity types which can use this type of sensor.
getApplicableTypes() - Method in class org.simbrain.world.odorworld.sensors.Sensor: Return a list of entity types which can use this type of sensor.
getApplyButton() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel
getArchivedActions() - Method in class org.simbrain.workspace.ArchiveContents
getArchivedComponent(String) - Method in class org.simbrain.workspace.ArchiveContents: Returns the component associated with the uri.
getArchivedComponents() - Method in class org.simbrain.workspace.ArchiveContents: Returns an immutable list of the components in this archive.
getArchivedConsumer() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedCoupling
getArchivedCouplings() - Method in class org.simbrain.workspace.ArchiveContents: Returns an immutable list of the couplings in this archive.
getArchivedProducer() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedCoupling
getArgumentDataTypes() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getArgumentDataTypes() - Method in interface org.simbrain.workspace.Attribute: Returns the method signature for auxiliary arguments (see the javadocs above for more information on this).
getArgumentDataTypes() - Method in class org.simbrain.workspace.PotentialAttribute
getArgumentValues() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getArgumentValues() - Method in interface org.simbrain.workspace.Attribute: Returns the argument values auxiliary arguments (see the javadocs above for more information on this).
getArgumentValues() - Method in class org.simbrain.workspace.PotentialAttribute
getAttributeManager() - Method in class org.simbrain.workspace.WorkspaceComponent
getAttributeName() - Method in class org.simbrain.workspace.AttributeType
getAutoZoomMode() - Method in class org.simbrain.network.gui.NetworkPanel
getAuxiliaryObject() - Method in class org.simbrain.network.listeners.NetworkEvent
getAuxValue() - Method in class org.simbrain.network.core.Neuron
getAvailableActionList() - Method in class org.simbrain.network.core.NetworkUpdateManager: Returns a list of network update actions that can be added.
getAvailableActionList() - Method in class org.simbrain.workspace.updater.UpdateActionManager: Returns a list of network update actions that can be added.
getAverage(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Helper function for computing mean values of an array of doubles.
getAverageInput() - Method in class org.simbrain.network.core.Neuron
getB() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getB() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getB() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
getBackgroundColor() - Static method in class org.simbrain.network.gui.NetworkPanel
getBackgroundColor() - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
getBackgroundColor() - Method in class org.simbrain.world.odorworld.OdorWorldPanel
getBackgroundCurrent() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getBalloonLocationX(RotatingEntity) - Method in class org.simbrain.world.odorworld.OdorWorldRenderer
getBalloonLocationY(RotatingEntity) - Method in class org.simbrain.world.odorworld.OdorWorldRenderer
getBarColor() - Method in class org.simbrain.plot.barchart.BarChartModel
getBaseColor() - Method in class org.simbrain.util.projection.DataColoringManager
getBaseDescription() - Method in class org.simbrain.workspace.AttributeType: Returns the description string of this datatype, with a method name if there is one.
getBaseExcitatorySynapse() - Method in class org.simbrain.network.connections.RadialSimple
getBaseInhibitorySynapse() - Method in class org.simbrain.network.connections.RadialSimple
getBaseLine() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getBaseLine() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
getBaseLine() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
getBaseLineStrength() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
getBaseObject() - Method in interface org.simbrain.workspace.Attribute: Returns the base object associated with this attribute.
getBaseObject() - Method in class org.simbrain.workspace.PotentialAttribute
getBaseObjectKey() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getBaseProb() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
getBatchSize() - Method in class org.simbrain.network.subnetworks.SOMGroup: Get the Batch Size.
getBeginPosition() - Method in class org.simbrain.network.gui.NetworkPanel
getBeginPosition() - Method in class org.simbrain.world.textworld.TextWorld.TextItem
getBehavior() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Return the current behavior.
getBestFit(double[], int) - Method in enum org.simbrain.util.math.ProbDistribution
getBestFitParams(double[], int) - Method in enum org.simbrain.util.math.ProbDistribution
getBetweenLayerInterval() - Method in class org.simbrain.network.subnetworks.FeedForward
getBetweenNeuronInterval() - Method in class org.simbrain.network.groups.NeuronGroup
getBez1(Point2D, Point2D, NeuronGroupNode.Port) - Method in enum org.simbrain.util.widgets.DirectedCubicArrow.BezierTemplate
getBez2(Point2D, Point2D, NeuronGroupNode.Port) - Method in enum org.simbrain.util.widgets.DirectedCubicArrow.BezierTemplate
getBezier_1() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getBezier_2() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getBias() - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
getBias() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
getBias() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
getBias() - Method in interface org.simbrain.network.neuron_update_rules.interfaces.BiasedUpdateRule
getBias() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
getBias() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getBias() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getBiases() - Method in class org.simbrain.network.groups.NeuronGroup: Return biases as a double array.
getBins() - Method in class org.simbrain.plot.histogram.HistogramModel
getBins(int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the bins for a series.
getBites() - Method in class org.simbrain.world.odorworld.LifeCycle
getBitesToDie() - Method in class org.simbrain.world.odorworld.LifeCycle
getBounds() - Method in interface org.simbrain.util.genericframe.GenericFrame
getBounds() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Get bounds, based on current image.
getBuffer() - Method in class org.simbrain.network.core.Neuron
getBumpRate() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
getButtonPanel() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel: Return button panel in case user would like to add custom buttons.
getButtonPanel() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Return button panel in case user would like to add custom buttons.
getC() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getCanvas() - Method in class org.simbrain.network.gui.NetworkPanel
getCbDistribution() - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
getCbImplementation() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel
getCbNeuronType() - Method in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel
getCbSynapseType() - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel
getCbSynapseType() - Method in class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel
getCeiling() - Method in class org.simbrain.util.projection.DataColoringManager
getCenter() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Return the center of this node (the circle) in global coordinates.
getCenterLocation() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Returns the location of the center of this entity as a double array.
getCenterX() - Method in class org.simbrain.network.groups.NeuronGroup: Get the central x coordinate of this group, based on the positions of the neurons that comprise it.
getCenterX() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Returns the center x position of this entity.
getCenterX() - Method in class org.simbrain.world.visionworld.ReceptiveField: Return the center x coordinate for this receptive field.
getCenterY() - Method in class org.simbrain.network.groups.NeuronGroup: Get the central y coordinate of this group, based on the positions of the neurons that comprise it.
getCenterY() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Returns the center y position of this entity.
getCenterY() - Method in class org.simbrain.world.visionworld.ReceptiveField: Return the center y coordinate for this receptive field.
getChangeTableStructureAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for setting table structure.
getChartPanel() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel
getChartPanel() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel
getChartSeriesPaint() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
getCircle() - Static method in class org.simbrain.world.odorworld.entities.RotatingEntityManager: Returns circle image.
getClamped() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended
getClassName() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent
getClearGraphAction(RasterPlotPanel) - Static method in class org.simbrain.plot.rasterchart.RasterPlotActions: Clear the graph.
getClearGraphAction(TimeSeriesPlotPanel) - Static method in class org.simbrain.plot.timeseries.TimeSeriesPlotActions: Clear the graph.
getClearSourceNeuronsAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getClearWorkspaceAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getClipboardActions() - Method in class org.simbrain.network.gui.NetworkActionManager: Return clipboard actions.
getClipboardEntity() - Static method in class org.simbrain.world.odorworld.WorldClipboard
getClipping() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer
getClipping() - Method in class org.simbrain.util.randomizer.Randomizer
getClosestIndex(DataPoint) - Method in class org.simbrain.util.projection.Dataset: Returns the index of the closest point.
getClosestPoint(DataPoint) - Method in class org.simbrain.util.projection.NTree: Returns the closest point in the tree to the given point.
getClosestPoints(int, DataPoint) - Method in class org.simbrain.util.projection.NTree: Gets the closest points to the passed in point.
getClosestWord(double[]) - Method in class org.simbrain.world.textworld.DisplayWorld: Finds the closest vector in terms of Euclidean distance, then returns the String associated with it.
getCm() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getcMembrane() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getColor() - Method in class org.simbrain.util.projection.DataPointColored
getColor() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getColor(Class<?>) - Static method in class org.simbrain.workspace.CouplingManager: Associates attribute and coupling data types (classes) with colors used in displaying attributes and couplings.
getColor() - Method in class org.simbrain.world.odorworld.dialogs.OdorWorldDialog: Show the color pallette and get a color.
getColoringMethodString() - Method in class org.simbrain.util.projection.DataColoringManager: Get the coloring method as a string.
getColorManager() - Method in class org.simbrain.util.projection.Projector
getColumnClass(int) - Method in class org.simbrain.util.table.SimbrainDataTable
getColumnClass(int) - Method in class org.simbrain.util.table.TextTable
getColumnClass(int) - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
getColumnClass(int) - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
getColumnClass(int) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
getColumnClass(int) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
getColumnConsumer(int) - Method in class org.simbrain.world.dataworld.DataWorldComponent: Return the column consumer with specified index, or null if none found.
getColumnCount() - Method in class org.simbrain.util.table.SimbrainDataTable
getColumnCount() - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
getColumnCount() - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
getColumnCount() - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
getColumnCount() - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
getColumnList(List<Neuron>, int) - Static method in class org.simbrain.network.layouts.GridLayout: Returns a list of columns corresponding to a set of neurons assumed to be in the form of a grid.
getColumnName(int) - Method in class org.simbrain.util.table.SimbrainDataTable
getColumnName(int) - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
getColumnName(int) - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
getColumnName(int) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
getColumnName(int) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
getColumnProducer(int) - Method in class org.simbrain.world.dataworld.DataWorldComponent: Return the column producer with specified index, or null if none found.
getColumns() - Method in class org.simbrain.util.JMultiLineToolTip
getCompetitive() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork
getComponent(int, int) - Method in class org.simbrain.util.projection.Dataset: Get a specific coordinate of a specific datapoint.
getComponent() - Method in class org.simbrain.workspace.updater.UpdateComponent: Returns a reference to this component.
getComponent(String) - Method in class org.simbrain.workspace.Workspace: Get a component using its name id.
getComponent(String) - Method in class org.simbrain.workspace.WorkspaceComponentDeserializer: Returns the workspace component associated with the given uri.
getComponentId() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedUpdateAction
getComponentList() - Method in class org.simbrain.workspace.Workspace
getComponentList(Class<?>) - Method in class org.simbrain.workspace.Workspace: Returns all components of the specified type, e.g.
getComponentListeners() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Return list of component listeners.
getComponents() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Get a synchronized list of component.
getConnectedSynapses() - Method in class org.simbrain.network.gui.nodes.NeuronNode
getConnection() - Method in class org.simbrain.network.gui.dialogs.connect.AbstractConnectionPanel: Get the underlying connection object.
getConnection() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.AllToAllPanel
getConnection() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.OneToOnePanel: Get the underlying connection object.
getConnection() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.RadialPanel
getConnection() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel: Get the underlying connection object.
getConnectionActions() - Method in class org.simbrain.network.gui.NetworkActionManager
getConnectionDensity() - Method in class org.simbrain.network.connections.Sparse
getConnectionManager() - Method in class org.simbrain.network.groups.SynapseGroup
getConnectionMenu() - Method in class org.simbrain.network.gui.NetworkActionManager: Returns a menu for setting neuron connections.
getConnectOrientation() - Method in class org.simbrain.network.connections.OneToOne
getConnectorPanel() - Method in class org.simbrain.network.gui.dialogs.connect.CondensedConnectionPanel: Returns the density based connection panel so that other classes can set certain properties of the panel independent of this class.
getConnectors() - Method in class org.simbrain.network.connections.QuickConnectionManager
getConsumer() - Method in class org.simbrain.workspace.Coupling
getConsumerTypes() - Method in class org.simbrain.workspace.WorkspaceComponent
getConsumingColumnType() - Method in class org.simbrain.world.dataworld.DataWorldComponent
getContentPane() - Method in class org.simbrain.util.StandardDialog: This method gets the content pane for adding components.
getContextLayer() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork
getContextMenu() - Method in class org.simbrain.network.gui.NetworkPanel: Return the context menu for this Network panel.
getContextMenu() - Method in class org.simbrain.network.gui.nodes.InteractionBox
getContextMenu() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode.NeuronGroupInteractionBox
getContextMenu() - Method in class org.simbrain.network.gui.nodes.NeuronNode
getContextMenu() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return a context menu specific to this screen element.
getContextMenu() - Method in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox
getContextMenu() - Method in class org.simbrain.network.gui.nodes.SynapseNode
getContextMenu() - Method in class org.simbrain.network.gui.nodes.TextNode
getContextMenu() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
getContextMenu() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return the context menu for this sensor node.
getContextMenuAlt() - Method in class org.simbrain.network.gui.NetworkPanel
getCoolColor() - Static method in class org.simbrain.network.gui.nodes.NeuronNode
getCopy(Network, ArrayList<?>) - Static method in class org.simbrain.network.util.CopyPaste: Creates a copy of a list of network model elements: neurons, synapses, and groups.
getCopyAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the copy action.
getCopyItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getCoupling() - Method in class org.simbrain.workspace.updater.UpdateCoupling
getCoupling(String) - Method in class org.simbrain.workspace.Workspace: Returns the coupling associated with a string id.
getCouplingId() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedUpdateAction
getCouplingManager() - Method in class org.simbrain.workspace.Workspace: Returns the coupling manager for this workspace.
getCouplings() - Method in class org.simbrain.workspace.CouplingManager: Returns an unmodifiable list of all the couplings.
getCouplings(WorkspaceComponent, WorkspaceComponent) - Method in class org.simbrain.workspace.CouplingManager: Returns all couplings from the given source component to the given target component.
getCovariance(int, int) - Method in class org.simbrain.util.projection.Dataset: Returns the covariance of the ith component of the dataset with respect to the jth component.
getCovarianceMatrix() - Method in class org.simbrain.util.projection.Dataset: Returns a covariance matrix for the dataset.
getCurrentConnector() - Method in class org.simbrain.network.connections.QuickConnectionManager
getCurrentDirectory() - Method in class org.simbrain.workspace.Workspace
getCurrentFile() - Method in class org.simbrain.workspace.Workspace
getCurrentFile() - Method in class org.simbrain.workspace.WorkspaceComponent
getCurrentItem() - Method in class org.simbrain.world.textworld.TextWorld
getCurrentLayout() - Method in class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Returns the current layout being edited.
getCurrentLocation() - Method in class org.simbrain.util.SFileChooser: Returns the directory this chooser is in.
getCurrentlyEditableSynapses() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel
getCurrentlyHeardPhrases() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
getCurrentMethodString() - Method in class org.simbrain.util.projection.Projector: Used to get the String associated with the current projection method.
getCurrentObject() - Method in interface org.simbrain.util.propertyeditor.ComboBoxWrapper: Return the current object to be initially presented in the combo box.
getCurrentPoint() - Method in class org.simbrain.util.projection.Projector
getCurrentRow() - Method in interface org.simbrain.util.table.IterableRowsTable: Returns the current row.
getCurrentRow() - Method in class org.simbrain.util.table.NumericTable
getCurrentState() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
getCurrentValue() - Method in class org.simbrain.world.odorworld.sensors.SmellSensor
getCurrentValue(int) - Method in class org.simbrain.world.odorworld.sensors.SmellSensor: The current value at an index.
getCurrentVector() - Method in class org.simbrain.world.textworld.ReaderWorld: Returns the double array associated with the currently selected token (character or word).
getCursor() - Method in class org.simbrain.network.gui.EditMode: Return the cursor for this edit mode.
getCutAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the cut action.
getCutItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getD() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getData() - Method in class org.simbrain.plot.histogram.HistogramModel
getData() - Method in interface org.simbrain.util.math.NumericMatrix: Get the data.
getData() - Method in class org.simbrain.util.table.SimbrainJTable
getDataDirectory() - Static method in class org.simbrain.network.gui.trainer.TrainerGuiActions: Return the current data directory.
getDataModel() - Method in class org.simbrain.world.dataworld.DataWorldComponent: Returns the data model for this component.
getDataNames() - Method in class org.simbrain.plot.histogram.HistogramModel
getDataSeries() - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the set of colored data series.
getDataset() - Method in class org.simbrain.plot.barchart.BarChartModel: Return JFreeChart pie dataset.
getDataSet() - Method in class org.simbrain.plot.histogram.HistogramModel
getDataset() - Method in class org.simbrain.plot.piechart.PieChartModel
getDataset() - Method in class org.simbrain.plot.projection.ProjectionModel
getDataset() - Method in class org.simbrain.plot.rasterchart.RasterModel
getDataset() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
getDataset() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
getDatasetCopy() - Method in class org.simbrain.util.projection.Dataset
getDataType() - Method in class org.simbrain.util.table.NumericTable
getDataType() - Method in class org.simbrain.util.table.SimbrainDataTable: Returns the datatype (T) for a given table type.
getDataType() - Method in class org.simbrain.util.table.TextTable
getDataType() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getDataType() - Method in interface org.simbrain.workspace.Attribute: Returns the "main" data type of this attribute (see class javadocs above).
getDataType() - Method in class org.simbrain.workspace.AttributeType
getDataType() - Method in class org.simbrain.workspace.Coupling: Returns the datatype associated with this coupling.
getDataType() - Method in class org.simbrain.workspace.PotentialAttribute
getDecay() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getDecayAmount() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getDecayFraction() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getDecayFunction() - Method in class org.simbrain.util.environment.SmellSource
getDecayRate() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
getDecrementAmount() - Method in class org.simbrain.util.projection.DataColoringManager
getDefault_Pallet() - Static method in class org.simbrain.plot.histogram.HistogramPanel
getDefaultContextMenu() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Returns default actions for a context menu.
getDefaultContextMenu() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Creates default actions for all model group nodes.
getDefaultContextMenu() - Method in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Returns default actions for a context menu.
getDefaultFilter() - Method in class org.simbrain.world.visionworld.sensormatrix.AbstractSensorMatrix: Return the default filter for the sensors in this sensor matrix, if any.
getDefaultFilter() - Method in interface org.simbrain.world.visionworld.SensorMatrix: Return the default filter for the sensors in this sensor matrix, if any.
getDefaultFormat() - Method in class org.simbrain.workspace.WorkspaceComponent: The file extension for a component type, e.g.
getDefaultIncrement() - Static method in class org.simbrain.network.core.NeuronUpdateRule
getDefaultKappa() - Static method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
getDefaultLowBound() - Method in enum org.simbrain.util.math.ProbDistribution
getDefaultLowerBound() - Method in enum org.simbrain.util.math.SquashingFunction
getDefaultNumDatasets() - Static method in class org.simbrain.plot.histogram.HistogramPanel: Returns default number of datasets.
getDefaultParam1() - Method in enum org.simbrain.util.math.ProbDistribution
getDefaultParam2() - Method in enum org.simbrain.util.math.ProbDistribution
getDefaultPercentExcitatory() - Static method in class org.simbrain.network.connections.QuickConnectionManager
getDefaultUpBound() - Method in enum org.simbrain.util.math.ProbDistribution
getDefaultUpperBound() - Method in enum org.simbrain.util.math.SquashingFunction
getDefaultValue() - Method in class org.simbrain.util.table.NumericTable
getDefaultValue() - Method in class org.simbrain.util.table.SimbrainDataTable: Returns the default cell value for a given table type.
getDefaultValue() - Method in class org.simbrain.util.table.TextTable
getDelay() - Method in class org.simbrain.network.core.Synapse
getDelay(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
getDeleteAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the clear action.
getDeleteColumnAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for deleting a column from a jtable.
getDeleteItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getDeleteRowAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for deleting a row from to a jtable.
getDensityEsitmate() - Method in class org.simbrain.network.connections.Radial.DensityEstimator
getDerivative(double) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: The inverse of the activation function.
getDerivative(double) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.DifferentiableUpdateRule: The inverse of the activation function.
getDerivative(double) - Method in class org.simbrain.network.neuron_update_rules.LinearRule: The inverse of the activation function.
getDerivative(double) - Method in class org.simbrain.network.neuron_update_rules.SigmoidalRule: The inverse of the activation function.
getDescription() - Method in interface org.simbrain.network.core.NetworkUpdateAction: Provide a String description of this update method.
getDescription() - Method in class org.simbrain.network.core.NeuronUpdateRule: Returns a brief description of this update rule.
getDescription() - Method in class org.simbrain.network.core.SynapseUpdateRule: Returns a brief description of this update rule.
getDescription() - Method in class org.simbrain.network.layouts.GridLayout
getDescription() - Method in class org.simbrain.network.layouts.HexagonalGridLayout
getDescription() - Method in interface org.simbrain.network.layouts.Layout
getDescription() - Method in class org.simbrain.network.layouts.LineLayout
getDescription() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getDescription() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Returns a brief description of this update rule.
getDescription() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.RunningAverageRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.SigmoidalRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
getDescription() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getDescription() - Method in enum org.simbrain.network.subnetworks.Hopfield.HopfieldUpdate
getDescription() - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
getDescription() - Method in class org.simbrain.network.synapse_update_rules.HebbianRule
getDescription() - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
getDescription() - Method in class org.simbrain.network.synapse_update_rules.OjaRule
getDescription() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
getDescription() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
getDescription() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
getDescription() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder
getDescription() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay
getDescription() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder
getDescription() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.Step
getDescription() - Method in class org.simbrain.network.synapse_update_rules.StaticSynapseRule
getDescription() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
getDescription() - Method in class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule
getDescription() - Method in class org.simbrain.network.update_actions.BufferedUpdate
getDescription() - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
getDescription() - Method in class org.simbrain.network.update_actions.CustomUpdate
getDescription() - Method in class org.simbrain.network.update_actions.PriorityUpdate
getDescription() - Method in class org.simbrain.network.update_actions.UpdateGroup
getDescription() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getDescription() - Method in interface org.simbrain.workspace.Attribute: Returns a descriptive name for this attribute.
getDescription(String) - Method in class org.simbrain.workspace.AttributeType: Returns a description using a custom base name (e.g.
getDescription() - Method in class org.simbrain.workspace.PotentialAttribute: Returns a description of this potential attribute; used in GUI.
getDescription() - Method in class org.simbrain.workspace.updater.ComponentUpdatePart: Returns the description for this part.
getDescription() - Method in interface org.simbrain.workspace.updater.UpdateAction: Provide a String description of this update method.
getDescription() - Method in class org.simbrain.workspace.updater.UpdateActionCustom
getDescription() - Method in class org.simbrain.workspace.updater.UpdateAllBuffered
getDescription() - Method in class org.simbrain.workspace.updater.UpdateComponent: Provide a String description of this update method.
getDescription() - Method in class org.simbrain.workspace.updater.UpdateCoupling: Provide a String description of this update method.
getDescription() - Method in class org.simbrain.world.game.GameAttributes
getDescription() - Method in interface org.simbrain.world.threedee.Sensor
getDescription() - Method in class org.simbrain.world.threedee.sensors.Sight.SightSensor
getDescription() - Method in interface org.simbrain.world.visionworld.Filter: Return the description of this filter.
getDescription() - Method in class org.simbrain.world.visionworld.filter.PixelAccumulator
getDescription() - Method in class org.simbrain.world.visionworld.filter.RandomFilter
getDescription() - Method in class org.simbrain.world.visionworld.filter.RgbFilter: Return the description of this filter.
getDescription() - Method in class org.simbrain.world.visionworld.filter.UniformFilter
getDescription() - Method in class org.simbrain.world.visionworld.Sensor
getDesktop() - Method in class org.simbrain.workspace.gui.GuiComponent
getDesktop(Workspace) - Static method in class org.simbrain.workspace.gui.SimbrainDesktop
getDesktop() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Returns the internal desktop object.
getDesktop() - Method in class org.simbrain.workspace.gui.SimbrainScriptEditor
getDesktopComponent() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent
getDesktopComponent(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Returns the desktop component corresponding to a workspace component.
getDesktopComponent(String) - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Returns the desktop component corresponding to a named workspace component.
getDetailTriangle() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple
getDetailTriangle() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple
getDialog() - Method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Returns an dialog containing this property editor.
getDialog(ScriptEditor) - Method in class org.simbrain.util.scripteditor.ScriptEditor: Returns a standard dialog for editing a script.
getDIAMETER() - Static method in class org.simbrain.network.gui.nodes.NeuronNode
getDictionaryDirectory() - Static method in class org.simbrain.world.textworld.TextWorldActions: Return the current directory for the dictionary file.
getDimension() - Method in class org.simbrain.plot.projection.ProjectionComponent.Dimension
getDimension(int) - Method in class org.simbrain.plot.projection.ProjectionComponent: Return a dimension object.
getDimension() - Method in class org.simbrain.util.projection.DataPoint: Returns the number of components of the data vector.
getDimensions() - Method in class org.simbrain.util.projection.Dataset
getDimensions() - Method in class org.simbrain.util.projection.Projector: Number of dimensions of the underlying data.
getDir(File) - Static method in class org.simbrain.util.Utils: Get the directory component of a file.
getDirection() - Method in class org.simbrain.world.odorworld.effectors.Turning
getDispersion() - Method in class org.simbrain.util.environment.SmellSource: Return the dispersion.
getDispersionPanel() - Method in class org.simbrain.util.environment.SmellSourcePanel
getDisplayThreshold() - Method in class org.simbrain.world.textworld.DisplayWorld
getDistance(int, int) - Method in class org.simbrain.util.projection.Dataset: Get the distance between two points.
getDistance(DataPoint, DataPoint) - Method in class org.simbrain.util.projection.Dataset: Returns the euclidean distance between two points.
getDistance(DataPoint, DataPoint) - Static method in class org.simbrain.util.projection.NTree: Determines the Euclidean distance between two points.
getDistances() - Method in class org.simbrain.util.projection.Dataset: Returns a matrix of interpoint distances, between the points in the dataset.
getDistConst() - Method in class org.simbrain.network.connections.Radial
getDistributionName() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer: Returns the string name of the distribution.
getDistributionName() - Method in class org.simbrain.util.randomizer.Randomizer: Returns the string name of the distribution.
getDockingPoint(NeuronGroupNode.Port, SynapseGroupArrow) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
getDockingPorts() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
getDotSize() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
getDouble(String) - Static method in class org.simbrain.util.SimbrainPreferences: Retrieve a property whose value is a double.
getDoubleArray() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getDoubleMatrix(File) - Static method in class org.simbrain.util.Utils: Read a csv (comma-separated-values) files.
getDoubleStrings() - Method in class org.simbrain.util.projection.Dataset: Returns a matrix of strings, one row for each datapoint, representing the dataset.
getDoubleX() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Get the X position as a double.
getDoubleY() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Get the Y position as a double.
getDownstairs() - Method in class org.simbrain.util.projection.Projector: Convenience method to get downstairs dataset.
getDt() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getDuration() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getEditablePopField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getEditCombinedDataAction(NetworkPanel, Trainable) - Static method in class org.simbrain.network.gui.trainer.TrainerGuiActions: Action for viewing two datatables, one for input data; the other for training data.
getEditDataAction(NetworkPanel, List<Neuron>, NumericMatrix, String) - Static method in class org.simbrain.network.gui.trainer.TrainerGuiActions: Action for viewing data in a table that correlate with a set of neurons.
getEditMenuActions() - Method in class org.simbrain.world.visionworld.VisionWorld: Return a list of edit menu actions for this vision world.
getEditMode() - Method in class org.simbrain.network.gui.NetworkPanel: Return the current edit mode for this Network panel.
getEditorComponent() - Method in interface org.simbrain.world.visionworld.filter.editor.FilterEditor: Return the editor component for this filter editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.filter.editor.PixelAccumulatorEditor: Return the editor component for this filter editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.filter.editor.RandomFilterEditor: Return the editor component for this filter editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: Return the editor component for this filter editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.filter.editor.UniformFilterEditor: Return the editor component for this filter editor.
getEditorComponent() - Method in interface org.simbrain.world.visionworld.node.editor.PixelMatrixImageNodeEditor: Return the editor component for this pixel matrix image node editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.node.editor.PixelMatrixImageNodeTableEditor: Return the editor component for this pixel matrix image node editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.pixelmatrix.editor.BufferedImagePixelMatrixEditor: Return the editor component for this pixel matrix editor.
getEditorComponent() - Method in interface org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditor: Return the editor component for this pixel matrix editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.pixelmatrix.editor.ScreenCapturePixelMatrixEditor: Return the editor component for this pixel matrix editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.sensormatrix.editor.DenseSensorMatrixEditor: Return the editor component for this sensor matrix editor.
getEditorComponent() - Method in interface org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditor: Return the editor component for this sensor matrix editor.
getEditorComponent() - Method in class org.simbrain.world.visionworld.sensormatrix.editor.SparseSensorMatrixEditor: Return the editor component for this sensor matrix editor.
getEditSensorsAction() - Method in class org.simbrain.world.visionworld.VisionWorld: Return the edit sensors action for this vision world.
getEditSpikeRespondersPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
getEditToolBar() - Method in class org.simbrain.network.gui.NetworkPanel
getEeDistConst() - Method in class org.simbrain.network.connections.Radial
getEffector(int) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel: Helper method to get a reference to the effector displayed in a row.
getEffector(String, String) - Method in class org.simbrain.world.odorworld.OdorWorld: Returns the effector with the given id, or null if none is found.
getEffectors() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
getEiDistConst() - Method in class org.simbrain.network.connections.Radial
getEk() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getElapsedTime() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getElementAt(int) - Method in class org.simbrain.workspace.gui.couplingmanager.GenericListModel: Returns a specific consumer.
getEna() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getEnabled() - Method in class org.simbrain.network.groups.Subnetwork
getEndPosition() - Method in class org.simbrain.network.gui.NetworkPanel
getEndPosition() - Method in class org.simbrain.world.textworld.TextWorld.TextItem
getEndPt() - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow
getEndPt() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
getEndPt() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getEndPt() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getEndX(int, int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the end value for a bin.
getEndY(int, int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the end y-value for a bin (which is the same as the y-value, this method exists only to support the general form of the IntervalXYDataset interface).
getEntity(String) - Method in class org.simbrain.world.odorworld.OdorWorld: Returns the entity with the given id, or, failing that, a given name.
getEntityType() - Method in class org.simbrain.world.odorworld.entities.RotatingEntity
getEnumeration() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getEpsilon() - Method in class org.simbrain.util.projection.ProjectSammon
getError() - Method in class org.simbrain.network.trainers.BackpropTrainer: Get the current MSE error.
getError() - Method in class org.simbrain.network.trainers.BPTTTrainer
getError() - Method in class org.simbrain.network.trainers.IterableTrainer: Get the current MSE error.
getError() - Method in class org.simbrain.network.trainers.LMSIterative: Get the current MSE error.
getError() - Method in class org.simbrain.util.projection.IterableProjectionMethod: Returns the current error associated with this projection method.
getErrorListeners() - Method in class org.simbrain.network.trainers.IterableTrainer
getErrorThreshold() - Method in class org.simbrain.network.trainers.IterableTrainer
getEuclideanDist(Neuron, Neuron) - Static method in class org.simbrain.network.core.Network: Gets the Euclidean distance between two neurons' positions in coordinate space.
getEventListenerList() - Method in class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Return the EventListenerList backing this vision world model listener support class.
getException() - Method in class org.simbrain.workspace.updater.SynchronizingInvocationEvent
getExcitatoryColor() - Static method in class org.simbrain.network.gui.nodes.SynapseNode
getExcitatoryConductance() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getExcitatoryCurrent() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getExcitatoryMaxConductance() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getExcitatoryProbability() - Method in class org.simbrain.network.connections.RadialSimple
getExcitatoryPrototype() - Method in class org.simbrain.network.groups.SynapseGroup: Reveals the excitatory prototype synapse, allowing more detailed synapse values to be queried at the group level.
getExcitatoryRadius() - Method in class org.simbrain.network.connections.RadialSimple
getExcitatoryRandomizer() - Method in class org.simbrain.network.groups.SynapseGroup
getExcitatoryRandomizerPanel() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
getExcitatoryRatio() - Method in class org.simbrain.network.connections.QuickConnectionManager
getExcitatoryRatioParameter() - Method in class org.simbrain.network.groups.SynapseGroup: Returns the excitatory ratio parameter.
getExcitatoryRatioPrecise() - Method in class org.simbrain.network.groups.SynapseGroup
getExcitatoryReversal() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getExcitatoryStrengths() - Method in class org.simbrain.network.groups.SynapseGroup
getExcitatorySynapses(Collection<Synapse>) - Static method in class org.simbrain.network.connections.ConnectionUtilities
getExcitatorySynapses() - Method in class org.simbrain.network.groups.SynapseGroup
getExportDataHi(ProjectionModel) - Static method in class org.simbrain.plot.projection.ProjectionPlotActions: Export high dimensional data to .csv.
getExportDataLow(ProjectionModel) - Static method in class org.simbrain.plot.projection.ProjectionPlotActions: Export low dimensional data to .csv.
getExRandomizer() - Method in class org.simbrain.network.connections.QuickConnectionManager
getExRandomizer() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
getExReversal() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getExtension(File) - Static method in class org.simbrain.util.SFileChooser: Returns all the characters after the last period in the file name.
getExtension(String) - Static method in class org.simbrain.util.SFileChooser: Returns all the characters after the last period in the file name.
getExternalActivations() - Method in class org.simbrain.network.groups.NeuronGroup: Returns a vector of activations to be used by some object external to the neuron group.
getExtractDictionaryAction(TextWorld) - Static method in class org.simbrain.world.textworld.TextWorldActions: Action for loading a dictionary, by finding every distinct word and punctuation mark in a text file.
getExtractTokensFromVectorDict(TextWorld) - Static method in class org.simbrain.world.textworld.dictionary.TokenDictionaryPanel: An action for extracting tokens from the vector dictionary associated with the world object.
getExtraDataPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple
getExtraDataPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple
getFALSE() - Static method in class org.simbrain.util.widgets.TristateDropDown
getFanIn() - Method in class org.simbrain.network.core.Neuron
getFanInList() - Method in class org.simbrain.network.core.Neuron: Used for deletion to avoid a ConcurrentModificationException as well as conform to the other processes inovlved in removing synapses from a network.
getFanOut() - Method in class org.simbrain.network.core.Neuron
getFanOutList() - Method in class org.simbrain.network.core.Neuron: Used for deletion to avoid a ConcurrentModificationException as well as conform to the other processes inovlved in removing synapses from a network.
getFieldCount() - Method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Returns the number of items contained in the panel.
getFileMenuActions() - Method in class org.simbrain.world.visionworld.VisionWorld: Return a list of file menu actions for this vision world.
getFillAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for filling a table with specific values.
getFilter() - Method in class org.simbrain.world.visionworld.Sensor: Return the filter for this sensor.
getFiringProbability() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
getFiringThreshold() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
getFixedWidth() - Method in class org.simbrain.util.JMultiLineToolTip
getFlatGroupList() - Method in class org.simbrain.network.core.Network: Create a "flat" list of groups, which includes the top-level groups plus all subgroups.
getFlatNeuronGroupList() - Method in class org.simbrain.network.core.Network: Returns a list of all neuron groups.
getFlatNeuronList() - Method in class org.simbrain.network.core.Network: Create "flat" list of neurons, which includes the top-level neurons plus all group neurons.
getFlatNeuronList() - Method in class org.simbrain.network.groups.Subnetwork: Return a "flat" list containing every neuron in every neuron group in this subnetwork.
getFlatSynapseList() - Method in class org.simbrain.network.core.Network: Create "flat" list of synapses, which includes the top-level synapses plus all subnet synapses.
getFlatSynapseList() - Method in class org.simbrain.network.groups.Subnetwork: Return a "flat" list containing every synapse in every synapse group in this subnetwork.
getFloat(String) - Static method in class org.simbrain.util.SimbrainPreferences: Retrieve a property whose value is a float.
getFloor() - Method in class org.simbrain.util.projection.DataColoringManager
getFontName() - Method in class org.simbrain.network.core.NetworkTextObject
getFontSize() - Method in class org.simbrain.network.core.NetworkTextObject
getFormat() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent
getFormats() - Method in class org.simbrain.docviewer.DocViewerComponent
getFormats() - Method in class org.simbrain.workspace.WorkspaceComponent: Returns a list of the formats that this component supports.
getFourCorners() - Method in class org.simbrain.network.groups.NeuronGroup
getFrame() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Returns the main frame for the desktop.
getFrequency() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getG_Ca() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getG_e_bar() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getG_i_bar() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getG_K() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getG_L() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getG_L() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getGain() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getGeneratorlist() - Static method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel
getGetterSetter(int) - Method in class org.simbrain.workspace.AttributeList: Returns the getterSetter associated with this index.
getGlobalControlActions() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager: Return a list of network control actions.
getGlobalRunAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getGlobalStopAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getGlobalUpdateAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getGraphicalLowerBound() - Method in class org.simbrain.network.core.NeuronUpdateRule: Returns a value for lower bound to be used in computing the saturation of neuron nodes.
getGraphicalLowerBound() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getGraphicalLowerBound() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
getGraphicalLowerBound() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getGraphicalLowerBound() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getGraphicalUpperBound() - Method in class org.simbrain.network.core.NeuronUpdateRule: Returns a value for upper bound to be used in computing the saturation of neuron nodes.
getGraphicalUpperBound() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getGraphicalUpperBound() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
getGraphicalUpperBound() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getGraphicalUpperBound() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getGridPaint() - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Return the grid paint for this sensor matrix node.
getGridStroke() - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Return the grid stroke for this sensor matrix node.
getGridThreshold() - Method in class org.simbrain.network.groups.NeuronGroup
getGroup(String) - Method in class org.simbrain.network.core.Network: Find a group with a given string id.
getGroup() - Method in interface org.simbrain.network.gui.dialogs.group.GroupPropertiesPanel
getGroup() - Method in class org.simbrain.network.gui.dialogs.group.NeuronGroupPanel
getGroup() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getGroup() - Method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel
getGroup() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel
getGroup() - Method in class org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel
getGroup() - Method in class org.simbrain.network.gui.dialogs.network.WTAPropertiesPanel
getGroup() - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow
getGroup() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
getGroup() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getGroup() - Method in class org.simbrain.network.update_actions.UpdateGroup
getGroup2() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
getGroupAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getGroupByLabel(String) - Method in class org.simbrain.network.core.Network: Find group with a given label, or null if none found.
getGroupedObjects() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
getGroupIdGenerator() - Method in class org.simbrain.network.core.Network
getGroupList() - Method in class org.simbrain.network.core.Network: Returns the group list.
getGroupMenu() - Method in class org.simbrain.network.gui.NetworkActionManager: Returns a menu of model group actions.
getGroupsByLabel(String) - Method in class org.simbrain.network.core.Network: Find groups with a given label, or null if none found.
getGrowthRate() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
getH() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getHeading() - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Returns the current heading, in degrees.
getHeadingRadians() - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Returns the heading in radians.
getHearingSensorImage(Hearing) - Method in class org.simbrain.world.odorworld.OdorWorldRenderer: Draws the thought bubble.
getHeight() - Method in class org.simbrain.network.groups.NeuronGroup: Return the height of this group, based on the positions of the neurons that comprise it.
getHeight() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Returns the height of the visible portion of the desktop.
getHeight() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Gets this OdorWorldEntity's height, based on the size of the current image.
getHeight() - Method in class org.simbrain.world.odorworld.OdorWorld: Returns height of world in pixels.
getHeight() - Method in class org.simbrain.world.odorworld.sensors.TileSensor
getHeight() - Method in class org.simbrain.world.odorworld.TileMap: Gets the height of this TileMap (number of tiles down).
getHeight() - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Return the height of this pixel matrix.
getHeight() - Method in interface org.simbrain.world.visionworld.PixelMatrix: Return the height of this pixel matrix.
getHeight() - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Return the height of this pixel matrix.
getHeight() - Method in class org.simbrain.world.visionworld.ReceptiveField: Return the height of this receptive field.
getHelpPath() - Method in interface org.simbrain.network.gui.dialogs.group.GroupPropertiesPanel: Returns a string path to the documentation page for this group, relative to the top level Simbrain/doc directory.
getHelpPath() - Method in class org.simbrain.network.gui.dialogs.group.NeuronGroupPanel
getHelpPath() - Method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel
getHelpPath() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel: Returns a string path to the documentation page for this group, relative to the top level Simbrain/doc directory.
getHelpPath() - Method in class org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel: Returns a string path to the documentation page for this group, relative to the top level Simbrain/doc directory.
getHelpPath() - Method in class org.simbrain.network.gui.dialogs.network.WTAPropertiesPanel
getHiD1() - Method in class org.simbrain.util.projection.ProjectCoordinate
getHiD2() - Method in class org.simbrain.util.projection.ProjectCoordinate
getHiddenLayer() - Method in class org.simbrain.network.subnetworks.BPTTNetwork: Returns the hidden layer.
getHiddenLayer() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork
getHighlightColor() - Method in class org.simbrain.world.textworld.TextWorld
getHorizontalSpacing() - Method in class org.simbrain.network.util.CascadingNetworkBuilder
getHosts() - Method in class org.simbrain.network.update_actions.concurrency_tools.BufferedUpdateTask
getHotColor() - Static method in class org.simbrain.network.gui.nodes.NeuronNode
getHotColor() - Method in class org.simbrain.util.projection.DataColoringManager
getHotPointMode() - Method in class org.simbrain.util.projection.DataColoringManager
getHSpacing() - Method in class org.simbrain.network.layouts.GridLayout
getHSpacing() - Method in class org.simbrain.network.layouts.HexagonalGridLayout
getHypotheticalId() - Method in class org.simbrain.util.SimpleId: Returns what the simple identifier would be if a hypothetical construct requiring such an id were constructed and put into the network.
getI_bg() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getI_bg() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getiBg() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getiBg() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getId() - Method in class org.simbrain.network.core.Neuron
getId() - Method in class org.simbrain.network.core.Synapse
getId() - Method in class org.simbrain.network.groups.Group
getId() - Method in class org.simbrain.util.SimpleId: Returns a simple identifier.
getId() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent
getId() - Method in class org.simbrain.workspace.Coupling: Returns an id used for persistence.
getId(WorkspaceComponent) - Method in class org.simbrain.workspace.WorkspaceComponentSerializer: Returns the id associated with a component.
getId() - Method in class org.simbrain.world.odorworld.effectors.Effector
getId() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
getId() - Method in class org.simbrain.world.odorworld.sensors.Sensor
getId_no() - Method in class org.simbrain.network.update_actions.concurrency_tools.Consumer
getIdField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getIeDistConst() - Method in class org.simbrain.network.connections.Radial
getIiDistConst() - Method in class org.simbrain.network.connections.Radial
getImage(String) - Static method in class org.simbrain.resource.ResourceManager: Retrieve an Image based on its file name.
getImage() - Method in class org.simbrain.world.odorworld.entities.Animation: Gets this Animation's current image.
getImage() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Gets this OdorWorldEntity's current image.
getImage(String) - Static method in class org.simbrain.world.odorworld.resources.OdorWorldResourceManager: Retrieve an Image based on its file name.
getImage() - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Return an image for this pixel matrix, scaled to dimensions getWidth() x getHeight() if necessary.
getImage() - Method in interface org.simbrain.world.visionworld.PixelMatrix: Return an image for this pixel matrix, scaled to dimensions getWidth() x getHeight() if necessary.
getImage() - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Return an image for this pixel matrix, scaled to dimensions getWidth() x getHeight() if necessary.
getImageIcon(String) - Static method in class org.simbrain.resource.ResourceManager: Retrieve an ImageIcon based on its file name.
getImageIcon(String) - Static method in class org.simbrain.world.odorworld.resources.OdorWorldResourceManager: Retrieve an ImageIcon based on its file name.
getImageLocations() - Method in class org.simbrain.world.odorworld.entities.Animation
getImageMap() - Method in class org.simbrain.world.odorworld.entities.RotatingEntity
getImportData(ProjectionModel) - Static method in class org.simbrain.plot.projection.ProjectionPlotActions: Import high dimensional data from .csv.
getIncomingField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getIncomingSgs() - Method in class org.simbrain.network.groups.NeuronGroup
getIncomingWeights() - Method in class org.simbrain.network.groups.NeuronGroup: Return flat list of fanins for all neurons in group.
getIncrement() - Method in class org.simbrain.network.core.NeuronUpdateRule
getIncrement() - Method in class org.simbrain.network.core.Synapse
getIncrement(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
getIncrementAmount() - Method in class org.simbrain.util.projection.DataColoringManager
getIndex() - Method in class org.simbrain.plot.barchart.BarChartComponent.BarChartSetter
getIndex() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent.ScatterPlotSetter
getIndex(DataPoint) - Method in class org.simbrain.util.projection.NTree: Returns the index for the given point.
getIndex() - Method in class org.simbrain.world.dataworld.DataWorldComponent.ColumnAttribute
getIndexOfNeuronGroup(NeuronGroup) - Method in class org.simbrain.network.groups.Subnetwork: Returns the index of a neuron group.
getInhibitoryColor() - Static method in class org.simbrain.network.gui.nodes.SynapseNode
getInhibitoryConductance() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getInhibitoryMaxConductance() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getInhibitoryProbability() - Method in class org.simbrain.network.connections.RadialSimple
getInhibitoryPrototype() - Method in class org.simbrain.network.groups.SynapseGroup: Reveals the inhibitory prototype synapse, allowing more detailed synapse values to be queried at the group level.
getInhibitoryRadius() - Method in class org.simbrain.network.connections.RadialSimple
getInhibitoryRandomizer() - Method in class org.simbrain.network.groups.SynapseGroup
getInhibitoryRandomizerPanel() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
getInhibitoryReversal() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getInhibitoryStrengths() - Method in class org.simbrain.network.groups.SynapseGroup
getInhibitorySynapses(Collection<Synapse>) - Static method in class org.simbrain.network.connections.ConnectionUtilities
getInhibitorySynapses() - Method in class org.simbrain.network.groups.SynapseGroup
getInhibitoryThresholdConductance() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Returns the inhibitory conductance that would set this point neuron's voltage at its threshold potential.
getInitAlpha() - Method in class org.simbrain.network.subnetworks.SOMGroup: get Initial Alpha.
getInitialPosition() - Method in class org.simbrain.network.util.CascadingNetworkBuilder
getInitNeighborhoodSize() - Method in class org.simbrain.network.subnetworks.SOMGroup: Get the initial neighborhoodsize.
getInOutMode() - Method in class org.simbrain.network.gui.NetworkPanel
getInput(Neuron) - Method in enum org.simbrain.network.core.NeuronUpdateRule.InputType: Returns the total input to a neuron using either a post-synaptic response value calculated from each synapse and derived from the spike-train of the pre-synaptic neuron or a simple weighted sum of the product of the synapse values and their respective source neurons.
getInputData() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getInputData() - Method in class org.simbrain.network.trainers.TrainingSet
getInputDataMatrix() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Wrap input data in a DataMatrix Object.
getInputDataMatrix() - Method in class org.simbrain.network.trainers.TrainingSet: Wrap input data in a DataMatrix Object.
getInputLayer() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork
getInputLayer() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getInputLayer() - Method in class org.simbrain.network.subnetworks.FeedForward: Returns the input layer.
getInputLayer() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork
getInputLayer() - Method in class org.simbrain.network.subnetworks.SOMNetwork
getInputNeurons() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork
getInputNeurons() - Method in class org.simbrain.network.subnetworks.FeedForward: Convenience method for getting the neurons associated with the input group.
getInputNeurons() - Method in class org.simbrain.network.subnetworks.Hopfield
getInputNeurons() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Returns the list of input neurons.
getInputNeurons() - Method in class org.simbrain.network.subnetworks.SOMNetwork
getInputNeurons() - Method in interface org.simbrain.network.trainers.Trainable: Returns the list of input neurons.
getInputThreshold() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
getInputType() - Method in class org.simbrain.network.core.NeuronUpdateRule
getInputValue() - Method in class org.simbrain.network.core.Neuron
getInRandomizer() - Method in class org.simbrain.network.connections.QuickConnectionManager
getInRandomizer() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
getInReversal() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getInsertColumnAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for inserting a column in to a jtable.
getInsertRowAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for inserting a row in to a jtable.
getInstances() - Static method in class org.simbrain.workspace.gui.SimbrainDesktop
getInt(String) - Static method in class org.simbrain.util.SimbrainPreferences: Retrieve a property whose value is an integer.
getInteractionBox() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
getInteractionBox() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNode
getInteractionBoxes() - Method in interface org.simbrain.network.gui.nodes.GroupNode: Returns a list of child interaction boxes, or null if it does not contain an interaction box.
getInteractionBoxes() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
getInteractionBoxes() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode
getInteractionBoxes() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNode
getInteractionBoxes() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
getIntermedateLayers(Network, List<Neuron>, List<Neuron>) - Static method in class org.simbrain.network.util.SimnetUtils: Given a source and target set of neurons, find all layers of neurons connecting them, as follows.
getInternalFrame() - Method in class org.simbrain.util.scripteditor.ScriptEditor: Returns an internal frame for editing a script.
getInternalFrame(SimbrainDesktop, File) - Static method in class org.simbrain.workspace.gui.SimbrainScriptEditor: Returns an internal frame for editing a script.
getIntValue(JTextField) - Method in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: Returns the int value of the provided text field.
getInverse(double) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: The inverse of the activation function.
getInverse(double) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.InvertibleUpdateRule: The inverse of the activation function.
getItemCount(int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the number of data items for a series.
getIterateNetworkAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the iterate network action.
getIteration() - Method in class org.simbrain.network.trainers.CompetitiveTrainer: Return the current iteration.
getIteration() - Method in class org.simbrain.network.trainers.IterableTrainer: Return the current iteration.
getIteration() - Method in class org.simbrain.network.trainers.SOMTrainer: Return the current iteration.
getIterations() - Method in class org.simbrain.network.core.Network: Returns the current number of iterations.
getIterationsBeforeStopping() - Method in class org.simbrain.network.trainers.IterableTrainer
getJMenuBar() - Method in interface org.simbrain.util.genericframe.GenericFrame
getJumpHeight() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
getJumpHeight() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
getK() - Method in class org.simbrain.network.subnetworks.KWTA: Returns the initial number of neurons.
getKappa() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
getKey() - Method in class org.simbrain.world.visionworld.Sensor: Return a unique identifier for this sensor.
getKeyFromObject(Object) - Method in class org.simbrain.network.NetworkComponent
getKeyFromObject(Object) - Method in class org.simbrain.plot.projection.ProjectionComponent
getKeyFromObject(Object) - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
getKeyFromObject(Object) - Method in class org.simbrain.workspace.WorkspaceComponent: Returns a unique key associated with an object.
getKeyFromObject(Object) - Method in class org.simbrain.world.dataworld.DataWorldComponent
getKeyFromObject(Object) - Method in class org.simbrain.world.odorworld.OdorWorldComponent
getKeyFromObject(Object) - Method in class org.simbrain.world.visionworld.VisionWorldComponent
getKNearestNeighbors(int, DataPoint) - Method in class org.simbrain.util.projection.Dataset: returns k neighbors where the 0th item is the closest and the 1st item is the second closest etc.
getKthVariantDimension(int) - Method in class org.simbrain.util.projection.Dataset: Returns the k'th most variant dimesion.
getLabel() - Method in class org.simbrain.network.core.Neuron
getLabel() - Method in class org.simbrain.network.groups.Group
getLabel() - Method in class org.simbrain.world.odorworld.effectors.Effector
getLabel() - Method in class org.simbrain.world.odorworld.sensors.Sensor
getLabelsOfActiveNeurons(double) - Method in class org.simbrain.network.groups.NeuronGroup: Utility to method (used in couplings) to get a string showing the labels of all "active" neurons (neurons with activation above a threshold).
getLambda() - Method in class org.simbrain.network.connections.Radial
getLambda() - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
getLambda() - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
getLastActivation() - Method in class org.simbrain.network.util.NeuronWithMemory
getLastAddedPoint() - Method in class org.simbrain.util.projection.Dataset: Returns the last point added to this dataset.
getLastClickedPosition() - Method in class org.simbrain.network.gui.NetworkPanel
getLastPosition() - Method in class org.simbrain.world.textworld.TextWorld
getLastReplaceString() - Method in class org.simbrain.util.scripteditor.ScriptEditor
getLastSample() - Method in class org.simbrain.world.visionworld.Sensor: Return the last sample value for this sensor.
getLastSearchString() - Method in class org.simbrain.util.scripteditor.ScriptEditor
getLastSelectedNeuron() - Method in class org.simbrain.network.gui.NetworkPanel
getLastSpikeTime() - Method in class org.simbrain.network.core.SpikingNeuronUpdateRule
getLatch() - Method in class org.simbrain.workspace.updater.LatchCompletionSignal: Returns the latch underlying this signal.
getLayout() - Method in class org.simbrain.network.groups.NeuronGroup
getLayoutActions() - Method in class org.simbrain.network.gui.NetworkActionManager
getLayoutMenu() - Method in class org.simbrain.network.gui.NetworkActionManager: Returns a menu for setting neuron connections.
getLeakConductance() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getLeakConstant() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: ContinuousSigmoidalRule.leak
getLeakMaxConductance() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getLeakReversal() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getLeakReversal() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getLeakyLearningRate() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Return leaky learning rate.
getLearningRate() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Return the learning rate.
getLearningRate() - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
getLearningRate() - Method in class org.simbrain.network.synapse_update_rules.HebbianRule
getLearningRate() - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
getLearningRate() - Method in class org.simbrain.network.synapse_update_rules.OjaRule
getLearningRate() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
getLearningRate() - Method in class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule
getLearningRate() - Method in class org.simbrain.network.trainers.BackpropTrainer
getLearningRate() - Method in class org.simbrain.network.trainers.BPTTTrainer
getLearningRate() - Method in class org.simbrain.network.trainers.LMSIterative
getLearningRule() - Method in class org.simbrain.network.core.Synapse
getLearningRuleDescription(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
getLine() - Method in class org.simbrain.network.gui.nodes.SynapseNode
getLineColor() - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
getLineColor() - Static method in class org.simbrain.network.gui.nodes.SynapseNode
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.simbrain.util.ComboBoxRenderer: Puts images next to images in a combo box.
getListeners() - Method in class org.simbrain.network.trainers.Trainer
getLocation() - Method in class org.simbrain.util.environment.SmellSource
getLocation(double[]) - Method in class org.simbrain.util.environment.SmellSource: Return location of this smell source.
getLocation() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Returns the location of the entity as a double array.
getLocation() - Method in class org.simbrain.world.odorworld.sensors.SmellSensor
getLock() - Method in class org.simbrain.workspace.updater.ComponentUpdatePart: Returns the lock for this object.
getLocks() - Method in class org.simbrain.workspace.WorkspaceComponent: Returns the locks for the update parts.
getLogger(Class) - Static method in class org.simbrain.util.Logger
getLogger(String) - Static method in class org.simbrain.util.Logger
getLogger() - Method in class org.simbrain.workspace.WorkspaceComponent
getLogicalColumnCount() - Method in class org.simbrain.util.table.SimbrainDataTable: Returns the number of columns in the underlying data, which is one less than the number of columns in the table data.
getLogicalValueAt(int, int) - Method in class org.simbrain.util.table.SimbrainDataTable: Get the value of a specific cell in the data structure backing this table data structure.
getLogSaturation() - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
getLongDescription() - Method in interface org.simbrain.network.core.NetworkUpdateAction: Provide a longer description for tooltips, etc.
getLongDescription() - Method in class org.simbrain.network.groups.Subnetwork: Get long description for info box, formmated in html.
getLongDescription() - Method in class org.simbrain.network.update_actions.BufferedUpdate
getLongDescription() - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
getLongDescription() - Method in class org.simbrain.network.update_actions.CustomUpdate
getLongDescription() - Method in class org.simbrain.network.update_actions.PriorityUpdate
getLongDescription() - Method in class org.simbrain.network.update_actions.UpdateGroup
getLongDescription() - Method in interface org.simbrain.workspace.updater.UpdateAction: Provide a longer description for tooltips, etc.
getLongDescription() - Method in class org.simbrain.workspace.updater.UpdateActionCustom
getLongDescription() - Method in class org.simbrain.workspace.updater.UpdateAllBuffered
getLongDescription() - Method in class org.simbrain.workspace.updater.UpdateComponent
getLongDescription() - Method in class org.simbrain.workspace.updater.UpdateCoupling
getLoseValue() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Return the loser value.
getLoseValue() - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
getLowerBound() - Method in class org.simbrain.network.core.Neuron: Return the lower bound for the the underlying rule, if it is bounded.
getLowerBound() - Method in class org.simbrain.network.core.Synapse
getLowerBound(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Returns the lower bound.
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Returns the lower bound.
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getLowerBound() - Method in interface org.simbrain.network.neuron_update_rules.interfaces.BoundedUpdateRule: Returns the lower bound.
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
getLowerBound() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getLowerBound() - Method in class org.simbrain.plot.barchart.BarChartModel
getLowerBound() - Method in class org.simbrain.util.randomizer.Randomizer
getLowerBound() - Method in class org.simbrain.util.table.NumericTable: Lower bound for (e.g.) randomization.
getLowerDomainBoundary() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
getLowerRangeBoundary() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
getLowerThreshold() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getLowerValue() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
getLowerValue() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getLtpMod() - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
getM() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getM() - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
getMainPanel() - Method in class org.simbrain.network.gui.dialogs.connect.CondensedConnectionPanel: Returns the main panel where all the components are actually laid out.
getMainPanel() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionPanel
getMainPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel
getMainToolBar() - Method in class org.simbrain.network.gui.NetworkPanel
getMarqueeColor() - Static method in class org.simbrain.network.gui.nodes.SelectionMarquee
getMatchingScalar(String) - Method in class org.simbrain.world.textworld.ReaderWorld: Returns 1 if the current item is this character, or 0 otherwise.
getMatchingVector(String) - Method in class org.simbrain.world.textworld.ReaderWorld: Return the vector associated with the currently parsed token, or a default zero vector.
getMatrixRowCompression(double[][]) - Static method in class org.simbrain.util.math.SimbrainMath: Returns a row compressed representation of a weight matrix represented as a 2D array of doubles.
getMaxDiameter() - Static method in class org.simbrain.network.gui.nodes.SynapseNode
getMaxDim() - Method in class org.simbrain.network.groups.NeuronGroup
getMaximum(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Finds the largest value in a vector array.
getMaximum(Number[]) - Static method in class org.simbrain.util.math.SimbrainMath: Returns the maximum value of an array of numbers.
getMaximumDistance() - Method in class org.simbrain.util.projection.Dataset: Get the maximimum interpoint distance between points in the dataset.
getMaximumResponse() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay
getMaximumSize() - Method in interface org.simbrain.util.genericframe.GenericFrame
getMaximumSize(JComponent) - Method in class org.simbrain.util.MultiLineToolTipUI
getMaximumValue() - Method in class org.simbrain.world.visionworld.filter.RandomFilter: Return the maximum value for this random filter.
getMaxPossibleConnections() - Method in class org.simbrain.network.connections.Sparse
getMaxState() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
getMaxVisibleColumns() - Method in class org.simbrain.util.table.SimbrainJTableScrollPanel
getMaxVisibleRows() - Method in class org.simbrain.util.table.SimbrainJTableScrollPanel
getMaxX() - Method in class org.simbrain.network.groups.NeuronGroup: Returns the maximum X position of this group based on the neurons that comprise it.
getMaxY() - Method in class org.simbrain.network.groups.NeuronGroup: Returns the maximum Y position of this group based on the neurons that comprise it.
getMean() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.StatisticsBlock
getMean(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
getMean(int) - Method in class org.simbrain.util.projection.Dataset: Returns the mean of the dataset on a given dimension.
getMeanSquaredError(double[], double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Returns the mean squared error between a source and target vector.
getMedian() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.StatisticsBlock
getMedian(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
getMembranePotential() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getMemCapacitance() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getMenu() - Method in class org.simbrain.world.odorworld.OdorWorldDesktopComponent
getMenuCSV(boolean, boolean) - Method in class org.simbrain.util.table.SimbrainJTable: Return a menu with items for opening from and saving to .csv files.
getMenuEdit() - Method in class org.simbrain.util.table.SimbrainJTable: Return a menu with items for changing the table structure.
getMenuFill() - Method in class org.simbrain.util.table.SimbrainJTable: Return a menu with items for filling table values.
getMenuNormalize() - Method in class org.simbrain.util.table.SimbrainJTable: Return a menu with items for normalizing the data in a table.
getMenuRandomize() - Method in class org.simbrain.util.table.SimbrainJTable: Return a menu with items for randomizing table values.
getMethodBaseName() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getMethodName() - Method in interface org.simbrain.workspace.Attribute: Returns the name of the method associated with this attribute.
getMethodName() - Method in class org.simbrain.workspace.AttributeType
getMethodName() - Method in class org.simbrain.workspace.PotentialAttribute
getMiddleValue() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getMinDiameter() - Static method in class org.simbrain.network.gui.nodes.SynapseNode
getMinimum(Number[]) - Static method in class org.simbrain.util.math.SimbrainMath: Returns the minimum value of an array of numbers.
getMinimumDistance() - Method in class org.simbrain.util.projection.Dataset: Get the minimum interpoint distance between points in the dataset.
getMinimumNumRows(Trainable) - Method in class org.simbrain.network.trainers.IterableTrainer: Returns the number of rows in whichever dataset has fewer rows.
getMinimumSize(JComponent) - Method in class org.simbrain.util.MultiLineToolTipUI
getMinimumValue() - Method in class org.simbrain.world.visionworld.filter.RandomFilter: Return the minimum value for this random filter.
getMinX() - Method in class org.simbrain.network.groups.NeuronGroup: Returns the minimum X position of this group based on the neurons that comprise it.
getMinY() - Method in class org.simbrain.network.groups.NeuronGroup: Returns the minimum Y position of this group based on the neurons that comprise it.
getModel() - Method in class org.simbrain.network.gui.NeuronGroupSelectionPanel
getModel() - Method in class org.simbrain.plot.barchart.BarChartComponent: Returns model.
getModel() - Method in class org.simbrain.plot.histogram.HistogramComponent: Returns model.
getModel() - Method in class org.simbrain.plot.histogram.HistogramGui: Return a reference to the underlying data.
getModel() - Method in class org.simbrain.plot.histogram.HistogramPanel: Return reference to underlying data.
getModel() - Method in class org.simbrain.plot.piechart.PieChartComponent
getModel() - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent
getModel() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
getModel() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent
getModel() - Method in class org.simbrain.world.game.GameComponent: Returns the game model.
getModel() - Method in class org.simbrain.world.visionworld.VisionWorld: Return the model for this vision world.
getModelGroupNodeFilter() - Static method in class org.simbrain.network.gui.filters.Filters: Return the model group node filter.
getModifiableNeuronList() - Method in class org.simbrain.network.groups.Subnetwork: Returns a "flat" list containing every neuron in every neuron group in this subnetwork.
getMomentum() - Method in class org.simbrain.network.trainers.BackpropTrainer
getMomentum() - Method in class org.simbrain.network.trainers.BPTTTrainer
getMostActiveNeuron() - Method in class org.simbrain.network.groups.NeuronGroup: Returns the label of the most active neuron.
getMouse() - Static method in class org.simbrain.world.odorworld.entities.RotatingEntityManager: Tree map for mouse.
getMouseoverPaint() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return the mouseover paint for this sensor node.
getMyNextItemRow() - Method in class org.simbrain.util.LabelledItemPanel: Returns the current row.
getN() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getName() - Static method in class org.simbrain.network.connections.AllToAll: Returns a short name for this connection type, used in combo boxes.
getName() - Static method in class org.simbrain.network.connections.OneToOne: Returns a short name for this connection type, used in combo boxes.
getName() - Static method in class org.simbrain.network.connections.Sparse: Returns a short name for this connection type, used in combo boxes.
getName() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getName() - Method in enum org.simbrain.network.subnetworks.Hopfield.HopfieldUpdate
getName() - Static method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
getName() - Static method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
getName() - Method in class org.simbrain.util.Logger
getName() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent
getName() - Method in class org.simbrain.workspace.gui.GuiComponent: Return name of underlying component.
getName() - Method in class org.simbrain.workspace.WorkspaceComponent: Returns the name of this component.
getName() - Method in class org.simbrain.world.game.GameModel: Returns the name of the game.
getName() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Get the entity's name.
getNameField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getNameFromPath(String) - Static method in class org.simbrain.util.Utils: Extract file name from a path description.
getNames() - Static method in enum org.simbrain.util.math.ProbDistribution
getNeighborhoodDecayAmount() - Method in class org.simbrain.network.subnetworks.SOMGroup: Get neighborhoodDecayAmount.
getNeighborhoodSize() - Method in class org.simbrain.network.subnetworks.SOMGroup: Get the current neighborhood size.
getNetTimeConstant() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getNetwork() - Method in class org.simbrain.network.core.Neuron: Returns the root network this neuron is embedded in.
getNetwork() - Method in class org.simbrain.network.core.Synapse: Convenience method for getting a reference to the parent root network.
getNetwork() - Method in class org.simbrain.network.gui.NetworkPanel
getNetwork() - Method in class org.simbrain.network.NetworkComponent: Returns the root network.
getNetwork() - Method in class org.simbrain.network.subnetworks.BackpropNetwork
getNetwork() - Method in class org.simbrain.network.subnetworks.BPTTNetwork
getNetwork() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork
getNetwork() - Method in class org.simbrain.network.subnetworks.Hopfield
getNetwork() - Method in class org.simbrain.network.subnetworks.LMSNetwork
getNetwork() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Returns a reference to the subnetwork or synapse group being trained.
getNetwork() - Method in class org.simbrain.network.subnetworks.SOMNetwork
getNetwork() - Method in interface org.simbrain.network.trainers.Trainable: Returns a reference to the subnetwork or synapse group being trained.
getNetworkControlActions() - Method in class org.simbrain.network.gui.NetworkActionManager: Return a list of network control actions.
getNetworkDialog(NetworkPanel) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: This version of network dialog allows user to set User Preferences.
getNetworkDialog(NetworkPanel) - Method in class org.simbrain.network.gui.NetworkPanel: Returns a NetworkDialog.
getNetworkEditingActions() - Method in class org.simbrain.network.gui.NetworkActionManager: Return a list of network editing actions.
getNetworkModeActions() - Method in class org.simbrain.network.gui.NetworkActionManager: Return a list of network mode actions.
getNetworkPanel() - Method in class org.simbrain.network.desktop.NetworkDesktopComponent: Return the network panel for this network frame.
getNetworkPanel() - Method in class org.simbrain.network.gui.NetworkSelectionEvent: Return the source of this event as a NetworkPanel.
getNetworkPanel() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
getNetworkPanel() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return the network panel for this screen element.
getNetworkPanel() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode
getNetworkPanel() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNode
getNetworkScriptMenu(NetworkPanel) - Static method in class org.simbrain.network.desktop.NetworkScriptMenu: Create script menu.
getNeuron(int) - Method in class org.simbrain.network.core.Network
getNeuron(String) - Method in class org.simbrain.network.core.Network: Find a neuron with a given string id.
getNeuron() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Return the neuron for this neuron node.
getNeuronByLabel(String) - Method in class org.simbrain.network.core.Network: Returns the first neuron in the array returned by getNeuronsByLabel.
getNeuronConsumer(NetworkComponent, Neuron, String) - Static method in class org.simbrain.network.NetworkComponent: Helper method for making neuron consumers, since it happens in a few different places and is important to be consistent about.
getNeuronContextMenu(Neuron) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getNeuronContextMenu(Neuron) - Method in class org.simbrain.network.gui.NetworkPanel: Creates the context menu for neurons.
getNeuronCount() - Method in class org.simbrain.network.core.Network
getNeuronDialog(Collection<NeuronNode>) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getNeuronDialog(Collection<NeuronNode>) - Method in class org.simbrain.network.gui.NetworkPanel
getNeuronGroup(int) - Method in class org.simbrain.network.groups.Subnetwork: Get a neuron group by index.
getNeuronGroup() - Method in class org.simbrain.network.groups.Subnetwork: Get the first neuron group in the list.
getNeuronGroup() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Get a reference to the underlying neuron group.
getNeuronGroupByLabel(String) - Method in class org.simbrain.network.groups.Subnetwork: Find neuron group with a given label, or null if none found.
getNeuronGroupConsumer(NetworkComponent, NeuronGroup, String) - Static method in class org.simbrain.network.NetworkComponent: Helper method for making neuron group vector consumers, since it happens in a few different places and is important to be consistent about.
getNeuronGroupConsumerMenu(NeuronGroup) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getNeuronGroupConsumerMenu(NeuronGroup) - Method in class org.simbrain.network.gui.NetworkPanel: Creates the consumer menu for neuron groups.
getNeuronGroupCount() - Method in class org.simbrain.network.groups.Subnetwork: Get number of neuron groups or "layers" in the list.
getNeuronGroupDialog(NeuronGroupNode) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Creates a modeless version of the neuron group dialog relative to the SimbrainDesktop.
getNeuronGroupDialog(NeuronGroupNode) - Method in class org.simbrain.network.gui.NetworkPanel: Overridden by NetworkPanelDesktop to ensure modeless-ness relative to SimbrainDesktop.
getNeuronGroupList() - Method in class org.simbrain.network.groups.Subnetwork: Returns an unmodifiable version of the neuron group list.
getNeuronGroupNodeFilter() - Static method in class org.simbrain.network.gui.filters.Filters
getNeuronGroupProducer(NetworkComponent, NeuronGroup, String) - Static method in class org.simbrain.network.NetworkComponent: Helper method for making neuron group producers, since it happens in a few different places and is important to be consistent about.
getNeuronGroupProducerMenu(NeuronGroup) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getNeuronGroupProducerMenu(NeuronGroup) - Method in class org.simbrain.network.gui.NetworkPanel: Creates the producer menu for neuron groups.
getNeuronGroups() - Method in class org.simbrain.network.core.Network: Convenience method to return a list of neuron groups in the network.
getNeuronGroups() - Method in class org.simbrain.network.gui.NeuronGroupSelectionPanel
getNeuronGroupsAsList() - Method in class org.simbrain.network.groups.Subnetwork: Return neuron groups as a list.
getNeuronGroupsAsList() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Return neuron groups as a list.
getNeuronIdGenerator() - Method in class org.simbrain.network.core.Network: Return the generator for neuron ids.
getNeuroninfoPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel
getNeuronLayout() - Method in class org.simbrain.network.gui.dialogs.layout.AbstractLayoutPanel: Returns the layout object being edited by this panel.
getNeuronList() - Method in class org.simbrain.network.core.Network: Return the list of synapses.
getNeuronList() - Method in class org.simbrain.network.groups.NeuronGroup
getNeuronNodeFilter() - Static method in class org.simbrain.network.gui.filters.Filters: Return the neuron node filter.
getNeuronNodes() - Method in class org.simbrain.network.gui.NetworkPanel: Return a collection of all neuron nodes.
getNeuronOrSynapseNodeFilter() - Static method in class org.simbrain.network.gui.filters.Filters: Return the neuron or synapse node filter.
getNeuronPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: Directly access the neuron panel to utilize its methods without using this class as an intermediary.
getNeuronProducer(NetworkComponent, Neuron, String) - Static method in class org.simbrain.network.NetworkComponent: Helper method for making neuron producers, since it happens in a few different places and is important to be consistent about.
getNeuronsByLabel(String) - Method in class org.simbrain.network.core.Network: Search for a neuron by label.
getNeuronSet() - Method in class org.simbrain.network.subnetworks.Hopfield
getNeuronsInRadius(Neuron, int) - Method in class org.simbrain.network.groups.NeuronGroup: Returns all the neurons in this group within a certain radius of the given neuron.
getNeuronType() - Method in class org.simbrain.network.groups.NeuronGroup
getNeuronType() - Method in class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel.LayerCreationPanel: Return the current selected neuron type.
getNeuronType() - Method in class org.simbrain.network.util.CascadingNetworkBuilder
getNewBarChartAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewConsoleAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewDataWorldAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewDocViewerAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewGroupActions() - Method in class org.simbrain.network.gui.NetworkActionManager
getNewGroupMenu() - Method in class org.simbrain.network.gui.NetworkActionManager: Return a JMenu for creating new neuron groups.
getNewNetworkAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewNetworkActions() - Method in class org.simbrain.network.gui.NetworkActionManager
getNewNetworkMenu() - Method in class org.simbrain.network.gui.NetworkActionManager: Return a JMenu for creating new networks.
getNewNeuronAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the new neuron action.
getNewOdorWorldAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewPieChartPlotAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewScatterPlotAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewTimeSeriesPlotAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewVisionWorldAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNewWorldActions() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getNoiseGen() - Method in class org.simbrain.network.trainers.LMSOffline
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule: Return the noise generator.
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getNoiseGenerator() - Method in interface org.simbrain.network.neuron_update_rules.interfaces.NoisyUpdateRule: Return the noise generator.
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getNoiseGenerator() - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
getNoiseGenerator() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getNoiseLevel() - Method in class org.simbrain.util.environment.SmellSource: Return the noise level.
getNoiseVar() - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
getNoisyVector(double[], double) - Static method in class org.simbrain.util.math.SimbrainMath: Add noise to a vector and return the result.
getNormalizationFactor() - Method in class org.simbrain.network.synapse_update_rules.OjaRule
getNormalizeAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for normalizing selected parts of a table.
getNormalizedSeparatedInput(Neuron) - Method in enum org.simbrain.network.core.NeuronUpdateRule.InputType
getNormalizeInputs() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Return the normalize inputs value.
getNudgeAmount() - Static method in class org.simbrain.network.gui.NetworkPanel
getNULL() - Static method in class org.simbrain.util.widgets.TristateDropDown
getNumberOfActiveInputs(int) - Method in class org.simbrain.network.core.Neuron: Returns the number of neurons attaching to this one which have activity above a specified threshold.
getNumberOfPastes() - Method in class org.simbrain.network.gui.NetworkPanel
getNumBrachesPerNeuron() - Method in class org.simbrain.network.util.CascadingNetworkBuilder
getNumColumns() - Method in class org.simbrain.network.layouts.GridLayout
getNumColumns() - Method in class org.simbrain.network.layouts.HexagonalGridLayout
getNumericIndices() - Method in class org.simbrain.network.groups.SynapseGroup: A more compressed version of a weight matrix for cases where a weight matrix is needed, but may cause memory issues if fully instantiated.
getNumericIndices(ConnectionUtilities.SynapseParameterGetter<Number>) - Method in class org.simbrain.network.groups.SynapseGroup: A more compressed version of a weight matrix for cases where a weight matrix is needed, but may cause memory issues if fully instantiated.
getNumericValuesAsByteArray() - Method in class org.simbrain.network.core.Synapse
getNumLayers() - Method in class org.simbrain.network.util.CascadingNetworkBuilder
getNumNeurons() - Method in class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel.LayerCreationPanel: Return the number of neurons currently in this text field.
getNumNeurons() - Method in class org.simbrain.network.subnetworks.SOMGroup: Get the number of neurons.
getNumPoints() - Method in class org.simbrain.util.projection.Dataset
getNumPoints() - Method in class org.simbrain.util.projection.Projector: Returns the size of the dataset.
getNumSubSamples() - Static method in class org.simbrain.network.groups.NeuronGroup
getNumTargs() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
getNumThreads() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater
getNumUnits() - Method in class org.simbrain.network.subnetworks.Hopfield
getNumUnits() - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
getObject() - Method in class org.simbrain.network.listeners.NetworkEvent
getObjectFromKey(String) - Method in class org.simbrain.network.NetworkComponent
getObjectFromKey(String) - Method in class org.simbrain.plot.barchart.BarChartComponent
getObjectFromKey(String) - Method in class org.simbrain.plot.histogram.HistogramComponent
getObjectFromKey(String) - Method in class org.simbrain.plot.piechart.PieChartComponent
getObjectFromKey(String) - Method in class org.simbrain.plot.projection.ProjectionComponent
getObjectFromKey(String) - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent
getObjectFromKey(String) - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
getObjectFromKey(String) - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent
getObjectFromKey(String) - Method in class org.simbrain.workspace.WorkspaceComponent: Finds objects based on a key.
getObjectFromKey(String) - Method in class org.simbrain.world.dataworld.DataWorldComponent
getObjectFromKey(String) - Method in class org.simbrain.world.odorworld.OdorWorldComponent
getObjectFromKey(String) - Method in class org.simbrain.world.textworld.DisplayComponent
getObjectFromKey(String) - Method in class org.simbrain.world.textworld.ReaderComponent
getObjectFromKey(String) - Method in class org.simbrain.world.visionworld.VisionWorldComponent
getObjectList() - Method in class org.simbrain.world.odorworld.OdorWorld: Returns the list of entities.
getObjectNodeMap() - Method in class org.simbrain.network.gui.NetworkPanel
getObjectPropsItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getObjects() - Method in interface org.simbrain.util.propertyeditor.ComboBoxWrapper: Return the array of objects that the combo box will select among.
getOkButton() - Method in class org.simbrain.util.StandardDialog: Give other classes access to the Ok button.
getOldObject() - Method in class org.simbrain.network.listeners.NetworkEvent
getOldPixelMatrix() - Method in class org.simbrain.world.visionworld.VisionWorldModelEvent: Return the old pixel matrix for this vision world model event, if any.
getOldSelection() - Method in class org.simbrain.network.gui.NetworkSelectionEvent: Return the old selection.
getOldSelection() - Method in class org.simbrain.world.visionworld.SensorSelectionEvent: Return the old set of selected sensors.
getOldSensorMatrix() - Method in class org.simbrain.world.visionworld.VisionWorldModelEvent: Return the old sensor matrix for this vision world model event, if any.
getOneToOne() - Method in class org.simbrain.network.connections.QuickConnectionManager
getOpenCouplingListAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenCouplingManagerAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenCSVAction(SimbrainJTable, NumericMatrix) - Static method in class org.simbrain.network.gui.trainer.TrainerGuiActions: Action for opening data comma separated value file.
getOpenCSVAction(NumericTable, boolean, boolean) - Static method in class org.simbrain.util.table.TableActionManager: Action for opening from comma separate value file.
getOpenCSVAction(TextTable, boolean, boolean) - Static method in class org.simbrain.util.table.TableActionManager: Action for opening text table from comma separated value file.
getOpenDataWorldAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenNetworkAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenOdorWorldAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenPlotAction() - Method in class org.simbrain.plot.actions.PlotActionManager
getOpenSavePlotActions() - Method in class org.simbrain.plot.actions.PlotActionManager
getOpenSaveWorkspaceActions() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenWorkspaceAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenWorkspaceComponentListAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpenWorldActions() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getOpposingDefaultPosition(NeuronGroup) - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow: Based on the NeuronGroup at either end of this arrow, gives a "dummy" default opposing position.
getOpposingDefaultPosition(NeuronGroup) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional: Based on the NeuronGroup at either end of this arrow, gives a "dummy" default opposing position.
getOpposingDefaultPosition(NeuronGroup) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple: Returns a default position...
getOrientation() - Method in class org.simbrain.network.layouts.LineLayout
getOrientationTypes() - Static method in class org.simbrain.network.connections.OneToOne: Used for populating combo box with orientation types.
getOscInHost() - Method in class org.simbrain.world.oscworld.OscWorldComponent: Return the OSC in host name.
getOscInPort() - Method in class org.simbrain.world.oscworld.OscWorldComponent: Return the OSC in port number.
getOscOutHost() - Method in class org.simbrain.world.oscworld.OscWorldComponent: Return the OSC out host name.
getOscOutPort() - Method in class org.simbrain.world.oscworld.OscWorldComponent: Return the OSC out port number.
getOSMatches(String) - Static method in class org.simbrain.util.Utils: Decides if the operating system matches.
getOutgoingField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getOutgoingSg() - Method in class org.simbrain.network.groups.NeuronGroup
getOutgoingWeights() - Method in class org.simbrain.network.groups.NeuronGroup: Return flat list of fanouts for all neurons in group.
getOutlinedObjects() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode
getOutlinePadding() - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
getOutlinePaint() - Method in class org.simbrain.world.visionworld.node.AbstractPixelMatrixNode: Return the outline paint for this pixel matrix node.
getOutlinePaint() - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Return the outline paint for this sensor matrix node.
getOutlinePaint() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return the outline paint for this sensor node.
getOutlineStroke() - Method in class org.simbrain.world.visionworld.node.AbstractPixelMatrixNode: Return the outline stroke for this pixel matrix node.
getOutlineStroke() - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Return the outline stroke for this sensor matrix node.
getOutlineStroke() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return the outline stroke for this sensor node.
getOutputAmount() - Method in class org.simbrain.world.odorworld.sensors.Hearing
getOutputFunction() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getOutputLayer() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getOutputLayer() - Method in class org.simbrain.network.subnetworks.FeedForward: Returns the output layer.
getOutputLayer() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork
getOutputNeurons() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork
getOutputNeurons() - Method in class org.simbrain.network.subnetworks.FeedForward: Convenience method for getting the neurons associated with the output group.
getOutputNeurons() - Method in class org.simbrain.network.subnetworks.Hopfield
getOutputNeurons() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Returns the list of output neurons.
getOutputNeurons() - Method in class org.simbrain.network.subnetworks.SOMNetwork
getOutputNeurons() - Method in interface org.simbrain.network.trainers.Trainable: Returns the list of output neurons.
getOutputThreshold() - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
getOutputThresholdMomentum() - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
getPanel() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.group.NeuronGroupPanel
getPanel() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel
getPanel() - Method in class org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.network.WTAPropertiesPanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended
getPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple
getPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel
getPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
getPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple
getPanel() - Method in class org.simbrain.network.gui.trainer.DataPanel
getPanel() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineTrainingPanel
getPanel() - Method in class org.simbrain.network.gui.trainer.TrainingSetPanel
getPanel() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
getPanel() - Method in class org.simbrain.util.widgets.ApplyPanel
getPanel() - Method in interface org.simbrain.util.widgets.EditablePanel: This interface is only meant to be implemented by panels which edit model values.
getPanel() - Method in class org.simbrain.world.game.tictactoe.TicTacToeGui: Returns a game panel.
getPanel() - Method in class org.simbrain.world.textworld.dictionary.TokenDictionaryPanel
getPanel() - Method in class org.simbrain.world.textworld.dictionary.TokenToVectorPanel
getPanel() - Method in class org.simbrain.world.textworld.dictionary.VectorToTokenPanel
getParam1() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer
getParam1() - Method in class org.simbrain.util.randomizer.Randomizer: See the javadoc at Randomizer.param1.
getParam1FieldVal() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
getParam1Name() - Method in enum org.simbrain.util.math.ProbDistribution
getParam2() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer
getParam2() - Method in class org.simbrain.util.randomizer.Randomizer: See the javadoc at Randomizer.param2.
getParam2FieldVal() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
getParam2Name() - Method in enum org.simbrain.util.math.ProbDistribution
getParameter(T) - Method in interface org.simbrain.network.gui.ParameterGetter: A generic method set up with the intention of allowing programmers to create a simple function which retrieves an arbitrary parameter of an arbitrary type from an object (also of an arbitrary type).
getParameterFromSynapse(Synapse) - Method in interface org.simbrain.network.connections.ConnectionUtilities.SynapseParameterGetter: A generic getter intended to be used to return the value of some parameter of the given synapse.
getParent() - Method in class org.simbrain.workspace.PotentialAttribute
getParent() - Method in class org.simbrain.workspace.updater.ComponentUpdatePart: Returns the parent of this component.
getParent() - Method in class org.simbrain.world.odorworld.effectors.Effector
getParent() - Method in class org.simbrain.world.odorworld.LifeCycle
getParent() - Method in class org.simbrain.world.odorworld.sensors.Sensor
getParentComponent() - Method in interface org.simbrain.workspace.Attribute: Returns a reference to the parent component.
getParentComponent() - Method in class org.simbrain.workspace.AttributeType
getParentComponent() - Method in class org.simbrain.world.game.GameAttributes
getParentComponentRef() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getParentFrame() - Method in class org.simbrain.workspace.gui.GuiComponent: Returns the parent from of this view.
getParentGroup() - Method in class org.simbrain.network.core.Neuron: TODO: Possibly make this be a NeuronGroup.
getParentGroup() - Method in class org.simbrain.network.core.Synapse
getParentGroup() - Method in class org.simbrain.network.groups.Group
getParentGroupField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getParentNetwork() - Method in class org.simbrain.network.core.Synapse
getParentNetwork() - Method in class org.simbrain.network.groups.Group
getParentNodeFilter() - Static method in class org.simbrain.network.gui.filters.Filters: Return the parent node filter.
getParentNodes() - Method in class org.simbrain.network.gui.NetworkPanel: Return a collection of all parent nodes.
getParentRef() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedAttribute
getParentWorld() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
getParseStyle() - Method in class org.simbrain.world.textworld.ReaderWorld: Returns the current parse style inside a comboboxwrapper.
getPasteAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the paste action.
getPasteItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getPasteX() - Method in class org.simbrain.network.gui.NetworkPanel
getPasteY() - Method in class org.simbrain.network.gui.NetworkPanel
getPdf() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
getPdf() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer
getPdf() - Method in class org.simbrain.util.randomizer.Randomizer
getPeak() - Method in class org.simbrain.util.environment.SmellSource
getPenBackground() - Method in class org.simbrain.world.visionworld.node.PixelMatrixImageNode: Return the pen background color for this pixel matrix image node.
getPenForeground() - Method in class org.simbrain.world.visionworld.node.PixelMatrixImageNode: Return the pen foreground color for this pixel matrix image node.
getPercentExcitatory() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel: Returns the desired percent excitatory.
getPercentValidation() - Method in class org.simbrain.network.trainers.TrainingSet
getPerKChannels() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getPerNaChannels() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getPhase() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getPhi() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getPhrase() - Method in class org.simbrain.world.odorworld.effectors.Speech
getPhrase() - Method in class org.simbrain.world.odorworld.sensors.Hearing
getPixel(int, int) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Return the color of the pixel at the specified (x, y) coordinates.
getPixel(int, int) - Method in interface org.simbrain.world.visionworld.PixelMatrix: Return the color of the pixel at the specified (x, y) coordinates.
getPixel(int, int) - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Return the color of the pixel at the specified (x, y) coordinates.
getPixelMatrix() - Method in class org.simbrain.world.visionworld.ImmutableVisionWorldModel: Return the pixel matrix for this vision world model.
getPixelMatrix() - Method in class org.simbrain.world.visionworld.MutableVisionWorldModel: Return the pixel matrix for this vision world model.
getPixelMatrix() - Method in class org.simbrain.world.visionworld.node.AbstractPixelMatrixNode: Return the pixel matrix for this pixel matrix node.
getPixelMatrix() - Method in interface org.simbrain.world.visionworld.VisionWorldModel: Return the pixel matrix for this vision world model.
getPixelMatrix() - Method in class org.simbrain.world.visionworld.VisionWorldModelEvent: Return the pixel matrix for this vision world model event, if any.
getPlasticityType() - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
getPlotActions() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getPoint(int) - Method in class org.simbrain.util.projection.Dataset: Get a specified point in the dataset.
getPolarity() - Method in class org.simbrain.network.core.Neuron: Polarity of this neuron (excitatory, inhibitory, or none = null).
getPolarity() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer
getPopField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getPopLabel() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getPosition() - Method in class org.simbrain.network.core.Neuron: Returns position as a 2-d point.
getPosition() - Method in class org.simbrain.network.groups.NeuronGroup: Return current position (upper left corner of neuron in the farthest north-west position.
getPosition() - Method in class org.simbrain.world.textworld.TextWorld
getPotentialConsumers() - Method in class org.simbrain.network.NetworkComponent
getPotentialConsumers() - Method in class org.simbrain.plot.barchart.BarChartComponent
getPotentialConsumers() - Method in class org.simbrain.plot.histogram.HistogramComponent
getPotentialConsumers() - Method in class org.simbrain.plot.piechart.PieChartComponent
getPotentialConsumers() - Method in class org.simbrain.plot.projection.ProjectionComponent
getPotentialConsumers() - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent
getPotentialConsumers() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
getPotentialConsumers() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent
getPotentialConsumers() - Method in class org.simbrain.workspace.WorkspaceComponent: Return the potential consumers associated with this component.
getPotentialConsumers() - Method in class org.simbrain.world.dataworld.DataWorldComponent
getPotentialConsumers() - Method in class org.simbrain.world.odorworld.OdorWorldComponent
getPotentialConsumers() - Method in class org.simbrain.world.textworld.DisplayComponent
getPotentialProducers() - Method in class org.simbrain.network.NetworkComponent
getPotentialProducers() - Method in class org.simbrain.workspace.WorkspaceComponent: Return the potential producers associated with this component.
getPotentialProducers() - Method in class org.simbrain.world.dataworld.DataWorldComponent
getPotentialProducers() - Method in class org.simbrain.world.odorworld.OdorWorldComponent
getPotentialProducers() - Method in class org.simbrain.world.textworld.ReaderComponent
getPotentialProducers() - Method in class org.simbrain.world.visionworld.VisionWorldComponent
getPotentialTimeConstant() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getPreferredSize() - Method in interface org.simbrain.util.genericframe.GenericFrame
getPreferredSize(JComponent) - Method in class org.simbrain.util.MultiLineToolTipUI
getPrioritiesVisible() - Method in class org.simbrain.network.gui.NetworkPanel
getPriority() - Method in class org.simbrain.workspace.CouplingManager: Get the priority.
getPrioritySortedNeuronList() - Method in class org.simbrain.network.core.Network: TODO: Resolve priority update issue.
getProducer() - Method in class org.simbrain.workspace.Coupling
getProducerTypes() - Method in class org.simbrain.workspace.WorkspaceComponent
getProducingAttributes() - Method in class org.simbrain.world.threedee.sensors.Sight
getProducingColumnType() - Method in class org.simbrain.world.dataworld.DataWorldComponent
getProjectionMethod() - Method in class org.simbrain.util.projection.Projector
getProjectionMethods() - Method in class org.simbrain.util.projection.Projector
getProjectionModel() - Method in class org.simbrain.plot.projection.ProjectionComponent
getProjector() - Method in class org.simbrain.plot.projection.ProjectionComponent: Get reference to underlying projector object.
getProjector() - Method in class org.simbrain.plot.projection.ProjectionModel: Returns the projector.
getPropertiesDialogAction(Trainer) - Static method in class org.simbrain.network.gui.trainer.TrainerGuiActions: Show properties dialog for the indicated trainer.
getPropertiesDialogAction(RasterPlotPanel) - Static method in class org.simbrain.plot.rasterchart.RasterPlotActions: Shows a properties dialog for the trainer.
getPropertiesDialogAction(TimeSeriesPlotPanel) - Static method in class org.simbrain.plot.timeseries.TimeSeriesPlotActions: Shows a properties dialog for the trainer.
getPropertiesDialogAction(Object) - Static method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Returns an action for showing a property dialog for the provided objects.
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.InteractionBox
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode.NeuronGroupInteractionBox
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.NeuronNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return a property dialog for this screen element.
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Helper class to create the subnetwork dialog.
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.subnetworkNodes.BackpropNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.subnetworkNodes.CompetitiveNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.subnetworkNodes.ESNNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.subnetworkNodes.HopfieldNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.subnetworkNodes.LMSNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.subnetworkNodes.SOMNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.subnetworkNodes.SRNNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.SynapseNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.TextNode
getPropertyDialog() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
getPropertyTabAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getPropsItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getPrototypeResponder() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel
getPrototypeResponder() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel
getPrototypeResponder() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel
getPrototypeResponder() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel
getPrototypeResponder() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel
getPrototypeResponder() - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.AdExIFRulePanel
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.LogisticGeneratorPanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.RandomGeneratorPanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.SinusoidalGeneratorPanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.StochasticGeneratorPanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AdditiveRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.BinaryRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ContinuousSigmoidalRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.HodgkinHuxleyRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IACRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IntegrateAndFireRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IzhikevichRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.LinearRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.PointNeuronRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.RunningAverageRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SigmoidalRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SpikingThresholdRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ThreeValueRulePanel: Each neuron panel contains a static final subclass of NeuronUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPrototypeRule() - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel: Each synapse panel contains a static final subclass of SynapseUpdateRule variable called a prototype rule.
getPsr() - Method in class org.simbrain.network.core.Synapse
getPSRDecayTimeConstant() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.UDF
getPStyledText() - Method in class org.simbrain.network.gui.nodes.TextNode
getQuickConnector() - Method in class org.simbrain.network.gui.NetworkPanel
getQuitWorkspaceAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getRadius() - Method in class org.simbrain.world.odorworld.sensors.SmellSensor
getRandom() - Method in class org.simbrain.util.randomizer.PolarizedRandomizer: Returns a random number.
getRandom() - Method in class org.simbrain.util.randomizer.Randomizer: Returns a random number.
getRandomizeAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for randomizing selected parts of a table.
getRandomizeObjectsAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the randomize objects action.
getRandomizer() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
getRandomizers(List<NeuronUpdateRule>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel
getRandomProb() - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
getRandomValue() - Method in class org.simbrain.network.core.NeuronUpdateRule: Returns a random value between the upper and lower bounds of this neuron.
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule: Returns a random value between the upper and lower bounds of this neuron.
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo: Returns a random value between the upper and lower bounds of this neuron.
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule: Returns a random value between the upper and lower bounds of this neuron.
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule: Returns a random value between the upper and lower bounds of this neuron.
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Returns a random value between the upper and lower bounds of this neuron.
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule: Returns a random value between the upper and lower bounds of this neuron.
getRandomValue() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule: Returns a random value between the upper and lower bounds of this neuron.
getRangeLowerBound() - Method in class org.simbrain.plot.rasterchart.RasterModel
getRangeLowerBound() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
getRangeUpperBound() - Method in class org.simbrain.plot.rasterchart.RasterModel
getRangeUpperBound() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
getRasterModel() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel
getRateConstant() - Method in class org.simbrain.network.neuron_update_rules.RunningAverageRule
getReceptiveField() - Method in class org.simbrain.world.visionworld.Sensor: Return the receptive field for this sensor.
getReceptiveFieldHeight() - Method in class org.simbrain.world.visionworld.sensormatrix.AbstractSensorMatrix: Return the receptive field height for sensors in this sensor matrix.
getReceptiveFieldHeight() - Method in interface org.simbrain.world.visionworld.SensorMatrix: Return the receptive field height for sensors in this sensor matrix.
getReceptiveFieldWidth() - Method in class org.simbrain.world.visionworld.sensormatrix.AbstractSensorMatrix: Return the receptive field width for sensors in this sensor matrix.
getReceptiveFieldWidth() - Method in interface org.simbrain.world.visionworld.SensorMatrix: Return the receptive field width for sensors in this sensor matrix.
getReducedBounds() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Reduced bounds used for some entities, to improve the look of collisions and blocking.
getRefractoryPeriod() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getRefractoryPeriod() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getRefractoryPeriod() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getRefractoryPotential() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getRefreshAction() - Method in class org.simbrain.util.SceneGraphBrowser: Return the refresh action for this scene graph browser.
getRegularExpression() - Method in class org.simbrain.world.textworld.ReaderWorld
getRelAbs() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getRelativePath(String, String) - Static method in class org.simbrain.util.Utils: Helper method to create a relative path for use in saving simulation files which refer to files within directories.
getRemoveSourceAction(RasterPlotPanel) - Static method in class org.simbrain.plot.rasterchart.RasterPlotActions: Add a data source.
getRemoveSourceAction(TimeSeriesPlotPanel) - Static method in class org.simbrain.plot.timeseries.TimeSeriesPlotActions: Add a data source.
getRequiredSpacing() - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow
getRequiredSpacing() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
getRequiredSpacing() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getReservoirLayer() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getResetPotential() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getResistance() - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
getResistance() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getResponderList() - Static method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel
getResponderList(Collection<Synapse>) - Static method in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder: A method which takes in a list of synapses and returns a list of their spike responder, if they have any.
getResponseDuration() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.Step
getResponseHeight() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.Step
getResponseValue() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder
getRest() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getRestingPotential() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getResurrectionProb() - Method in class org.simbrain.world.odorworld.LifeCycle
getRotatingTileset(String, int) - Static method in class org.simbrain.world.odorworld.entities.RotatingEntityManager: Tree map for a rotating image from Reiner Prokein's collection.
getRowCompressedMatrixRepresentation() - Method in class org.simbrain.network.groups.SynapseGroup
getRowCount() - Method in class org.simbrain.util.table.SimbrainDataTable
getRowCount() - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
getRowCount() - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
getRowCount() - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
getRowCount() - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
getRowHeadings() - Method in class org.simbrain.util.table.SimbrainJTable
getRuleList(List<Neuron>) - Static method in class org.simbrain.network.core.Neuron: A method that returns a list of all the neuron update rules associated with a list of neurons.
getRuleList(Collection<Synapse>) - Static method in class org.simbrain.network.core.Synapse: A method which takes in a collection of synapses and returns a list of their update rules in the order in which they appear in the original collection, if that collection supports a consistent order.
getRulelist() - Static method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel
getRuleList() - Static method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel
getRunNetworkAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the run network action.
getRunToolBar() - Method in class org.simbrain.network.gui.NetworkPanel
getSaveCSVAction(SimbrainDataTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for saving to comma separated value file.
getSavedTime() - Method in class org.simbrain.workspace.Workspace
getSavePlotAction() - Method in class org.simbrain.plot.actions.PlotActionManager
getSavePlotAsAction() - Method in class org.simbrain.plot.actions.PlotActionManager
getSaveWorkspaceAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getSaveWorkspaceAsAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getScalingFactor() - Method in class org.simbrain.world.odorworld.effectors.StraightMovement
getScriptActions(SimbrainDesktop) - Method in class org.simbrain.workspace.gui.WorkspaceActionManager: Make a list of script actions by iterating through script menu directory.
getScriptFile() - Method in class org.simbrain.util.scripteditor.ScriptEditor
getScriptString() - Method in class org.simbrain.network.update_actions.CustomUpdate
getScriptString() - Method in class org.simbrain.workspace.updater.UpdateActionCustom
getScroller() - Method in class org.simbrain.network.gui.trainer.DataPanel
getSelectableFilter() - Static method in class org.simbrain.network.gui.filters.Filters: Return the parent node filter.
getSelectableNodes() - Method in class org.simbrain.network.gui.NetworkPanel: Return a collection of all persistent nodes, that is all neuron nodes and all synapse nodes.
getSelectAllAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the select all action.
getSelectAllNeuronsAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the select all neurons action.
getSelectAllWeightsAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the select all weights action.
getSelectedAttributes() - Method in class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel: Returns selected attributes.
getSelectedColumn() - Method in class org.simbrain.util.table.SimbrainJTable: Returns the currently selected column.
getSelectedEntity() - Method in class org.simbrain.world.odorworld.OdorWorldPanel
getSelectedItem() - Method in class org.simbrain.workspace.gui.couplingmanager.GenericListModel: Returns the selected item.
getSelectedModelElements() - Method in class org.simbrain.network.gui.NetworkPanel: Returns model Network elements corresponding to selected screen elements.
getSelectedModelNeuronGroups() - Method in class org.simbrain.network.gui.NetworkPanel: Returns selected neuron groups.
getSelectedModelNeurons() - Method in class org.simbrain.network.gui.NetworkPanel: Returns selected Neurons.
getSelectedModelSynapseGroups() - Method in class org.simbrain.network.gui.NetworkPanel: Returns selected synapse groups.
getSelectedModelSynapses() - Method in class org.simbrain.network.gui.NetworkPanel: Returns selected synapses.
getSelectedNeuronGroups() - Method in class org.simbrain.network.gui.NetworkPanel
getSelectedNeurons() - Method in class org.simbrain.network.gui.NetworkPanel: Returns selected Neurons.
getSelectedPaint() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return the selected paint for this sensor node.
getSelectedPoint() - Method in class org.simbrain.util.table.SimbrainJTable
getSelectedPoint() - Method in class org.simbrain.world.odorworld.OdorWorldPanel: Returns the last point clicked on.
getSelectedRow() - Method in class org.simbrain.util.table.SimbrainJTable: Returns the currently selected row.
getSelectedScreenElements() - Method in class org.simbrain.network.gui.NetworkPanel: Return a collection of all persistent nodes, that is all neuron nodes and all synapse nodes.
getSelectedSynapses() - Method in class org.simbrain.network.gui.NetworkPanel: Returns selected Synapses.
getSelectedText() - Method in class org.simbrain.network.gui.NetworkPanel: Returns the selected Text objects.
getSelectIncomingWeightsAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getSelection() - Method in class org.simbrain.network.gui.NetworkPanel: Return the selection as a collection of selected elements.
getSelection() - Method in class org.simbrain.network.gui.NetworkSelectionEvent: Return the selection.
getSelection() - Method in class org.simbrain.network.gui.NetworkSelectionModel: Return the selection as an unmodifiable collection of selected elements.
getSelection() - Method in class org.simbrain.world.visionworld.SensorSelectionEvent: Return the set of selected sensors.
getSelection() - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Return an unmodifiable collection of selected sensors.
getSelectionColor() - Static method in class org.simbrain.network.gui.nodes.SelectionHandle
getSelectionEditModeAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getSelectOutgoingWeightsAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getSelfConnectionActions() - Method in class org.simbrain.network.gui.NetworkActionManager: (Not current used).
getSemiSaturationConstant() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getSensor(int) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel: Helper method to get a reference to the sensor displayed in a row.
getSensor(String, String) - Method in class org.simbrain.world.odorworld.OdorWorld: Returns the sensor with the given id, or null if none is found.
getSensor() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return the sensor for this sensor node.
getSensor(int, int) - Method in class org.simbrain.world.visionworld.sensormatrix.DenseSensorMatrix: Return the sensor in this sensor matrix at the specified row and column, if any.
getSensor(int, int) - Method in interface org.simbrain.world.visionworld.SensorMatrix: Return the sensor in this sensor matrix at the specified row and column, if any.
getSensor(int, int) - Method in class org.simbrain.world.visionworld.sensormatrix.SparseSensorMatrix: Return the sensor in this sensor matrix at the specified row and column, if any.
getSensorMatrix() - Method in class org.simbrain.world.visionworld.ImmutableVisionWorldModel: Return the sensor matrix for this vision world model.
getSensorMatrix() - Method in class org.simbrain.world.visionworld.MutableVisionWorldModel: Return the sensor matrix for this vision world model.
getSensorMatrix() - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Return the sensor matrix for this sensor matrix node.
getSensorMatrix() - Method in interface org.simbrain.world.visionworld.VisionWorldModel: Return the sensor matrix for this vision world model.
getSensorMatrix() - Method in class org.simbrain.world.visionworld.VisionWorldModelEvent: Return the sensor matrix for this vision world model event, if any.
getSensors() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
getSensorSelectionModel() - Method in class org.simbrain.world.visionworld.VisionWorld: Return the sensor selection model for this vision world.
getSeparatedInput(Neuron) - Method in enum org.simbrain.network.core.NeuronUpdateRule.InputType: Returns the total excitatory and inhibitory inputs to a neuron separated.
getSerializePriority() - Method in class org.simbrain.workspace.WorkspaceComponent
getSeriesCount() - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the number of series in the dataset.
getSeriesData() - Method in class org.simbrain.plot.histogram.HistogramModel: Return the underlying series data.
getSeriesKey(int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: A bit expensive...
getSetAutoZoomMenuItem() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the set auto zoom check box menu item.
getSetNeuronPropertiesAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the neuron properties action.
getSetRandomizerPropsAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getSetSourceNeuronsAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the set source neurons action.
getSetSynapsePropertiesAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the synapse properties action.
getSetTableBoundsAction(NumericTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for setting table bounds.
getSetter(int) - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent: Return the setter with specified index, or null if none found.
getSetTextPropertiesAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowAdjustConnectivityDialog() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowAdjustSynapsesDialog() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowDebugAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowEditToolBarMenuItem() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the show edit tool bar menu item.
getShowMainToolBarMenuItem() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the show main tool bar menu item.
getShowNetworkHierarchyPanel() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowNetworkPreferencesAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the show network preferences action.
getShowPlotAction(NetworkPanel, IterableTrainer) - Static method in class org.simbrain.network.gui.trainer.TrainerGuiActions: Show an error plot for this trainer.
getShowPreferencesDialogAction(TextWorld) - Static method in class org.simbrain.world.textworld.TextWorldActions: Action for displaying a default preference dialog.
getShowPrioritiesAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowPropertyDialogAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getShowRunToolBarMenuItem() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the run clamp tool bar menu item.
getShowScriptEditorAction() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getShowSubnetOutline() - Method in class org.simbrain.network.gui.NetworkPanel
getShowTime() - Method in class org.simbrain.network.gui.NetworkPanel
getShowTrainerAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowUpdaterDialog() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowUpdaterDialog() - Method in class org.simbrain.workspace.gui.WorkspaceActionManager
getShowWeightMatrixAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getShowWeightsAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getShuffleAction(SimbrainDataTable<?>) - Static method in class org.simbrain.util.table.TableActionManager: Action for shuffling the rows of a table.
getSimbrainInterpreter(JConsole, Workspace) - Static method in class org.simbrain.console.ConsoleDesktopComponent: Returns a Simbrain interpreter.
getSimbrainProperties() - Static method in class org.simbrain.util.Utils: Return the Simbrain properties file, or null if it is not found.
getSimpleDescription(String) - Method in class org.simbrain.workspace.AttributeType: Like getDescription(String) but does not add the method base name.
getSimpleName() - Method in class org.simbrain.workspace.gui.GuiComponent: Retrieves a simple version of a component name from its class, e.g.
getSimpleName() - Method in class org.simbrain.workspace.WorkspaceComponent: Retrieves a simple version of a component name from its class, e.g.
getSize() - Method in interface org.simbrain.util.genericframe.GenericFrame
getSize() - Method in class org.simbrain.workspace.gui.couplingmanager.GenericListModel: Returns the number of consumers in the list.
getSlope() - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
getSlope() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
getSlope() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
getSlopeFactor() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getSmallWtThreshold() - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
getSmellSource() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
getSolutionType() - Method in class org.simbrain.network.trainers.LMSOffline: Returns the current solution type inside a comboboxwrapper.
getSom() - Method in class org.simbrain.network.subnetworks.SOMNetwork
getSource() - Method in class org.simbrain.network.core.Synapse
getSource() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getSource() - Method in class org.simbrain.network.gui.nodes.SynapseNode
getSource() - Method in class org.simbrain.network.listeners.NetworkEvent: Event's default getSource() just returns the same object as this class's getObject() method.
getSourceColor() - Static method in class org.simbrain.network.gui.nodes.SourceHandle
getSourceModelGroups() - Method in class org.simbrain.network.gui.NetworkPanel: Returns neuron groups which are "source elements" that can be connected to other neuron groups.
getSourceModelNeurons() - Method in class org.simbrain.network.gui.NetworkPanel
getSourceNeuronGroup() - Method in class org.simbrain.network.groups.SynapseGroup
getSourceNeurons() - Method in class org.simbrain.network.groups.SynapseGroup: Return a list of source neurons associated with the synapses in this group.
getSourceNode() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getSpaceHorizontalAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the space horizontal action.
getSpaceVerticalAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the space vertical action.
getSpacing() - Method in class org.simbrain.network.layouts.LineLayout
getSparse() - Method in class org.simbrain.network.connections.QuickConnectionManager
getSpeechBalloon(Speech) - Method in class org.simbrain.world.odorworld.OdorWorldRenderer: Draws the speech balloon.
getSpikeIndexes() - Method in class org.simbrain.network.groups.NeuronGroup: Returns an array of spike indices used in couplings, (e.g.
getSpikeResponder() - Method in class org.simbrain.network.core.Synapse
getSpikeResponderDescription(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
getSpikeResponsePanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel
getSpikingColor() - Static method in class org.simbrain.network.gui.nodes.NeuronNode
getSpkBuffer() - Method in class org.simbrain.network.core.Neuron
getSprites() - Method in class org.simbrain.world.odorworld.TileMap: Gets an Iterator of all the Sprites in this map, excluding the player OdorWorldEntity.
getSquashFunctionType() - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
getSquashFunctionType() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
getStartPort() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getStartPt() - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow
getStartPt() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
getStartPt() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getStartPt() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getStartX(int, int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the start value for a bin.
getStartY(int, int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the start y-value for a bin (which is the same as the y-value, this method exists only to support the general form of the IntervalXYDataset interface).
getState() - Method in class org.simbrain.network.core.Network: Returns the "state" of the network--the activation level of its neurons.
getState() - Method in class org.simbrain.util.widgets.StopLight
getState(int, int) - Method in class org.simbrain.world.game.tictactoe.TicTacToeModel: Returns the state of a given square.
getStateInfo() - Method in class org.simbrain.network.groups.Group
getStdDev() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.StatisticsBlock
getStdDev(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
getSteepness() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getStepsPerSequences() - Method in class org.simbrain.network.subnetworks.BPTTNetwork
getStimulus(double) - Method in class org.simbrain.util.environment.SmellSource: Calculate what impact the object will have on the creature's receptors (input nodes) based on its distance from this object and its features (whether it is a "noisy object", and how the stimulus decays).
getStimulus(int, double) - Method in class org.simbrain.util.environment.SmellSource: Calculate what impact the object will have on the creature's receptors (input nodes) based on its distance from this object and its features (whether it is a "noisy object", and how the stimulus decays).
getStimulusDimension() - Method in class org.simbrain.util.environment.SmellSource: Return the number of dimensions in the stimulus vector.
getStimulusString() - Method in class org.simbrain.util.environment.SmellSource: Return the stimulus string.
getStimulusVector() - Method in class org.simbrain.util.environment.SmellSource: Return the stimulus vector.
getStopNetworkAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the stop network action.
getStoppingCond() - Method in class org.simbrain.network.trainers.IterableTrainer: Returns the current solution type inside a comboboxwrapper.
getStoppingCondition() - Method in class org.simbrain.network.trainers.IterableTrainer
getStrength() - Method in class org.simbrain.network.core.Synapse
getStrength() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
getStrength() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesSimple
getString(String) - Static method in class org.simbrain.util.SimbrainPreferences: Retrieve a property whose value is a string.
getString() - Method in class org.simbrain.world.textworld.DisplayWorld.StringDataPoint: Get the associated string.
getStringConsumer() - Method in class org.simbrain.world.textworld.DisplayComponent: Returns a String consumer, which reads in from a text producer and sends that text straight to the display world.
getStringMatrix(File) - Static method in class org.simbrain.util.Utils: Read a csv (comma-separated-values) files.
getStrokeWidth() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getSubnetwork() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Get reference to model subnetwork.
getSumDistances() - Method in class org.simbrain.util.projection.Dataset
getSummary() - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel: Provides a string summary of the field values.
getSummedIncomingWeights() - Method in class org.simbrain.network.core.Neuron: Returns the sum of the strengths of the weights attaching to this neuron.
getSymmetricSynapse() - Method in class org.simbrain.network.core.Synapse: Returns symmetric synapse if there is one, null otherwise.
getSynapse(String) - Method in class org.simbrain.network.core.Network: Find a synapse with a given string id.
getSynapse(Neuron, Neuron) - Static method in class org.simbrain.network.core.Network: Returns a reference to the synapse connecting two neurons, or null if there is none.
getSynapse() - Method in class org.simbrain.network.gui.nodes.SynapseNode
getSynapseConsumer(NetworkComponent, Synapse, String) - Static method in class org.simbrain.network.NetworkComponent: Helper method for making synapse consumers, since it happens in a few different places and is important to be consistent about.
getSynapseContextMenu(Synapse) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getSynapseContextMenu(Synapse) - Method in class org.simbrain.network.gui.NetworkPanel
getSynapseCount() - Method in class org.simbrain.network.core.Network
getSynapseDialog(Collection<SynapseNode>) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getSynapseDialog(Collection<SynapseNode>) - Method in class org.simbrain.network.gui.NetworkPanel
getSynapseGroup() - Method in class org.simbrain.network.connections.Sparse
getSynapseGroup(NeuronGroup, NeuronGroup) - Method in class org.simbrain.network.core.Network: Returns the synapse group between some source neuron group and some target neuron group, if it exists.
getSynapseGroup(int) - Method in class org.simbrain.network.groups.Subnetwork: Get a synapse group by index.
getSynapseGroup() - Method in class org.simbrain.network.groups.Subnetwork: Get the first synapse group in the list.
getSynapseGroup() - Method in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox
getSynapseGroup() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNode
getSynapseGroupByLabel(String) - Method in class org.simbrain.network.groups.Subnetwork: Find synapse group with a given label, or null if none found.
getSynapseGroupConsumerMenu(SynapseGroup) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getSynapseGroupConsumerMenu(SynapseGroup) - Method in class org.simbrain.network.gui.NetworkPanel: Creates the consumer menu for synapse groups.
getSynapseGroupCount() - Method in class org.simbrain.network.groups.Subnetwork: Get number of synapse groups in the list.
getSynapseGroupDialog(SynapseGroupInteractionBox) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Creates a modeless version of the synapse group dialog relative to the SimbrainDesktop.
getSynapseGroupDialog(SynapseGroupInteractionBox) - Method in class org.simbrain.network.gui.NetworkPanel: Creates a synapse group dialog from a synapse group interaction box, overrriden in NetworkPanelDesktop to make it modeless relative to the SimbrainDesktop.
getSynapseGroupList() - Method in class org.simbrain.network.groups.Subnetwork: Returns an unmodifiable version of the synapse group list.
getSynapseGroupProducerMenu(SynapseGroup) - Method in class org.simbrain.network.desktop.NetworkPanelDesktop
getSynapseGroupProducerMenu(SynapseGroup) - Method in class org.simbrain.network.gui.NetworkPanel: Creates the producer menu for synapse groups.
getSynapseGroups() - Method in class org.simbrain.network.core.Network: Convenience method to return a list of synapse groups in the network.
getSynapseGroups() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
getSynapseIdGenerator() - Method in class org.simbrain.network.core.Network: Return the generator for synapse ids.
getSynapseList() - Method in class org.simbrain.network.core.Network: Return the list of synapses.
getSynapseList() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog
getSynapseNodeFilter() - Static method in class org.simbrain.network.gui.filters.Filters: Return the synapse node filter.
getSynapseNodes() - Method in class org.simbrain.network.gui.NetworkPanel: Return a collection of all synapse nodes.
getSynapsePanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel
getSynapseProducer(NetworkComponent, Synapse, String) - Static method in class org.simbrain.network.NetworkComponent: Helper method for making synapse producers, since it happens in a few different places and is important to be consistent about.
getSynapseVisibilityThreshold() - Static method in class org.simbrain.network.core.Network
getSynapticInput() - Method in class org.simbrain.network.core.Neuron: Sums the weighted synaptic inputs to a given neuron based on that synapse's spike responder.
getSyncCount() - Method in class org.simbrain.network.update_actions.concurrency_tools.SynchronizationPoint
getSyncCounter() - Method in class org.simbrain.network.update_actions.concurrency_tools.SynchronizationPoint
getSynpaseDecayPercent() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup
getTable() - Method in class org.simbrain.network.gui.dialogs.TestInputPanel
getTable() - Method in class org.simbrain.network.gui.trainer.DataPanel
getTable() - Method in class org.simbrain.network.gui.WeightMatrixViewer
getTarget() - Method in class org.simbrain.network.core.Synapse
getTarget() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getTarget() - Method in class org.simbrain.network.gui.nodes.SynapseNode
getTargetData() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getTargetData() - Method in class org.simbrain.network.trainers.TrainingSet
getTargetDataMatrix() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Wrap target data in a DataMatrix Object.
getTargetDataMatrix() - Method in class org.simbrain.network.trainers.TrainingSet: Wrap target data in a DataMatrix Object.
getTargetNeuronGroup() - Method in class org.simbrain.network.groups.SynapseGroup
getTargetNeurons() - Method in class org.simbrain.network.groups.SynapseGroup: Return a list of target neurons associated with the synapses in this group.
getTargetNode() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
getTargetValue() - Method in class org.simbrain.network.core.Neuron
getTau_minus() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
getTau_plus() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
getTauW() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getTemp() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getTemplate() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getTemplateExcitatorySynapse() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel
getTemplateInhibitorySynapse() - Method in class org.simbrain.network.gui.dialogs.connect.ConnectionSynapsePropertiesPanel
getTemplateRule() - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel
getTemplateSelectedRule() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
getTemplateSynapse() - Static method in class org.simbrain.network.core.Synapse: Returns a "template" synapse.
getTemplateSynapse(SynapseUpdateRule) - Static method in class org.simbrain.network.core.Synapse: Returns a template synapse with a specified learning rule.
getTerminus(SynapseGroupArrow) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
GetterSetter() - Constructor for class org.simbrain.workspace.AttributeList.GetterSetter
getTestData() - Method in class org.simbrain.network.groups.NeuronGroup
getTestInputAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getText() - Method in class org.simbrain.docviewer.DocViewerComponent
getText() - Method in class org.simbrain.network.core.NetworkTextObject
getText() - Method in class org.simbrain.util.scripteditor.ScriptEditor: Returns the main text (in the underlying text area).
getText() - Method in class org.simbrain.world.textworld.TextWorld
getText() - Method in class org.simbrain.world.textworld.TextWorld.TextItem
getTextAction(TextWorld) - Static method in class org.simbrain.world.textworld.TextWorldActions: Action for loading text in to a display or reader world.
getTextArea() - Method in class org.simbrain.util.scripteditor.ScriptEditor
getTextEditModeAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the text edit mode action.
getTextHandle() - Method in class org.simbrain.network.gui.NetworkPanel
getTextList() - Method in class org.simbrain.network.core.Network
getTextNodeFilter() - Static method in class org.simbrain.network.gui.filters.Filters: Return the text node filter.
getTextNodes() - Method in class org.simbrain.network.gui.NetworkPanel: Return a collection of all text nodes.
getTextObject() - Method in class org.simbrain.network.gui.nodes.TextNode
getTfLowBound() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
getTfLowBound() - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
getTfUpBound() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
getTfUpBound() - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
getTheBooleanObject() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheColor() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheDecayFunction() - Method in class org.simbrain.util.environment.SmellSource
getTheDouble() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheDoubleObject() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheFloat() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheFloatObject() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheInt() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheIntObject() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheLong() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheLongObject() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheParseStyle() - Method in class org.simbrain.world.textworld.ReaderWorld: Get the current parse style.
getTheShort() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheShortObject() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheString() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
getTheta() - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
getTheta(NeuronGroupNode.Port) - Static method in class org.simbrain.util.widgets.DirectedCubicArrow
getTheta() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getTheta() - Method in class org.simbrain.world.odorworld.sensors.SmellSensor
getThreshold() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
getThreshold() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getThreshold() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getThreshold() - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
getThreshold() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getThreshold() - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
getThreshold() - Method in class org.simbrain.world.odorworld.effectors.Speech
getThresholdPotential() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getThrowable() - Method in class org.simbrain.workspace.updater.SynchronizingInvocationEvent
getTile(int, int) - Method in class org.simbrain.world.odorworld.TileMap: Gets the tile at the specified location.
getTime() - Method in class org.simbrain.network.core.Network: Returns the current time in ms based on the network Network.timeStep.
getTime() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Returns the 'time' or number of update iterations that have passed.
getTime() - Method in class org.simbrain.workspace.Workspace: Returns global time.
getTimeConstant() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
getTimeConstant() - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
getTimeConstant() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getTimeConstant() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
getTimeConstant() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
getTimeConstant() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay
getTimeLabel() - Method in class org.simbrain.network.core.Network
getTimeSeriesModel() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel
getTimeStep() - Method in class org.simbrain.network.core.Network
getTimeString() - Static method in class org.simbrain.util.Utils: Helper method that returns the date and time in a format that can be used to create filenames.
getTimeType() - Method in class org.simbrain.network.core.Network
getTimeType() - Method in class org.simbrain.network.core.Neuron: Returns the time type of this neuron's update rule.
getTimeType() - Method in class org.simbrain.network.core.NeuronUpdateRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.core.SpikingNeuronUpdateRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.LinearRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.RunningAverageRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.SigmoidalRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule: Returns the type of time update (discrete or continuous) associated with this neuron.
getTimeType() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
getTimeType() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getTitle() - Method in interface org.simbrain.util.genericframe.GenericFrame
getTokenDictionary() - Method in class org.simbrain.world.textworld.TextWorld
getTokenToVectorDict() - Method in class org.simbrain.world.textworld.ReaderWorld
getTolerance() - Method in class org.simbrain.util.projection.Projector
getToolbarCSV(boolean, boolean) - Method in class org.simbrain.util.table.SimbrainJTable: Return a toolbar with buttons for opening from and saving to .csv files.
getToolbarEditRows() - Method in class org.simbrain.util.table.SimbrainJTable: Return a toolbar with buttons for editing the rows of a table.
getToolbarEditTable() - Method in class org.simbrain.util.table.SimbrainJTable: Return a toolbar with buttons for editing the table cells.
getToolbarModeSelect() - Method in class org.simbrain.world.textworld.ReaderPanel: Return a toolbar with buttons for switching between word and character mode.
getToolbarNormalize() - Method in class org.simbrain.util.table.SimbrainJTable
getToolbarOpenClose(GenericFrame, ScriptEditor) - Method in class org.simbrain.util.scripteditor.ScriptEditor: Return a toolbar with buttons for opening from and saving to .bsh files.
getToolbarRandomize() - Method in class org.simbrain.util.table.SimbrainJTable
getToolTipText() - Method in class org.simbrain.network.core.Neuron: Forward to update rule's tool tip method, which returns string for tool tip or short description.
getToolTipText(Neuron) - Method in class org.simbrain.network.core.NeuronUpdateRule: Returns string for tool tip or short description.
getToolTipText() - Method in class org.simbrain.network.core.Synapse: Returns string for tool tip or short description.
getToolTipText(Synapse) - Method in class org.simbrain.network.core.SynapseUpdateRule: Returns string for tool tip or short description.
getToolTipText() - Method in class org.simbrain.network.gui.nodes.InteractionBox
getToolTipText() - Method in class org.simbrain.network.gui.nodes.NeuronNode
getToolTipText() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return a String to use as tool tip text for this screen element.
getToolTipText() - Method in class org.simbrain.network.gui.nodes.SynapseNode
getToolTipText() - Method in class org.simbrain.network.gui.nodes.TextNode
getToolTipText() - Method in class org.simbrain.network.gui.nodes.ToolTipTextUpdater: Return a string to use as tool tip text.
getToolTipText() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
getToolTipText(Neuron) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getToolTipText(Neuron) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
getToolTipText() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return the tool tip text for this sensor node.
getTotalInput() - Method in class org.simbrain.network.core.Neuron
getTotalSmellVectorLength() - Method in class org.simbrain.world.odorworld.OdorWorld
getTrainable(Group, List<Neuron>, List<Neuron>, double[][], double[][]) - Static method in class org.simbrain.network.trainers.Trainer: Utility method for creating a trainable object.
getTrainableNetwork() - Method in class org.simbrain.network.trainers.Trainer
getTrainer() - Method in class org.simbrain.network.gui.trainer.IterativeControlsPanel
getTrainer() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.CompetitiveTrainerControlsPanel
getTrainer() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel
getTrainer() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.SOMTrainerControlsPanel
getTrainer() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Return a trainer object that can be used to train this ESN.
getTrainingSet() - Method in class org.simbrain.network.subnetworks.BackpropNetwork
getTrainingSet() - Method in class org.simbrain.network.subnetworks.BPTTNetwork
getTrainingSet() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork
getTrainingSet() - Method in class org.simbrain.network.subnetworks.Hopfield
getTrainingSet() - Method in class org.simbrain.network.subnetworks.LMSNetwork
getTrainingSet() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Returns the the training set, which contains input and target data.
getTrainingSet() - Method in class org.simbrain.network.subnetworks.SOMNetwork
getTrainingSet() - Method in interface org.simbrain.network.trainers.Trainable: Returns the the training set, which contains input and target data.
getTransparency() - Method in class org.simbrain.util.widgets.DirectedCubicArrow
getTRUE() - Static method in class org.simbrain.util.widgets.TristateDropDown
getTsClipping() - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel
getTsClipping() - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
getType() - Method in class org.simbrain.network.core.Neuron: The name of the update rule of this neuron; it's "type".
getType() - Method in class org.simbrain.network.core.Synapse: The name of the learning rule of the synapse; it's "type".
getType() - Method in class org.simbrain.network.groups.NeuronLayer
getType() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder
getType() - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the histogram type.
getType() - Method in class org.simbrain.world.odorworld.entities.BasicEntity: Getter which returns data that can be used in a combo box (the property editor dialog).
getType() - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Getter which returns data that can be used in a combo box (the property editor dialog).
getTypeDescription() - Method in class org.simbrain.network.groups.NeuronGroup: Return a human-readable name for this type of neuron group.
getTypeDescription() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup
getTypeDescription() - Method in class org.simbrain.network.subnetworks.SOMGroup
getTypeDescription() - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
getTypeDescription() - Method in class org.simbrain.world.odorworld.effectors.Effector: Short description of the effector type.
getTypeDescription() - Method in class org.simbrain.world.odorworld.effectors.Speech
getTypeDescription() - Method in class org.simbrain.world.odorworld.effectors.StraightMovement
getTypeDescription() - Method in class org.simbrain.world.odorworld.effectors.Turning
getTypeDescription() - Method in class org.simbrain.world.odorworld.sensors.BumpSensor
getTypeDescription() - Method in class org.simbrain.world.odorworld.sensors.Hearing
getTypeDescription() - Method in class org.simbrain.world.odorworld.sensors.Sensor: Short description of the sensor type.
getTypeDescription() - Method in class org.simbrain.world.odorworld.sensors.SmellSensor
getTypeDescription() - Method in class org.simbrain.world.odorworld.sensors.TileSensor
getTypeDescriptor(Class<?>) - Static method in class org.simbrain.workspace.CouplingManager: Associates attribute and coupling data types (classes) with text descriptions used in displaying attributes.
getTypeField() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getTypeName() - Method in class org.simbrain.workspace.AttributeType
getUndoManager() - Method in class org.simbrain.network.gui.NetworkPanel
getUngroupAction() - Method in class org.simbrain.network.gui.NetworkActionManager
getUnits() - Static method in class org.simbrain.network.core.Network
getUpdate(CompletionSignal) - Method in class org.simbrain.workspace.updater.ComponentUpdatePart: Get's a runnable that counts down the latch after completion.
getUpdateAction() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedUpdateAction
getUpdateComplete() - Method in class org.simbrain.network.gui.NetworkPanel
getUpdateDelay() - Method in class org.simbrain.workspace.Workspace
getUpdateFunc() - Method in class org.simbrain.network.subnetworks.Hopfield
getUpdateFuncFromName(String) - Static method in enum org.simbrain.network.subnetworks.Hopfield.HopfieldUpdate
getUpdateFuncNames() - Static method in enum org.simbrain.network.subnetworks.Hopfield.HopfieldUpdate
getUpdateInfoPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel
getUpdateInfoPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
getUpdateManager() - Method in class org.simbrain.network.core.Network
getUpdateManager() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Returns a reference to the update manager.
getUpdateMethod() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup
getUpdateMethodDesecription() - Method in class org.simbrain.network.groups.Group: Returns a description of this group's update method, which is displayed in the update manager panel.
getUpdateMethodDesecription() - Method in class org.simbrain.network.groups.NeuronGroup
getUpdateMethodDesecription() - Method in class org.simbrain.network.groups.Subnetwork
getUpdateMethodDesecription() - Method in class org.simbrain.network.groups.SynapseGroup: Returns a description of this group's update method, which is displayed in the update manager panel.
getUpdateMethodDesecription() - Method in class org.simbrain.network.subnetworks.BPTTNetwork
getUpdateMethodDesecription() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getUpdateMethodDesecription() - Method in class org.simbrain.network.subnetworks.FeedForward
getUpdateMethodDesecription() - Method in class org.simbrain.network.subnetworks.Hopfield
getUpdateMethodDesecription() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Returns a description of this group's update method, which is displayed in the update manager panel.
getUpdateOn() - Method in class org.simbrain.workspace.WorkspaceComponent
getUpdateParts() - Method in class org.simbrain.workspace.WorkspaceComponent: Returns the collection of update parts for this component.
getUpdatePriority() - Method in class org.simbrain.network.core.Neuron
getUpdater() - Method in class org.simbrain.workspace.Workspace: Returns a reference to the workspace updater.
getUpdaterListeners() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Return list of updater listeners.
getUpdateRule() - Method in class org.simbrain.network.core.Neuron: Returns the current update rule.
getUpdateRuleDescription() - Method in class org.simbrain.network.core.Neuron: Returns the current update rule's description (name).
getUpdateType() - Method in class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel
getUpperBound() - Method in class org.simbrain.network.core.Neuron: Return the upper bound for the the underlying rule, if it is bounded.
getUpperBound() - Method in class org.simbrain.network.core.Synapse
getUpperBound(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Returns the upper bound.
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Returns the upper bound.
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.IACRule
getUpperBound() - Method in interface org.simbrain.network.neuron_update_rules.interfaces.BoundedUpdateRule: Returns the upper bound.
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
getUpperBound() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getUpperBound() - Method in class org.simbrain.plot.barchart.BarChartModel
getUpperBound() - Method in class org.simbrain.util.randomizer.Randomizer
getUpperBound() - Method in class org.simbrain.util.table.NumericTable: Upper bound for (e.g.) randomization.
getUpperDomainBoundary() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
getUpperLeft(List<Object>) - Static method in class org.simbrain.network.util.SimnetUtils: Return the upper left corner of a list of objects, based on neurons.
getUpperRangeBoundary() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
getUpperThreshold() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getUpperValue() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
getUpperValue() - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
getUpstairs() - Method in class org.simbrain.util.projection.Projector: Convenience method to get upstairs dataset.
getUri() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent.ArchivedDesktopComponent
getUri() - Method in class org.simbrain.workspace.ArchiveContents.ArchivedComponent
getUseAdaptation() - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
getUseGlobalSettingsChkBx() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
getUseLeakyLearning() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Return the leaky learning value.
getUseNoise() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
getUseSlidingOutputThreshold() - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
getV() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getV_m1() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getV_m2() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getV_mem() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getV_Peak() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getV_Reset() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getV_Th() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getV_w1() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getV_w2() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getVal(int) - Method in class org.simbrain.workspace.AttributeList: Return the value of the getter at the specified index.
getValidationError() - Method in class org.simbrain.network.trainers.IterableTrainer: Get the current MSE error.
getValue() - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder
getValue() - Method in class org.simbrain.plot.projection.ProjectionComponent.Dimension: Returns current value.
getValue() - Method in class org.simbrain.workspace.AttributeList.GetterSetter
getValue() - Method in interface org.simbrain.workspace.Producer: Return the value for this producer.
getValue() - Method in class org.simbrain.world.dataworld.DataWorldComponent.ColumnAttribute: Returns the value of the current row at the specified index.
getValue() - Method in class org.simbrain.world.odorworld.sensors.Hearing
getValue() - Method in class org.simbrain.world.odorworld.sensors.TileSensor
getValue() - Method in interface org.simbrain.world.threedee.Sensor
getValue() - Method in class org.simbrain.world.threedee.sensors.Sight.SightSensor
getValue() - Method in class org.simbrain.world.visionworld.filter.UniformFilter: Return the value for this uniform filter.
getValue() - Method in class org.simbrain.world.visionworld.Sensor
getValueAt(int, int) - Method in class org.simbrain.util.table.SimbrainDataTable
getValueAt(int, int) - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
getValueAt(int, int) - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
getValueAt(int, int) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
getValueAt(int, int) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
getValueCurrentRow(int) - Method in class org.simbrain.util.table.NumericTable: Get the value of the specified column in the current row.
getValuesPanel() - Method in class org.simbrain.util.environment.SmellSourcePanel
getVClampOn() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
getVector() - Method in class org.simbrain.util.projection.DataPoint: Returns the underlying data vector.
getVectorCurrentRow() - Method in class org.simbrain.util.table.NumericTable: Return the current row of doubles as an array.
getVectorNorm(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Returns the Euclidean norm of the supplied vector.
getVectorString(double[], String) - Static method in class org.simbrain.util.Utils: Convert an array of doubles into a String.
getVectorString(String, String) - Static method in class org.simbrain.util.Utils: Convert a delimited string of doubles into an array of doubles.
getVectorToTokenDict() - Method in class org.simbrain.world.textworld.DisplayWorld
getVelocityX() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Gets the horizontal velocity of this OdorWorldEntity in pixels per millisecond.
getVelocityY() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Gets the vertical velocity of this OdorWorldEntity in pixels per millisecond.
getVerticalSpacing() - Method in class org.simbrain.network.util.CascadingNetworkBuilder
getViewGroupNode() - Method in class org.simbrain.network.gui.NetworkPanel
getViewMenuActions() - Method in class org.simbrain.world.visionworld.VisionWorld: Return a list of view menu actions for this vision world.
getVisibleConsumerTypes() - Method in class org.simbrain.workspace.WorkspaceComponent: Return visible consumer types.
getVisibleProducerTypes() - Method in class org.simbrain.workspace.WorkspaceComponent: Return visible producer types.
getVisionWorld() - Method in class org.simbrain.world.visionworld.SensorSelectionEvent: Return the source of this event as a vision world.
getVisionWorld() - Method in class org.simbrain.world.visionworld.VisionWorldComponent: Returns vision world canvas.
getVisionWorldDesktopComponent() - Method in class org.simbrain.world.visionworld.VisionWorld
getVisionWorldModel() - Method in class org.simbrain.world.visionworld.VisionWorldModelEvent: Return the source of this event as a vision world model.
getvRest_Ca() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getvRest_k() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getvRest_L() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getVSpacing() - Method in class org.simbrain.network.layouts.GridLayout
getVSpacing() - Method in class org.simbrain.network.layouts.HexagonalGridLayout
getW() - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
getW() - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
getW_K() - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
getW_minus() - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
getW_minus() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
getW_plus() - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
getW_plus() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
getWallItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getWallPropsItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getWandEditModeAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the wand edit mode action.
getWandRadius() - Static method in class org.simbrain.network.gui.EditMode
getWeight(int, int) - Method in class org.simbrain.network.core.Network: Gets the synapse at particular point.
getWeightedInputs() - Method in class org.simbrain.network.core.Neuron: Sums the weighted signals that are sent to this node.
getWeightMatrix() - Method in class org.simbrain.network.groups.SynapseGroup: For large, sparse synapse groups this will cause a heap overflow.
getWeightMatrix(List<Neuron>, List<Neuron>) - Static method in class org.simbrain.network.util.SimnetUtils: Gets a matrix of Synapse objects, formatted like the getWeights method.
getWeightMatrixPanel(WeightMatrixViewer) - Static method in class org.simbrain.network.gui.WeightMatrixViewer: Embed the scrollpanel in a widget with a toolbar.
getWeights(List<Neuron>, List<Neuron>) - Static method in class org.simbrain.network.util.SimnetUtils: Returns the weights connecting two lists of neurons as an N x M matrix of doubles, where N is the number of source neurons, and M is the number of target neurons.
getWeightsVisible() - Method in class org.simbrain.network.gui.NetworkPanel
getWeightVector() - Method in class org.simbrain.network.groups.SynapseGroup: Return weight strengths as a double vector.
getWhen() - Method in class org.simbrain.workspace.updater.SynchronizingInvocationEvent
getWhereToAdd() - Method in class org.simbrain.network.gui.NetworkPanel
getWidth() - Method in class org.simbrain.network.groups.NeuronGroup: Return the width of this group, based on the positions of the neurons that comprise it.
getWidth() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Returns the width of the visible portion of the desktop.
getWidth() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Gets this OdorWorldEntity's width, based on the size of the current image.
getWidth() - Method in class org.simbrain.world.odorworld.OdorWorld: Returns width of world in pixels.
getWidth() - Method in class org.simbrain.world.odorworld.sensors.TileSensor
getWidth() - Method in class org.simbrain.world.odorworld.TileMap: Gets the width of this TileMap (number of tiles across).
getWidth() - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Return the width of this pixel matrix.
getWidth() - Method in interface org.simbrain.world.visionworld.PixelMatrix: Return the width of this pixel matrix.
getWidth() - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Return the width of this pixel matrix.
getWidth() - Method in class org.simbrain.world.visionworld.ReceptiveField: Return the width of this receptive field.
getWindowSize() - Method in class org.simbrain.plot.rasterchart.RasterModel
getWindowSize() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
getWinValue() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Return the winner value.
getWinValue() - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
getWorkspace() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Returns the workspace.
getWorkspace() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater
getWorkspace() - Method in class org.simbrain.workspace.WorkspaceComponent: Returns the workspace associated with this component.
getWorkspaceComponent() - Method in class org.simbrain.workspace.gui.GuiComponent: Returns the workspace component wrapped by this instance.
getWorkspaceComponentListeners() - Method in class org.simbrain.workspace.WorkspaceComponent: Returns the WorkspaceComponentListeners on this component.
getWorkspaceParameters() - Method in class org.simbrain.workspace.ArchiveContents
getWorld() - Method in class org.simbrain.world.odorworld.OdorWorldComponent: Returns a reference to the odor world.
getWorld() - Method in class org.simbrain.world.odorworld.OdorWorldPanel
getWorld() - Method in class org.simbrain.world.textworld.DisplayComponent
getWorld() - Method in class org.simbrain.world.textworld.DisplayPanel
getWorld() - Method in class org.simbrain.world.textworld.ReaderComponent
getWorld() - Method in class org.simbrain.world.textworld.ReaderPanel
getWorldPanel() - Method in class org.simbrain.world.odorworld.OdorWorldDesktopComponent: Return the odor world.
getWrapAround() - Method in class org.simbrain.world.odorworld.OdorWorld
getX() - Method in class org.simbrain.network.core.NetworkTextObject
getX() - Method in class org.simbrain.network.core.Neuron
getX(int, int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the X value for a bin.
getX() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent.ScatterPlotSetter
getX() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Gets this OdorWorldEntity's current x position.
getX() - Method in class org.simbrain.world.odorworld.sensors.TileSensor
getX() - Method in class org.simbrain.world.visionworld.ReceptiveField: Return the x offset for this receptive field.
getxAxisName() - Method in class org.simbrain.plot.histogram.HistogramPanel
getXML() - Method in class org.simbrain.network.NetworkComponent
getXML() - Method in class org.simbrain.plot.barchart.BarChartComponent
getXML() - Method in class org.simbrain.plot.histogram.HistogramComponent
getXML() - Method in class org.simbrain.plot.piechart.PieChartComponent
getXML() - Method in class org.simbrain.plot.projection.ProjectionComponent
getXML() - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent
getXML() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
getXML() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent
getXML() - Method in class org.simbrain.workspace.WorkspaceComponent: Override for use with open service.
getXML() - Method in class org.simbrain.world.dataworld.DataWorldComponent
getXML() - Method in class org.simbrain.world.odorworld.OdorWorldComponent
getXpos() - Method in class org.simbrain.network.gui.nodes.NeuronNode
getXStream() - Static method in class org.simbrain.network.core.Network: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.plot.barchart.BarChartModel: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.plot.ChartModel: Creates an xtream object with relevant fields omitted.
getXStream() - Static method in class org.simbrain.plot.piechart.PieChartModel: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.plot.projection.ProjectionModel: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.plot.rasterchart.RasterModel: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.plot.scatterplot.ScatterPlotModel: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.plot.timeseries.TimeSeriesModel: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.util.table.SimbrainDataTable: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.world.odorworld.OdorWorld: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.world.textworld.DisplayWorld: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.world.textworld.ReaderWorld: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.world.textworld.TextWorld: Returns a properly initialized xstream object.
getXStream() - Static method in class org.simbrain.world.visionworld.AbstractVisionWorldModel: Returns a properly initialized xstream object.
getY() - Method in class org.simbrain.network.core.NetworkTextObject
getY() - Method in class org.simbrain.network.core.Neuron
getY(int, int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Returns the y-value for a bin (calculated to take into account the histogram type).
getY() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent.ScatterPlotSetter
getY() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Gets this OdorWorldEntity's current y position.
getY() - Method in class org.simbrain.world.odorworld.sensors.TileSensor
getY() - Method in class org.simbrain.world.visionworld.ReceptiveField: Return the y offset for this receptive field.
getyAxisName() - Method in class org.simbrain.plot.histogram.HistogramPanel
getYpos() - Method in class org.simbrain.network.gui.nodes.NeuronNode
getZ() - Method in class org.simbrain.network.core.Neuron
getZeroFillAction(SimbrainJTable) - Static method in class org.simbrain.util.table.TableActionManager: Action for zeroing out cells of a table.
getZeroSelectedObjectsAction() - Method in class org.simbrain.network.gui.NetworkActionManager: Return the clear neurons action.
getZeroWeightColor() - Static method in class org.simbrain.network.gui.nodes.SynapseNode
getZoomListener() - Method in class org.simbrain.network.gui.nodes.InteractionBox
getZoomToFitPageAction() - Method in class org.simbrain.network.gui.NetworkActionManager
GlobalRunAction - Class in org.simbrain.workspace.actions: Run network action.
GlobalRunAction(Workspace) - Constructor for class org.simbrain.workspace.actions.GlobalRunAction: Create a new run network action with the specified network panel.
GlobalStopAction - Class in org.simbrain.workspace.actions: Run network action.
GlobalStopAction(Workspace) - Constructor for class org.simbrain.workspace.actions.GlobalStopAction: Create a new run network action with the specified network panel.
GlobalUpdateAction - Class in org.simbrain.workspace.actions: Open data world in current workspace.
GlobalUpdateAction(Workspace) - Constructor for class org.simbrain.workspace.actions.GlobalUpdateAction: Create an open data world with the specified workspace.
goStraight(double) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Move the entity in a straight line relative to its current heading.
green - Variable in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: The green threshold.
GRID_HEIGHT - Static variable in class org.simbrain.plot.histogram.HistogramPanel: The grid height of this panel, for use by possible parent panels.
GRID_WIDTH - Static variable in class org.simbrain.plot.histogram.HistogramPanel: The grid width of this panel, for use by possible parent panels.
GridLayout - Class in org.simbrain.network.layouts: Lay neurons out in a grid.
GridLayout(double, double, int) - Constructor for class org.simbrain.network.layouts.GridLayout: Create a grid layout with a specific number of columns.
GridLayout(double, double) - Constructor for class org.simbrain.network.layouts.GridLayout: Create a grid layout that automatically produces a square grid based on number of neurons.
GridLayout() - Constructor for class org.simbrain.network.layouts.GridLayout: Default constructor.
GridLayoutPanel - Class in org.simbrain.network.gui.dialogs.layout: GridLayoutPanel allows the user to define the layout of a network.
GridLayoutPanel(GridLayout) - Constructor for class org.simbrain.network.gui.dialogs.layout.GridLayoutPanel: Default constructor.
Group - Class in org.simbrain.network.groups: Group: a logical group of neurons and / or synapses.
Group(Network) - Constructor for class org.simbrain.network.groups.Group: Construct a model group with a reference to its root network.
GroupAction - Class in org.simbrain.network.gui.actions: Group selected objects.
GroupAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.GroupAction: Group selected objects.
GroupAdapter - Class in org.simbrain.network.listeners: Adapter class for GroupListener.
GroupAdapter() - Constructor for class org.simbrain.network.listeners.GroupAdapter
groupAdded(NetworkEvent<Group>) - Method in class org.simbrain.network.listeners.GroupAdapter
groupAdded(NetworkEvent<Group>) - Method in interface org.simbrain.network.listeners.GroupListener: Invoked when a group is added.
groupAdded(NetworkEvent<Group>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
groupChanged(NetworkEvent<Group>, String) - Method in class org.simbrain.network.listeners.GroupAdapter
groupChanged(NetworkEvent<Group>, String) - Method in interface org.simbrain.network.listeners.GroupListener: Invoked when a group is changed.
groupChanged(NetworkEvent<Group>, String) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
GroupDeserializer - Class in org.simbrain.network.util.io_utilities: A class for storing static methods for custom deserialization of custom serializations of group objects in Simbrain.
GroupDeserializer() - Constructor for class org.simbrain.network.util.io_utilities.GroupDeserializer
GroupListener - Interface in org.simbrain.network.listeners: Listener interface for receiving network events relating to model groups.
GroupNode - Interface in org.simbrain.network.gui.nodes: Interface for all PNodes representing Simbrain groups.
groupParameterChanged(NetworkEvent<Group>) - Method in class org.simbrain.network.listeners.GroupAdapter
groupParameterChanged(NetworkEvent<Group>) - Method in interface org.simbrain.network.listeners.GroupListener: Invoked when a group is changed.
groupParameterChanged(NetworkEvent<Group>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
GroupPropertiesPanel - Interface in org.simbrain.network.gui.dialogs.group: Interface for panels that allow the properties of neuron groups to be edited.
groupRemoved(NetworkEvent<Group>) - Method in class org.simbrain.network.listeners.GroupAdapter
groupRemoved(NetworkEvent<Group>) - Method in interface org.simbrain.network.listeners.GroupListener: Invoked when a group is removed.
groupRemoved(NetworkEvent<Group>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
groupSelectedObjects() - Method in class org.simbrain.network.gui.NetworkPanel: Create a group of GUI objects.
GroupSerializer - Class in org.simbrain.network.util.io_utilities: A class for storing static methods for custom serialization of group objects in Simbrain.
GroupSerializer() - Constructor for class org.simbrain.network.util.io_utilities.GroupSerializer
GroupSerializer.Precision - Enum in org.simbrain.network.util.io_utilities: A flag for how decimal values should be serialized and methods for converting doubles or doubles as long bits appropriately.
groupUpdated(Group) - Method in class org.simbrain.network.listeners.GroupAdapter
groupUpdated(Group) - Method in interface org.simbrain.network.listeners.GroupListener: The state of the neurons or synapses in the group has changed.
groupUpdated(Group) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
GuiComponent<E extends WorkspaceComponent> - Class in org.simbrain.workspace.gui: A gui view on a WorkspaceComponent.
GuiComponent(GenericFrame, E) - Constructor for class org.simbrain.workspace.gui.GuiComponent: Construct a workspace component.
guiToggled() - Method in interface org.simbrain.workspace.WorkspaceComponentListener: Called when the component's gui(s) are turned on or off.

H

hasChanged() - Method in class org.simbrain.util.table.SimbrainJTable
hasChangedSinceLastSave() - Method in class org.simbrain.plot.barchart.BarChartComponent
hasChangedSinceLastSave() - Method in class org.simbrain.plot.histogram.HistogramComponent
hasChangedSinceLastSave() - Method in class org.simbrain.plot.piechart.PieChartComponent
hasChangedSinceLastSave() - Method in class org.simbrain.plot.projection.ProjectionComponent
hasChangedSinceLastSave() - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent
hasChangedSinceLastSave() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
hasChangedSinceLastSave() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent
hasChangedSinceLastSave() - Method in class org.simbrain.workspace.WorkspaceComponent: Returns true if it's changed since the last save.
hasCollided() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
hasContextMenu() - Method in class org.simbrain.network.gui.nodes.InteractionBox
hasContextMenu() - Method in class org.simbrain.network.gui.nodes.NeuronNode
hasContextMenu() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return true if this screen element has a context menu.
hasContextMenu() - Method in class org.simbrain.network.gui.nodes.SynapseNode
hasContextMenu() - Method in class org.simbrain.network.gui.nodes.TextNode
hasContextMenu() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
hasExcitatory() - Method in class org.simbrain.network.groups.SynapseGroup
hasFocus() - Method in class org.simbrain.world.visionworld.node.PixelMatrixImageNode: Return true if this pixel matrix image node has focus.
hashCode() - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset
hashCode() - Method in class org.simbrain.workspace.Coupling
hasInhibitory() - Method in class org.simbrain.network.groups.SynapseGroup
hasParentGroup() - Method in class org.simbrain.network.groups.Group: Returns true if this group has a parent group (i.e.
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.InteractionBox
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode.NeuronGroupInteractionBox
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.NeuronNode
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return true if this screen element has a property dialog.
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.SynapseNode
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.TextNode
hasPropertyDialog() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
hasToolTipText() - Method in class org.simbrain.network.gui.nodes.InteractionBox
hasToolTipText() - Method in class org.simbrain.network.gui.nodes.NeuronNode
hasToolTipText() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return true if this screen element has tool tip text.
hasToolTipText() - Method in class org.simbrain.network.gui.nodes.SynapseNode
hasToolTipText() - Method in class org.simbrain.network.gui.nodes.TextNode
hasToolTipText() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
hasUserCancelled() - Method in class org.simbrain.util.StandardDialog: This method returns true if the User cancelled the dialog otherwise false.
hasUserCancelled() - Method in class org.simbrain.workspace.gui.WorkspaceChangedDialog
Hearing - Class in org.simbrain.world.odorworld.sensors: Implement a simple hearing sensor.
Hearing(OdorWorldEntity, String, double) - Constructor for class org.simbrain.world.odorworld.sensors.Hearing: Construct the hearing sensor.
HearingSensorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel to add a hearing sensor to an entity.
HearingSensorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.HearingSensorPanel: Constructor for the case where a sensor is being created.
HearingSensorPanel(OdorWorldEntity, Hearing) - Constructor for class org.simbrain.world.odorworld.dialogs.HearingSensorPanel: Constructor for the case where a sensor is being edited.
hearingSensorType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
HebbianCPCARule - Class in org.simbrain.network.synapse_update_rules: HebbianCPCA.
HebbianCPCARule() - Constructor for class org.simbrain.network.synapse_update_rules.HebbianCPCARule
HebbianCPCARulePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: HebbianCPCAPanel.
HebbianCPCARulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel: This method is the default constructor.
HebbianRule - Class in org.simbrain.network.synapse_update_rules: Hebbian implements a standard Hebbian learning rule.
HebbianRule() - Constructor for class org.simbrain.network.synapse_update_rules.HebbianRule
HebbianRulePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: HebbianSynapsePanel.
HebbianRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel: This method is the default constructor.
HebbianThresholdRule - Class in org.simbrain.network.synapse_update_rules: HebbianThresholdSynapse.
HebbianThresholdRule() - Constructor for class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
HebbianThresholdRulePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: HebbianThresholdSynapsePanel.
HebbianThresholdRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel: This method is the default constructor.
height - Variable in class org.simbrain.workspace.gui.WorkspaceChangedDialog
height - Variable in class org.simbrain.world.threedee.sensors.Sight
HexagonalGridLayout - Class in org.simbrain.network.layouts: Lay neurons out in a hexagonal grid.
HexagonalGridLayout(double, double, int) - Constructor for class org.simbrain.network.layouts.HexagonalGridLayout: Create a layout.
HexagonalGridLayout() - Constructor for class org.simbrain.network.layouts.HexagonalGridLayout: Default Constructor.
HexagonalGridLayoutPanel - Class in org.simbrain.network.gui.dialogs.layout: HexagonalGridLayoutPanel allows the user to define the layout of a network.
HexagonalGridLayoutPanel(HexagonalGridLayout) - Constructor for class org.simbrain.network.gui.dialogs.layout.HexagonalGridLayoutPanel: Default constructor.
highlight(int, int) - Method in class org.simbrain.world.textworld.ReaderPanel: Highlight word beginning at begin nd ending at end.
HistogramComponent - Class in org.simbrain.plot.histogram: The Component representation of a histogram.
HistogramComponent(String) - Constructor for class org.simbrain.plot.histogram.HistogramComponent: Create new Histogram Component.
HistogramComponent(String, HistogramModel) - Constructor for class org.simbrain.plot.histogram.HistogramComponent: Create new Histogram Component from a specified model.
HistogramGui - Class in org.simbrain.plot.histogram: Display a Histogram in the Simbrain Desktop.
HistogramGui(GenericFrame, HistogramComponent) - Constructor for class org.simbrain.plot.histogram.HistogramGui: Construct the GUI.
HistogramModel - Class in org.simbrain.plot.histogram: Underlying model for the histogram data, in the form of a list of double arrays, one array per histogram.
HistogramModel() - Constructor for class org.simbrain.plot.histogram.HistogramModel: Creates a blank histogram.
HistogramModel(int) - Constructor for class org.simbrain.plot.histogram.HistogramModel: Creates a histogram with no data and a specified number of datsets.
HistogramModel(int, int) - Constructor for class org.simbrain.plot.histogram.HistogramModel
HistogramModel(List<double[]>, List<String>, int) - Constructor for class org.simbrain.plot.histogram.HistogramModel: Creates a histogram with the provided number of bins, data set(s), and data name(s), but does not include titles for the histogram, the x axis or the y axis.
HistogramModel(List<double[]>, List<String>, int, String, String, String) - Constructor for class org.simbrain.plot.histogram.HistogramModel: Creates a histogram with the provided number of bins, data set(s), data name(s), title, and x and y axis titles.
HistogramModel(List<double[]>, List<String>, int, String, String, String, Color[]) - Constructor for class org.simbrain.plot.histogram.HistogramModel: Creates a histogram with the provided number of bins, data set(s), data name(s), title, and x and y axis titles.
HistogramPanel - Class in org.simbrain.plot.histogram: Panel to display histogram.
HistogramPanel(HistogramModel) - Constructor for class org.simbrain.plot.histogram.HistogramPanel: Construct a new histogram panel.
HodgkinHuxleyRule - Class in org.simbrain.network.neuron_update_rules: Hodgkin-Huxley Neuron.
HodgkinHuxleyRule() - Constructor for class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
HodgkinHuxleyRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: Hodgkin-Huxley Rule Panel TODO: No Implementation.
HodgkinHuxleyRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.HodgkinHuxleyRulePanel: Creates HodgkinHuxley preferences panel.
Hopfield - Class in org.simbrain.network.subnetworks: Hopfield is a basic implementation of a discrete Hopfield network.
Hopfield(Network, int) - Constructor for class org.simbrain.network.subnetworks.Hopfield: Creates a new Hopfield network.
Hopfield.HopfieldUpdate - Enum in org.simbrain.network.subnetworks: Main forms of Hopfield update rule.
HopfieldCreationDialog - Class in org.simbrain.network.gui.dialogs.network: DiscreteHopfieldDialog is a dialog box for creating discrete Hopfield networks.
HopfieldCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.HopfieldCreationDialog: This method is the default constructor.
HopfieldEditTrainDialog - Class in org.simbrain.network.gui.dialogs.network: Dialog for setting the properties of Hopfield networks and training them.
HopfieldEditTrainDialog(NetworkPanel, Hopfield) - Constructor for class org.simbrain.network.gui.dialogs.network.HopfieldEditTrainDialog: Construct the dialog.
HopfieldNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of Hopfield Network.
HopfieldNode(NetworkPanel, Hopfield) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.HopfieldNode: Create a Hopfield Network PNode.
HopfieldPropertiesPanel - Class in org.simbrain.network.gui.dialogs.network: DiscreteHopfieldPropertiesDialog is a dialog box for setting the properties of a discrete Hopfield network.
HopfieldPropertiesPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel: Constructor for creating Hopfield networks.
HopfieldPropertiesPanel(NetworkPanel, Hopfield) - Constructor for class org.simbrain.network.gui.dialogs.network.HopfieldPropertiesPanel: Constructor for editing.
hopfieldPropsPanel - Variable in class org.simbrain.network.gui.dialogs.network.HopfieldEditTrainDialog: The main panel.
HopfieldTrainer - Class in org.simbrain.network.trainers: Trainer for a Hopfield network.
HopfieldTrainer(Hopfield) - Constructor for class org.simbrain.network.trainers.HopfieldTrainer: Construct the Hopfield trainer.

I

IACRule - Class in org.simbrain.network.neuron_update_rules: IACNeuron implements an Interactive Activation and Competition neuron.
IACRule() - Constructor for class org.simbrain.network.neuron_update_rules.IACRule
IACRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: IACNeuronPanel.
IACRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.IACRulePanel: This method is the default constructor.
IGNORE - Static variable in interface org.simbrain.workspace.updater.CompletionSignal: Simple signal with no implementation.
image - Variable in class org.simbrain.world.threedee.sensors.Sight
ImagePreviewPanel - Class in org.simbrain.util
ImagePreviewPanel() - Constructor for class org.simbrain.util.ImagePreviewPanel
ImmutableVisionWorldModel - Class in org.simbrain.world.visionworld: Immutable implementation of VisionWorldModel.
ImmutableVisionWorldModel(PixelMatrix, SensorMatrix) - Constructor for class org.simbrain.world.visionworld.ImmutableVisionWorldModel: Create a new immutable vision world model with the specified pixel matrix and sensor matrix.
importData(File) - Method in class org.simbrain.util.projection.Projector: Add new high-d datapoints and reinitialize the datasets.
IN_OUT_FONT - Static variable in class org.simbrain.network.gui.nodes.NeuronNode: Font for input and output labels.
increment - Variable in class org.simbrain.network.core.NeuronUpdateRule: Amount by which to increment or decrement neuron.
incrementActivation(Neuron) - Method in class org.simbrain.network.core.NeuronUpdateRule: Increment a neuron by increment.
incrementActivation(double, double) - Method in class org.simbrain.util.projection.DataPointColored: Increment the activation of this point (for frequency based coloring).
incrementIteration() - Method in class org.simbrain.network.trainers.CompetitiveTrainer: Increment the iteration number by 1.
incrementIteration() - Method in class org.simbrain.network.trainers.IterableTrainer: Increment the iteration number by 1.
incrementIteration() - Method in class org.simbrain.network.trainers.SOMTrainer: Increment the iteration number by 1.
incrementSelectedObjects() - Method in class org.simbrain.network.gui.NetworkPanel: Increases neuron and synapse activation levels.
incrementWeight() - Method in class org.simbrain.network.core.Synapse: Increment this weight by increment.
inFanInOfSomeNode(Synapse) - Method in class org.simbrain.network.groups.NeuronGroup: Returns true if the provided synapse is in the fan-in weight vector of some node in this neuron group.
init(Synapse) - Method in class org.simbrain.network.core.SynapseUpdateRule: Initialize the update rule and make necessary changes to the parent synapse.
init() - Method in class org.simbrain.network.gui.dialogs.text.TextDialog: Initializes font chooser dialog.
init() - Method in class org.simbrain.network.gui.trainer.IterativeControlsPanel: Initialize the panel.
init() - Method in class org.simbrain.network.gui.trainer.SimpleTrainerControlPanel: Initialize the panel.
init() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.CompetitiveTrainerControlsPanel: Initialize the panel.
init() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.SOMTrainerControlsPanel: Initialize the panel.
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule: TODO: Doesn't feel like good API...
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule: TODO: Doesn't feel like good API...
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule: TODO: Doesn't feel like good API...
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
init(Neuron) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.ActivityGenerator: TODO: Doesn't feel like good API...
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.RunningAverageRule
init(Neuron) - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.HebbianRule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.OjaRule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.UDF: Initializes this UDF object based on the synapse it governs.
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.StaticSynapseRule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
init(Synapse) - Method in class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule
init() - Method in class org.simbrain.network.update_actions.CustomUpdate: Initialize the interpreter.
init(int) - Method in class org.simbrain.plot.projection.ProjectionModel: Initialize the projection model with a certain number of data sources.
init() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel: Initialize Chart Panel.
init() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Initialize Chart Panel.
init() - Method in class org.simbrain.util.projection.ProjectCoordinate
init() - Method in class org.simbrain.util.projection.ProjectionMethod: Perform any initialization necessary for a given projection method.
init() - Method in class org.simbrain.util.projection.ProjectNNSubspace
init(int) - Method in class org.simbrain.util.projection.Projector: Initialize projector to accept data of a specified dimension.
init() - Method in class org.simbrain.util.projection.ProjectPCA
init() - Method in class org.simbrain.util.projection.ProjectSammon
init() - Method in class org.simbrain.util.projection.ProjectTriangulate
init(int, int) - Method in class org.simbrain.util.table.NumericTable: Initialize the table.
init(int, int) - Method in class org.simbrain.util.table.TextTable: Initialize the table.
init() - Method in class org.simbrain.workspace.gui.WorkspaceChangedDialog: Initialize the panel.
init() - Method in class org.simbrain.workspace.updater.UpdateActionCustom: Initialize the interpreter.
initDefaultTabs() - Method in class org.simbrain.network.gui.dialogs.network.SupervisedTrainingDialog: This method initializes the components on the panel.
initGui() - Method in class org.simbrain.network.gui.NetworkPanel: Initialize the Gui.
INITIAL_DATA_SOURCES - Static variable in class org.simbrain.plot.histogram.HistogramModel: Default number of data sources for plot initialization.
initializeConsumers() - Method in class org.simbrain.plot.projection.ProjectionComponent: Initialize consumers.
initializeImages() - Method in class org.simbrain.world.odorworld.entities.Animation: Initialize images relative to their locations.
initializeInputLayer(NeuronGroup) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Initializes the input layer from a neuron group and adds it to the ESN.
initializeOutput(NeuronGroup) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Initializes the output layer and adds it to the ESN.
initializeReservoir(NeuronGroup, SynapseGroup, double) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Initializes the reservoir.
initializeSynapseVisibility() - Method in class org.simbrain.network.groups.SynapseGroup: Determine whether this synpasegroup should initially have its synapses displayed.
initialSfunction - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: The initially selected squashing function (or NULL_STRING), used for determining how to fill field values based on the selected implementation.
initJTable() - Method in class org.simbrain.util.table.SimbrainJTable: Initialize the table.
initListeners() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel: Initializes the listener on the apply button, allowing the values in the randomizer to be committed, and if editing, immediately causing the synapses in question to undergo randomization.
initMenu() - Method in class org.simbrain.world.odorworld.OdorWorldMenu: Build the popup menu displayed when users right-click in world.
initNetwork() - Method in class org.simbrain.network.subnetworks.BackpropNetwork
initNetwork() - Method in class org.simbrain.network.subnetworks.BPTTNetwork
initNetwork() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork
initNetwork() - Method in class org.simbrain.network.subnetworks.Hopfield
initNetwork() - Method in class org.simbrain.network.subnetworks.LMSNetwork
initNetwork() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork
initNetwork() - Method in class org.simbrain.network.subnetworks.SOMNetwork
initNetwork() - Method in interface org.simbrain.network.trainers.Trainable: Initialize the network.
initPanel(SimbrainJTable) - Method in class org.simbrain.world.textworld.dictionary.VectorDictionaryPanel: Build and initialize the panel.
initSpikeResponder() - Method in class org.simbrain.network.core.Synapse: Set a default spike responder if the source neuron is a spiking neuron, else set the spikeResponder to null.
initTrainer(boolean) - Method in class org.simbrain.network.gui.trainer.IterativeControlsPanel: Called whenever the trainer should be reinitialized.
inputNeurons - Variable in class org.simbrain.network.gui.trainer.DataPanel: The neurons that this data will be sent as input to.
inputScrollPane - Variable in class org.simbrain.world.textworld.ReaderPanel: The main scroll panel.
inputType - Variable in class org.simbrain.network.core.NeuronUpdateRule
inRandomizerEnabled() - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
insertColumn(int, T) - Method in class org.simbrain.util.table.MutableTable: Insert a new column at the specified position.
insertColumn(int) - Method in class org.simbrain.util.table.MutableTable: Insert a new column at the specified position, using the default data.
insertRow(int, T) - Method in class org.simbrain.util.table.MutableTable: Insert a new row at the specified position.
insertRow(int) - Method in class org.simbrain.util.table.MutableTable: Insert a new row at the specified position, using the default data.
installUI(JComponent) - Method in class org.simbrain.util.MultiLineToolTipUI
instantiateTemplateSynapse(Neuron, Neuron, Network) - Method in class org.simbrain.network.core.Synapse: A template synapse is a synapse that has no proper references, but is used for setting properties.
IntegrateAndFireRule - Class in org.simbrain.network.neuron_update_rules: IntegrateAndFireNeuron implements an integrate and fire neuron.
IntegrateAndFireRule() - Constructor for class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
IntegrateAndFireRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: IntegrateAndFireNeuronPanel.
IntegrateAndFireRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.IntegrateAndFireRulePanel: Creates a new instance of the integrate and fire neuron panel.
InteractionBox - Class in org.simbrain.network.gui.nodes: Interaction Box: graphical element for interacting with a group.
InteractionBox(NetworkPanel) - Constructor for class org.simbrain.network.gui.nodes.InteractionBox: Create a new tab node.
interactionBox - Variable in class org.simbrain.network.gui.nodes.SynapseGroupNode: The interaction box for this neuron group.
InterceptingEventQueue - Class in org.simbrain.workspace.updater: An event queue implementing the TaskSynchronizationManager interface.
InterceptingEventQueue(Workspace) - Constructor for class org.simbrain.workspace.updater.InterceptingEventQueue: Creates a new instance for the given workspace.
interpreter - Variable in class org.simbrain.workspace.gui.SimbrainDesktop: Interpreter for terminal.
intersection(Collection, Collection) - Static method in class org.simbrain.util.Utils: Re-implementation of same method from org.apache.commons.collections.CollectionUtils.
intersectParam(Point2D, Point2D, Point2D, Point2D) - Static method in class org.simbrain.util.math.SimbrainMath: Returns the intersection parameters for two line segments.
intersects(Collection<T>, Collection<T>) - Static method in class org.simbrain.util.Utils: True if collection A has a non-empty intersection with collection B, false otherwise.
InvalidDataException - Exception in org.simbrain.network.trainers: Data has been supplied to a trainer object, or modified, in an improper way.
InvalidDataException(String) - Constructor for exception org.simbrain.network.trainers.InvalidDataException: Construct the exception.
invAtan(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: Returns the result of the inverse arctangent or tangent function.
inverf(double) - Static method in class org.simbrain.util.math.SimbrainMath: Calculates the inverse of the error function.
inverseVal(double, double, double, double) - Method in enum org.simbrain.util.math.SquashingFunction: Gives the value of the inverse of the given squashing function for some input value, a ceiling, floor, and slope.
InvertibleUpdateRule - Interface in org.simbrain.network.neuron_update_rules.interfaces: Indicates that an update rule is invertible.
invLogistic(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: Returns the results of the inverse of the standard sigmoidal (logistic) function.
invoke() - Method in interface org.simbrain.network.core.NetworkUpdateAction: Invoke this action.
invoke() - Method in class org.simbrain.network.update_actions.BufferedUpdate
invoke() - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
invoke() - Method in class org.simbrain.network.update_actions.CustomUpdate
invoke() - Method in class org.simbrain.network.update_actions.PriorityUpdate
invoke() - Method in class org.simbrain.network.update_actions.UpdateGroup
invoke() - Method in interface org.simbrain.workspace.updater.UpdateAction: Invoke this action.
invoke() - Method in class org.simbrain.workspace.updater.UpdateActionCustom: Invoke this action.
invoke() - Method in class org.simbrain.workspace.updater.UpdateAllBuffered: Invoke this action.
invoke() - Method in class org.simbrain.workspace.updater.UpdateComponent: Invoke this action.
invoke() - Method in class org.simbrain.workspace.updater.UpdateCoupling: Invoke this action.
invokeMain(String, String[]) - Static method in class org.simbrain.workspace.gui.SplashWindow: Invokes the main method of the provided class name.
invTanh(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: The inverse hyperbolic tangent given an upper and lower limit and slope for a particular value for the hyperbolic tangent before being inverted.
isActivated() - Method in class org.simbrain.world.odorworld.effectors.Speech
isActivated() - Method in class org.simbrain.world.odorworld.sensors.Hearing
isAddNoise - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: Add noise combo box.
isAddNoise() - Method in class org.simbrain.util.environment.SmellSource: Return add noise.
isAdjusting() - Method in class org.simbrain.network.gui.NetworkSelectionModel: Return true if this model will be adjusting over a series of rapid changes.
isAllClamped() - Method in class org.simbrain.network.groups.NeuronGroup: Returns true if all the neurons in this group are clamped.
isAllowSelfConnect() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
isAllowSelfConnections() - Method in class org.simbrain.network.connections.RadialSimple
isAllUnclamped() - Method in class org.simbrain.network.groups.NeuronGroup: Returns true if all the neurons in this group are unclamped.
isAutoDomain() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
isAutoFind() - Method in class org.simbrain.util.projection.ProjectCoordinate
isAutoRange() - Method in class org.simbrain.plot.barchart.BarChartModel
isAutoRange() - Method in class org.simbrain.plot.rasterchart.RasterModel
isAutoRange() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
isAutoRange() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
isBlocked() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Returns true if the entity is blocked from moving.
isBold() - Method in class org.simbrain.network.core.NetworkTextObject
isByPriority() - Method in class org.simbrain.network.subnetworks.Hopfield
isCellEditable(int, int) - Method in class org.simbrain.util.table.SimbrainDataTable
isCellEditable(int, int) - Method in class org.simbrain.util.table.SimbrainJTable
isCellEditable(int, int) - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
isCellEditable(int, int) - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
isCellEditable(int, int) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
isCellEditable(int, int) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
isClamped() - Method in class org.simbrain.network.core.Neuron
isClipped() - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
isClipped() - Method in class org.simbrain.network.neuron_update_rules.DecayRule
isClipped() - Method in class org.simbrain.network.neuron_update_rules.IACRule
isClipped() - Method in interface org.simbrain.network.neuron_update_rules.interfaces.ClippableUpdateRule: Is clipping turned on or not.
isClipped() - Method in class org.simbrain.network.neuron_update_rules.LinearRule
isClipped() - Method in class org.simbrain.network.synapse_update_rules.StaticSynapseRule: Return clipped.
isConnected(Synapse) - Method in class org.simbrain.network.core.Neuron: True if the synapse is connected to this neuron, false otherwise.
isConsistent(Collection, Class<?>, String) - Static method in class org.simbrain.network.gui.NetworkUtils: Checks to see if all the objects in a list return the same value for a method which the user provides by name.
isConsistent(Collection<T>, ParameterGetter<T, V>) - Static method in class org.simbrain.network.gui.NetworkUtils
isDead() - Method in class org.simbrain.world.odorworld.LifeCycle
isDebugEnabled() - Method in class org.simbrain.util.Logger
isDisplayPopUpMenu() - Method in class org.simbrain.util.table.SimbrainJTable
isDisplaySynapses() - Method in class org.simbrain.network.groups.SynapseGroup
isDown() - Method in class org.simbrain.util.widgets.DropDownTriangle
isDraggable() - Method in class org.simbrain.network.gui.nodes.InteractionBox
isDraggable() - Method in class org.simbrain.network.gui.nodes.NeuronNode
isDraggable() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return true if this screen element is draggable.
isDraggable() - Method in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox
isDraggable() - Method in class org.simbrain.network.gui.nodes.SynapseNode
isDraggable() - Method in class org.simbrain.network.gui.nodes.TextNode
isDraggable() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
isDrawOutline() - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
isEditable() - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
isEffectorsEnabled() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
isEmpty() - Method in class org.simbrain.network.core.Network: Returns true if all objects are gone from this network.
isEmpty() - Method in class org.simbrain.network.groups.Group: Whether this group is empty or not.
isEmpty() - Method in class org.simbrain.network.groups.NeuronGroup
isEmpty() - Method in class org.simbrain.network.groups.Subnetwork
isEmpty() - Method in class org.simbrain.network.groups.SynapseGroup: Whether this group is empty or not.
isEmpty() - Static method in class org.simbrain.network.gui.Clipboard
isEmpty() - Method in class org.simbrain.network.gui.NetworkSelectionModel: Return true if the selection is empty.
isEmpty() - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Return true if this sensor selection model is empty.
isEnabled() - Method in class org.simbrain.network.core.Synapse: Whether this synapse is enabled or not.
isEnabled(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
isEnabled() - Method in class org.simbrain.util.SwitchableActionListener
isEnabled() - Method in class org.simbrain.util.SwitchableChangeListener
isEnabled() - Method in class org.simbrain.util.SwitchablePropertyChangeListener
isEqualizeEfferents() - Method in class org.simbrain.network.connections.Sparse
isFillBackground() - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
isFireUpdates() - Method in class org.simbrain.network.core.Network
isFixedWidth() - Method in class org.simbrain.plot.rasterchart.RasterModel
isFixedWidth() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
isFrozen() - Method in class org.simbrain.network.core.Synapse
isFrozen(SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
isGenerator() - Method in class org.simbrain.network.core.Neuron
isGrouped() - Method in class org.simbrain.network.gui.nodes.ScreenElement
isGuiOn() - Method in class org.simbrain.network.gui.NetworkPanel
isGuiOn() - Method in class org.simbrain.workspace.WorkspaceComponent
isHebbian() - Method in class org.simbrain.network.synapse_update_rules.STDPRule
isInBoundsX(float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Check whether, if the provided point is used to set the x (upper left) coordinate of the entity, the bounds of the object will be in bounds.
isInBoundsY(float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Check whether, if the provided point is used to set the y (upper left) coordinate of the entity, the bounds of the object will be in bounds.
isInputMode() - Method in class org.simbrain.network.groups.NeuronGroup
isItalic() - Method in class org.simbrain.network.core.NetworkTextObject
isIterable() - Method in class org.simbrain.util.projection.ProjectionMethod: Convenience method to determine if instances of this are instances of IterableProjectionMethod.
isIterationMode() - Method in class org.simbrain.util.table.NumericTable
isLinked() - Method in class org.simbrain.util.widgets.LinkIcon
isMacOSX() - Static method in class org.simbrain.util.Utils: Determines whether the system is a Mac os x.
isManualColumns() - Method in class org.simbrain.network.layouts.GridLayout
isManualColumns() - Method in class org.simbrain.network.layouts.HexagonalGridLayout
isMarkedForDeletion() - Method in class org.simbrain.network.groups.Group
isMouseover() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return true if the mouse is over this sensor node.
isMultiFlag() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple
isNoiseAdded() - Method in class org.simbrain.network.trainers.LMSOffline
isNull() - Method in class org.simbrain.util.widgets.TristateDropDown: Determines if value is null.
isObjectsBlockMovement() - Method in class org.simbrain.world.odorworld.OdorWorld
isometricView() - Method in class org.simbrain.world.visionworld.VisionWorld: Switch to the isometric view.
IsometricViewAction - Class in org.simbrain.world.visionworld.action: Isometric view action.
IsometricViewAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.IsometricViewAction: Create a new isometric view action.
isPermitDensityEditing() - Method in class org.simbrain.network.connections.Sparse
isPolarized() - Method in class org.simbrain.network.core.Neuron: If the neuron is polarized, it will be excitatory or inhibitory.
isRecordAsSpikes() - Method in class org.simbrain.network.groups.NeuronGroup
isRecording() - Method in class org.simbrain.network.groups.NeuronGroup
isRecurrent() - Method in class org.simbrain.network.groups.SynapseGroup: Check whether this synapse group connects a neuron group to itself.
isRecurrentConnection() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
isReplace() - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Are we replacing rules or editing them? Replacing happens when AbstractNeuronRulePanel.commitChanges(List) is called on a neuron panel whose rule is different from the rules of the neurons being edited.
isReplace() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Are we replacing rules or editing them? Replacing happens when AbstractSpikeResponsePanel.commitChanges(Collection) is called on a synapse panel whose rule is different from the rules of the synapses being edited.
isReplace() - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Are we replacing rules or editing them? Replacing happens when AbstractSynapseRulePanel.commitChanges(Collection) is called on a synapse panel whose rule is different from the rules of the synapses being edited.
isRidgeRegression() - Method in class org.simbrain.network.trainers.LMSOffline
isRunning() - Method in class org.simbrain.network.gui.NetworkPanel
isRunning() - Method in class org.simbrain.plot.projection.ProjectionModel
isRunning() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Returns whether the updater is set to run.
isSelectable() - Method in class org.simbrain.network.gui.nodes.InteractionBox
isSelectable() - Method in class org.simbrain.network.gui.nodes.NeuronNode
isSelectable() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return true if this screen element is selectable.
isSelectable() - Method in class org.simbrain.network.gui.nodes.SynapseNode
isSelectable() - Method in class org.simbrain.network.gui.nodes.TextNode
isSelectable() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
isSelected(Object) - Method in class org.simbrain.network.gui.NetworkPanel: Return true if the specified element is selected.
isSelected(Object) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Return true if the specified element is selected.
isSelected() - Method in class org.simbrain.util.widgets.TristateDropDown: Determines if index is selected true.
isSelected() - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Return true if this sensor node is selected.
isSelected(Sensor) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Return true if the specified sensor is selected.
isSelection() - Method in class org.simbrain.network.gui.EditMode: Return true if this edit mode is SELECTION.
isSelectionEmpty() - Method in class org.simbrain.network.gui.NetworkPanel: Return true if the selection is empty.
isSelfConnectionAllowed() - Method in class org.simbrain.network.connections.AllToAll
isSelfConnectionAllowed() - Method in class org.simbrain.network.connections.Sparse
isSensorsEnabled() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
isShowHistory() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
isShowSensors() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
isSkipsSynapticUpdates() - Method in class org.simbrain.network.core.NeuronUpdateRule
isSkipsSynapticUpdates() - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
isSpike() - Method in class org.simbrain.network.core.Neuron
isSpikingNeuron() - Method in class org.simbrain.network.core.NeuronUpdateRule
isSpikingNeuron() - Method in class org.simbrain.network.core.SpikingNeuronUpdateRule: A helper method which identifies this and all subclasses as variations of spiking neurons.
isSpikingNeuronGroup() - Method in class org.simbrain.network.groups.NeuronGroup
isText() - Method in class org.simbrain.network.gui.EditMode: Return true if this edit mode is TEXT.
isTheBool() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
isTopLevelGroup() - Method in class org.simbrain.network.groups.Group: Returns true if this group is "top level" (has no parent group).
isTraceEnabled() - Method in class org.simbrain.util.Logger
isUnique(DataPoint, double) - Method in class org.simbrain.util.projection.NTree: Checks whether the given point already exists in the tree with the specified tolerance.
isUpdateCompleted() - Method in class org.simbrain.network.core.Network: Used by Network thread to ensure that an update cycle is complete before updating again.
isUpdateCompleted() - Method in class org.simbrain.network.trainers.CompetitiveTrainer
isUpdateCompleted() - Method in class org.simbrain.network.trainers.IterableTrainer
isUpdateCompleted() - Method in class org.simbrain.network.trainers.SOMTrainer
isUpdateCompleted() - Method in class org.simbrain.plot.projection.ProjectionModel: Swing update flag.
isUseApplyButton() - Method in class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel
isUseBidirectionalConnections() - Method in class org.simbrain.network.connections.OneToOne
isUseExcitatoryRandomization() - Method in class org.simbrain.network.connections.QuickConnectionManager
isUseFullRepOnSave() - Method in class org.simbrain.network.groups.SynapseGroup
isUseGroupLevelSettings() - Method in class org.simbrain.network.groups.SynapseGroup
isUseInhibitoryRandomization() - Method in class org.simbrain.network.connections.QuickConnectionManager
isUseRandom() - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
isUseSubSampling() - Static method in class org.simbrain.network.groups.NeuronGroup
isUseSuperclass() - Method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor
isValidData() - Method in class org.simbrain.util.StandardDialog: This method is used to validate the current dialog box.
isVisible() - Method in class org.simbrain.workspace.AttributeType
isWand() - Method in class org.simbrain.network.gui.EditMode: Return true if this edit mode is WAND.
isWorkAvailable() - Method in class org.simbrain.network.update_actions.concurrency_tools.SynchronizationPoint
IterableProjectionMethod - Class in org.simbrain.util.projection: IterableProjectionMethod extends projection method and provides tools for iterating a projection method.
IterableProjectionMethod(Projector) - Constructor for class org.simbrain.util.projection.IterableProjectionMethod: Construct the projection method.
IterableRowsTable - Interface in org.simbrain.util.table: Interface for tables (subclasses of SimbrainJTable) that have concept of "current row" implemented which allows the table to iterated from row to row when updated.
IterableTrainer - Class in org.simbrain.network.trainers: Superclass for all types of trainer which can be iterated and which return an error when they are iterated.
IterableTrainer(Trainable) - Constructor for class org.simbrain.network.trainers.IterableTrainer: Construct the iterable trainer.
IterableTrainer.StoppingCondition - Enum in org.simbrain.network.trainers: Stopping condition.
iterate() - Method in class org.simbrain.network.trainers.IterableTrainer: Iterate the training algorithm and stop iteration based on the selected stopping condition.
iterate() - Method in class org.simbrain.util.projection.IterableProjectionMethod: Iterate, if it is iterable.
iterate() - Method in class org.simbrain.util.projection.Projector: Iterate the dataset once.
iterate() - Method in class org.simbrain.util.projection.ProjectSammon
iterate(int) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Iterate the updater for a specified number of iterations.
iterate(CountDownLatch, int) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Iterate a set number of iterations against a latch.
iterate() - Method in class org.simbrain.workspace.Workspace: Update the workspace a single time.
iterate(int) - Method in class org.simbrain.workspace.Workspace: Iterate for a specified number of steps.
iterate(CountDownLatch, int) - Method in class org.simbrain.workspace.Workspace: Iterated for a specified number of iterations using a latch.
iterate(CountDownLatch) - Method in class org.simbrain.workspace.Workspace: Iterate using a latch, which is counted down after the iteration completes.
iterateBtn - Variable in class org.simbrain.plot.projection.ProjectionGui: Iterate once.
IterateNetworkAction - Class in org.simbrain.network.gui.actions.network: Iterate network action.
IterateNetworkAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.network.IterateNetworkAction: Create a new iterate network action with the specified network panel.
IterativeControlsPanel - Class in org.simbrain.network.gui.trainer: The main controller panel for iterative learning, with buttons etc.
IterativeControlsPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.trainer.IterativeControlsPanel: Construct the panel with no trainer.
IterativeControlsPanel(NetworkPanel, IterableTrainer) - Constructor for class org.simbrain.network.gui.trainer.IterativeControlsPanel: Construct the panel with a trainer specified.
IterativeTrainingPanel - Class in org.simbrain.network.gui.trainer: Combines an iterative control panel and training set panel to provide the primary access point for training neural networks using iterative methods.
IterativeTrainingPanel(NetworkPanel, IterableTrainer) - Constructor for class org.simbrain.network.gui.trainer.IterativeTrainingPanel: Construct a rule chooser panel.
iterator() - Method in class org.simbrain.util.projection.NTree: Returns an iterator over this tree
iterator() - Method in class org.simbrain.workspace.gui.couplingmanager.GenericListModel: The Iterator for the items in the model.
iterator() - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Return an iterator over the selected sensors.
IzhikevichRule - Class in org.simbrain.network.neuron_update_rules: IzhikevichNeuron.
IzhikevichRule() - Constructor for class org.simbrain.network.neuron_update_rules.IzhikevichRule
IzhikevichRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: IzhikevichNeuronPanel.
IzhikevichRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.IzhikevichRulePanel: Creates an instance of this panel.

J

JMultiLineToolTip - Class in org.simbrain.util
JMultiLineToolTip() - Constructor for class org.simbrain.util.JMultiLineToolTip
JumpAndDecay - Class in org.simbrain.network.synapse_update_rules.spikeresponders: JumpAndDecay.
JumpAndDecay() - Constructor for class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
JumpAndDecayPanel - Class in org.simbrain.network.gui.dialogs.synapse.spike_responders: JumpAndDecayPanel.
JumpAndDecayPanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: This method is the default constructor.

K

KeyBindings - Class in org.simbrain.network.gui: Add key bindings to network panel.
KeyBindings() - Constructor for class org.simbrain.network.gui.KeyBindings
keyPressed(KeyEvent) - Method in class org.simbrain.workspace.gui.WorkspaceKeyAdapter: Responds to key pressed events.
keyPressed(KeyEvent) - Method in class org.simbrain.world.odorworld.OdorWorldPanel: Task to perform when keyboard button is pressed.
keyReleased(KeyEvent) - Method in class org.simbrain.world.odorworld.OdorWorldPanel: Task to perform when keyboard button is released.
keyTyped(KeyEvent) - Method in class org.simbrain.world.odorworld.OdorWorldPanel: Task to perform when keyboard button is typed.
KL_Divergence(Distribution, double[][]) - Static method in enum org.simbrain.util.math.ProbDistribution: The Kullback-Leibler divergence between some distribution and a set of observations.
KWTA - Class in org.simbrain.network.subnetworks: KwtaNetwork implements a k Winner Take All network.
KWTA(Network, int) - Constructor for class org.simbrain.network.subnetworks.KWTA: Default constructor.
KWTA.PointNeuronComparator - Class in org.simbrain.network.subnetworks: Used to sort PointNeurons by excitatory conductance.
KwtaCreationDialog - Class in org.simbrain.network.gui.dialogs.network: KwtaDialog is used as an assistant to create Kwta networks.
KwtaCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.KwtaCreationDialog: This method is the default constructor.
KwtaPropertiesDialog - Class in org.simbrain.network.gui.dialogs.network: WkTAPropertiesDialog is a dialog box for setting the properties of a k-winner take all network.
KwtaPropertiesDialog(KWTA) - Constructor for class org.simbrain.network.gui.dialogs.network.KwtaPropertiesDialog: Default constructor.

L

labelChanged(NetworkEvent<Neuron>) - Method in class org.simbrain.network.listeners.NeuronAdapter
labelChanged(NetworkEvent<Neuron>) - Method in interface org.simbrain.network.listeners.NeuronListener: Notify this listener of a text labelchanged event.
labelChanged(NetworkEvent<Neuron>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
LabelledItem - Class in org.simbrain.util.widgets: Simple utility for making rows with a label and a component.
LabelledItem(String, JComponent) - Constructor for class org.simbrain.util.widgets.LabelledItem: Construct the labelled item.
LabelledItemPanel - Class in org.simbrain.util: LabelledItemPanel provides a panel for laying out labeled elements neatly with all the labels and elements aligned down the screen.
LabelledItemPanel() - Constructor for class org.simbrain.util.LabelledItemPanel: This method is the default constructor.
LabelledItemPanel - Class in org.simbrain.util.propertyeditor.gui: LabelledItemPanel provides a panel for laying out labelled elements neatly with all the labels and elements aligned down the screen.
LabelledItemPanel() - Constructor for class org.simbrain.util.propertyeditor.gui.LabelledItemPanel: This method is the default constructor.
lastCharNL - Static variable in class org.simbrain.console.CommandLineReader
LatchCompletionSignal - Class in org.simbrain.workspace.updater: Signal implementation that wraps a count-down latch.
LatchCompletionSignal(CountDownLatch) - Constructor for class org.simbrain.workspace.updater.LatchCompletionSignal: Creates a new instance with the given latch.
LatchCompletionSignal(int) - Constructor for class org.simbrain.workspace.updater.LatchCompletionSignal: Creates a new instance which waits for a single done call.
LatchCompletionSignal() - Constructor for class org.simbrain.workspace.updater.LatchCompletionSignal: Creates a new instance which waits for a single done call.
LayerCreationPanel(HashMap<String, NeuronUpdateRule>, String, int) - Constructor for class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel.LayerCreationPanel: Construct a layer creation panel.
LayerCreationPanel(String, int) - Constructor for class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel.LayerCreationPanel: Construct a layer creation panel using default neuron types.
LayeredNetworkCreationPanel - Class in org.simbrain.network.gui.dialogs.network: Panel for creating a feed-forward layered network.
LayeredNetworkCreationPanel(int, Window) - Constructor for class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel: Constructs a labeled item panel dialog for the creation of a simple recurrent network.
LayeredNetworkCreationPanel.LayerCreationPanel - Class in org.simbrain.network.gui.dialogs.network: JPanel which contains information about one layer of a layered network.
layout - Variable in class org.simbrain.network.gui.dialogs.layout.AbstractLayoutPanel: The layout object represented by this panel.
layout(Point2D, Point2D) - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow: Lays out the arrow(s) between the two specified points.
layout(Point2D, Point2D) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
layout(Point2D, Point2D) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
Layout - Interface in org.simbrain.network.layouts: Interface for all neuron layout managers, which arrange a set of neurons in different ways.
layout - Variable in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: The layout.
layoutChildren() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Override PNode layoutChildren method in order to properly set the positions of children nodes.
layoutChildren() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Override pnode layoutChildren to get objects placed in correct spots.
layoutChildren() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional: Override PNode layoutChildren method in order to properly set the positions of children nodes.
layoutChildren() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeRecurrent
layoutChildren() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple: Override PNode layoutChildren method in order to properly set the positions of children nodes.
layoutChildren() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeVisible: Override PNode layoutChildren method in order to properly set the positions of children nodes.
layoutChildren(Point2D, NeuronGroupNode.Port, Point2D, NeuronGroupNode.Port) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
layoutChildrenQuiet(Point2D, Point2D) - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow: Lays out the child nodes of the class implementing this interface in a way that expressly ensures that layoutChildren() will not be called concurrently until this method has fully completed.
layoutChildrenQuiet(Point2D, Point2D) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
layoutChildrenQuiet(Point2D, Point2D) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
LayoutDialog - Class in org.simbrain.network.gui.dialogs.layout: LayoutPanel allows the user to define the layout of a network.
LayoutDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.layout.LayoutDialog: Constructor for creating dialog.
LayoutDialog(Layout, NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.layout.LayoutDialog: Constructor for creating independent dialog.
layoutNetwork() - Method in class org.simbrain.network.subnetworks.CompetitiveNetwork: Set the layout of the network.
layoutNetwork() - Method in class org.simbrain.network.subnetworks.SOMNetwork: Set the layout of the network.
layoutNeurons(List<Neuron>) - Method in class org.simbrain.network.layouts.GridLayout: Layout a list of neurons.
layoutNeurons(List<Neuron>) - Method in class org.simbrain.network.layouts.HexagonalGridLayout
layoutNeurons(List<Neuron>) - Method in interface org.simbrain.network.layouts.Layout: Layout a list of neurons.
layoutNeurons(List<Neuron>) - Method in class org.simbrain.network.layouts.LineLayout
layoutPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
LEARNING_RATE_DEFAULT - Static variable in class org.simbrain.network.synapse_update_rules.STDPRule: Default Learning rate.
learningRate - Variable in class org.simbrain.network.synapse_update_rules.STDPRule: General learning rate.
LEFT - Static variable in class org.simbrain.world.odorworld.effectors.Turning: Direction value to turn left.
LifeCycle - Class in org.simbrain.world.odorworld: Manage the lifecycle of an entity that can come into and go out of existence.
LifeCycle(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.LifeCycle
LinearRule - Class in org.simbrain.network.neuron_update_rules: LinearNeuron is a standard linear neuron.
LinearRule() - Constructor for class org.simbrain.network.neuron_update_rules.LinearRule
LinearRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: LinearNeuronPanel.
LinearRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.LinearRulePanel: Creates an instance of this panel.
LineLayout - Class in org.simbrain.network.layouts: Lay neurons out in a line.
LineLayout(double, LineLayout.LineOrientation) - Constructor for class org.simbrain.network.layouts.LineLayout: Create a layout.
LineLayout(double, double, double, LineLayout.LineOrientation) - Constructor for class org.simbrain.network.layouts.LineLayout: Create a line layout with all values specified.
LineLayout() - Constructor for class org.simbrain.network.layouts.LineLayout: Default Constructor.
LineLayout.LineOrientation - Enum in org.simbrain.network.layouts: Orientation of the line.
LineLayoutPanel - Class in org.simbrain.network.gui.dialogs.layout: LayoutPanel allows the user to define the layout of a network.
LineLayoutPanel(LineLayout) - Constructor for class org.simbrain.network.gui.dialogs.layout.LineLayoutPanel: Default constructor.
LinkIcon - Class in org.simbrain.util.widgets: This class consists of a graphical lock that when clicked changes to an open lock and back to a locked lock when clicked again.
LinkIcon(boolean) - Constructor for class org.simbrain.util.widgets.LinkIcon: Create a lock icon either in the locked or unlocked state.
listener - Variable in class org.simbrain.workspace.gui.WorkspaceChangedDialog
listeners - Variable in class org.simbrain.world.game.tictactoe.TicTacToeModel
LMSCreationDialog - Class in org.simbrain.network.gui.dialogs.network: LMSDialog is a dialog box for creating an LMS network.
LMSCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.LMSCreationDialog: This method is the default constructor.
LMSEditorDialog - Class in org.simbrain.network.gui.dialogs.network: LMSEditorDialog is a dialog box for editing a LMS network.
LMSEditorDialog(NetworkPanel, LMSNetwork) - Constructor for class org.simbrain.network.gui.dialogs.network.LMSEditorDialog: Default constructor.
LMSIterative - Class in org.simbrain.network.trainers: Train using least mean squares.
LMSIterative(Trainable) - Constructor for class org.simbrain.network.trainers.LMSIterative: Construct a least mean squares iterative panel.
LMSNetwork - Class in org.simbrain.network.subnetworks: A Least Mean Squares network.
LMSNetwork(Network, int, int, Point2D) - Constructor for class org.simbrain.network.subnetworks.LMSNetwork: Construct a new LMS Network.
LMSNetworkNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of a group of a LMS network.
LMSNetworkNode(NetworkPanel, LMSNetwork) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.LMSNetworkNode: Create a layered network.
LMSOffline - Class in org.simbrain.network.trainers: Offline/Batch Learning with least mean squares.
LMSOffline(Trainable) - Constructor for class org.simbrain.network.trainers.LMSOffline: Construct the LMSOOffline object, with a trainable network the Synapse group where the new synapses will be placed.
LMSOffline.SolutionType - Enum in org.simbrain.network.trainers: Solution methods for offline LMS.
LMSOfflineControlPanel - Class in org.simbrain.network.gui.trainer.subnetworkTrainingPanels: Control panel (buttons etc.) for least mean squares offline trainers.
LMSOfflineControlPanel(Window) - Constructor for class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel: Build the panel.
LMSOfflineControlPanel(LMSOffline, Window) - Constructor for class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel: Build the panel.
LMSOfflineTrainingPanel - Class in org.simbrain.network.gui.trainer.subnetworkTrainingPanels: Combines an LMS Offline control panel and training set panel to provide the primary access point for training neural networks using offline least mean squares.
LMSOfflineTrainingPanel(NetworkPanel, LMSOffline, Window) - Constructor for class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineTrainingPanel: Build the panel.
LoadNeuronScriptAction - Class in org.simbrain.network.gui.actions.neuron: :oad custom update script.
LoadNeuronScriptAction(Neuron) - Constructor for class org.simbrain.network.gui.actions.neuron.LoadNeuronScriptAction: Load a custom neuron script.
loadStimulusVectors(double[][]) - Method in class org.simbrain.world.odorworld.OdorWorld: Use the provided set of vectors (stored as a 2-d array of doubles, one vector per row) to set the stimulus vectors on all odor world entities, in the order in which they are stored in the internal list (which should match the order in which they were added to the world).
loadTokenDictionary(String[][]) - Method in class org.simbrain.world.textworld.TextWorld: Reset the dictionary (e.g.
loadTokenToVectorDict(String[][]) - Method in class org.simbrain.world.textworld.ReaderWorld: Loads a vector to token dictionary.
loadVectorToTokenDict(String[][]) - Method in class org.simbrain.world.textworld.DisplayWorld: Loads a new vector to token dictionary stored as a matrix of Strings.
LOCAL_FORMATTER - Static variable in class org.simbrain.util.SimbrainConstants: Convenience constant referring to current Locale.
log10of2 - Static variable in class org.simbrain.util.math.SimbrainMath
log2(double) - Static method in class org.simbrain.util.math.SimbrainMath
LOGGER - Variable in class org.simbrain.network.gui.actions.network.IterateNetworkAction
Logger - Class in org.simbrain.util: A (hackish?) way to remove remove dependency on log4j in jar files.
Logger() - Constructor for class org.simbrain.util.Logger
logger - Variable in class org.simbrain.util.projection.Dataset: Logger.
LOGGER - Static variable in class org.simbrain.workspace.updater.UpdateAllBuffered: The static logger for the class.
LOGGER - Static variable in class org.simbrain.workspace.updater.WorkspaceUpdater: The static logger for the class.
logistic(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: The logistic function given an upper and lower limit and slope for a particular value.
LogisticGeneratorPanel - Class in org.simbrain.network.gui.dialogs.neuron.generator_panels: LogisticNeuronPanel TODO: Work into new Input Generator Framework, currently no implementation.
LogisticGeneratorPanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.generator_panels.LogisticGeneratorPanel: Creates an instance of this panel.
LogisticRule - Class in org.simbrain.network.neuron_update_rules.activity_generators: LogisticNeuron updates using the logistic equation, which is chaotic for the default growth rate.
LogisticRule(LogisticRule, Neuron) - Constructor for class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
LogisticRule() - Constructor for class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
LogSTDPRule - Class in org.simbrain.network.synapse_update_rules: An implementation of Log-STDP as introduced in: Gilson M, Fukai T (2011) Stability versus Neuronal Specialization for STDP: Long-Tail Weight Distributions Solve the Dilemma.
LogSTDPRule() - Constructor for class org.simbrain.network.synapse_update_rules.LogSTDPRule
lower - Variable in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: The output lower bound.
lowerBound - Variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: The lower bound of the activity if clipping is used.
lowerBound - Variable in class org.simbrain.util.randomizer.Randomizer: Lower bound of the random distribution.

M

MACHEPS - Static variable in class org.simbrain.util.math.Matrices: The difference between 1 and the smallest exactly representable number greater than one.
main(String[]) - Static method in class org.simbrain.console.CommandLineReader
main(String[]) - Static method in class org.simbrain.network.gui.dialogs.connect.ConnectionPanel: Test the connection panel.
main(String[]) - Static method in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog: Main function to test dialog.
main(String[]) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel
main(String[]) - Static method in class org.simbrain.network.gui.NeuronGroupSelectionPanel
main(String[]) - Static method in class org.simbrain.network.gui.trainer.IterativeTrainingPanel: Test method for GUI layout.
main(String[]) - Static method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel
main(String[]) - Static method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate: Test main to demonstrate performance improvements over serial updates without a GUI.
main(String[]) - Static method in class org.simbrain.network.util.io_utilities.GroupSerializer: Test Main
main(String[]) - Static method in class org.simbrain.util.math.SimbrainMath: Test randPermuteWithExclusion.
main(String[]) - Static method in class org.simbrain.util.propertyeditor.gui.TestObject: Simple test routine.
main(String[]) - Static method in class org.simbrain.util.randomizer.gui.RandomizerPanel
main(String[]) - Static method in class org.simbrain.util.widgets.DropDownTriangle
main(String[]) - Static method in class org.simbrain.workspace.gui.SimbrainDesktop: Simbrain main method.
main(String[]) - Static method in class org.simbrain.workspace.gui.Splasher: Shows the splash screen, launches the application and then disposes the splash screen.
MainLayoutPanel - Class in org.simbrain.network.gui.dialogs.layout: All the functions of a layout selector in one panel.
MainLayoutPanel(Window) - Constructor for class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Creates the main layout panel with default values.
MainLayoutPanel(boolean, Window) - Constructor for class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Creates the main layout panel with default initially selected layout, but where the reveal option can be set.
MainLayoutPanel(Layout, boolean, Window) - Constructor for class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Creates the main layout panel.
mainPanel - Variable in class org.simbrain.network.gui.dialogs.connect.AbstractConnectionPanel: Main panel.
mainTab - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: Main tab.
makeConnections() - Method in class org.simbrain.network.groups.SynapseGroup: The "build" method which actually constructs the group in terms of populating it with synapses.
masterLayout() - Method in class org.simbrain.util.widgets.ApplyPanel: Lay out the panel.
Matrices - Class in org.simbrain.util.math
Matrices() - Constructor for class org.simbrain.util.math.Matrices
matrix - Variable in class org.simbrain.world.threedee.sensors.Sight
max(int, int) - Static method in class org.simbrain.util.math.SimbrainMath: Return the greater of two integers.
max(double[], double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Finds the longer of two arrays.
MAX - Static variable in class org.simbrain.util.projection.NTree: The number of elements to allow in a leaf before splitting
mean - Variable in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
median - Variable in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
MidiWorld - Class in org.simbrain.world.midiworld: MIDI world.
MidiWorld() - Constructor for class org.simbrain.world.midiworld.MidiWorld: Create a new MIDI world.
midpoint(Point2D, Point2D) - Method in interface org.simbrain.network.gui.nodes.SynapseGroupArrow: Returns the midpoint for for
midpoint(Point2D, Point2D) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional: Returns the midpoint for for
midpoint(Point2D, Point2D) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
midpoint(Point2D, Point2D) - Static method in class org.simbrain.util.math.SimbrainMath
mirror(Dataset) - Method in class org.simbrain.util.projection.Dataset: Makes this dataset a copy of the passed in dataset.
modelCleared(NetworkEvent) - Method in class org.simbrain.network.gui.NetworkPanel
modifyRowsColumns(int, int, T) - Method in class org.simbrain.util.table.MutableTable: Adds or removes rows (from the bottom) and columns (from the left).
moorePenroseSolution(Trainable) - Method in class org.simbrain.network.trainers.LMSOffline: Moore penrose.
MorrisLecarRule - Class in org.simbrain.network.neuron_update_rules
MorrisLecarRule() - Constructor for class org.simbrain.network.neuron_update_rules.MorrisLecarRule
mouseClicked(PInputEvent) - Method in class org.simbrain.network.gui.DragEventHandler
mouseClicked(PInputEvent) - Method in class org.simbrain.network.gui.WandEventHandler
mouseClicked(MouseEvent) - Method in class org.simbrain.util.widgets.DropDownTriangle
mouseClicked(MouseEvent) - Method in class org.simbrain.util.widgets.LinkIcon
mouseClicked(MouseEvent) - Method in class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel
mouseClicked(PInputEvent) - Method in class org.simbrain.world.visionworld.SelectionEventHandler
mouseEntered(PInputEvent) - Method in class org.simbrain.network.gui.nodes.ToolTipTextUpdater
mouseEntered(MouseEvent) - Method in class org.simbrain.util.widgets.DropDownTriangle
mouseEntered(MouseEvent) - Method in class org.simbrain.util.widgets.LinkIcon
mouseEntered(MouseEvent) - Method in class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel
mouseExited(PInputEvent) - Method in class org.simbrain.network.gui.nodes.ToolTipTextUpdater
mouseExited(MouseEvent) - Method in class org.simbrain.util.widgets.DropDownTriangle
mouseExited(MouseEvent) - Method in class org.simbrain.util.widgets.LinkIcon
mouseExited(MouseEvent) - Method in class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel
mousePressed(PInputEvent) - Method in class org.simbrain.network.gui.ContextMenuEventHandler
mousePressed(PInputEvent) - Method in class org.simbrain.network.gui.DragEventHandler
mousePressed(PInputEvent) - Method in class org.simbrain.network.gui.TextEventHandler
mousePressed(PInputEvent) - Method in class org.simbrain.network.gui.WandEventHandler
mousePressed(MouseEvent) - Method in class org.simbrain.util.widgets.DropDownTriangle
mousePressed(MouseEvent) - Method in class org.simbrain.util.widgets.LinkIcon
mousePressed(MouseEvent) - Method in class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel
mousePressed(PInputEvent) - Method in class org.simbrain.world.visionworld.SelectionEventHandler
mouseReleased(PInputEvent) - Method in class org.simbrain.network.gui.ContextMenuEventHandler
mouseReleased(MouseEvent) - Method in class org.simbrain.util.widgets.DropDownTriangle
mouseReleased(MouseEvent) - Method in class org.simbrain.util.widgets.LinkIcon
mouseReleased(MouseEvent) - Method in class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel
mouseReleased(PInputEvent) - Method in class org.simbrain.world.visionworld.SelectionEventHandler
moveEast(double) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Move the object east by the specified amount in pixels.
moveNorth(double) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Move the object north by the specified amount in pixels.
moveSouth(double) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Move the object south by the specified amount in pixels.
moveWest(double) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Move the object west by the specified amount in pixels.
MultiLineToolTipUI - Class in org.simbrain.util
MultiLineToolTipUI() - Constructor for class org.simbrain.util.MultiLineToolTipUI
multVector(double[], double) - Static method in class org.simbrain.util.math.SimbrainMath: Finds the entry-wise product of a vector and scalar.
MutableTable<T> - Class in org.simbrain.util.table: Superclass for tables which can be modified.
MutableTable() - Constructor for class org.simbrain.util.table.MutableTable
MutableVisionWorldModel - Class in org.simbrain.world.visionworld: Mutable implementation of VisionWorldModel.
MutableVisionWorldModel() - Constructor for class org.simbrain.world.visionworld.MutableVisionWorldModel: Create a new mutable vision world model.
MutableVisionWorldModel(PixelMatrix, SensorMatrix) - Constructor for class org.simbrain.world.visionworld.MutableVisionWorldModel: Create a new immutable vision world model with the specified pixel matrix and sensor matrix.
MyGlassPane() - Constructor for class org.simbrain.workspace.actions.OpenCouplingListAction.MyGlassPane
MyHighlightPainter(Color) - Constructor for class org.simbrain.world.textworld.ReaderPanel.MyHighlightPainter: Sets the color of highlighter.

N

NakaRushtonRule - Class in org.simbrain.network.neuron_update_rules: NakaRushtonNeuron is a firing-rate based neuron which is intended to model spike rates of real neurons.
NakaRushtonRule() - Constructor for class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Default constructor.
NakaRushtonRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: NakaRushtonNeuronPanel.
NakaRushtonRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Creates a new Naka-Rushton neuron panel.
needsReInit() - Method in class org.simbrain.util.projection.IterableProjectionMethod
Network - Class in org.simbrain.network.core: Network provides core neural network functionality and is the the main API for external calls.
Network() - Constructor for class org.simbrain.network.core.Network: Used to create an instance of network (Default constructor).
network - Variable in class org.simbrain.network.trainers.Trainer: The trainable object to be trained.
Network.PriorityComparator - Class in org.simbrain.network.core: Comparator for sorting neurons by update priority.
Network.TimeType - Enum in org.simbrain.network.core: Two types of time used in simulations.
NetworkActionManager - Class in org.simbrain.network.gui: Network action manager.
NetworkActionManager(NetworkPanel) - Constructor for class org.simbrain.network.gui.NetworkActionManager: Create a new network action manager for the specified network panel.
NetworkAdapter - Class in org.simbrain.network.listeners: Adapter class for NeuronListener.
NetworkAdapter() - Constructor for class org.simbrain.network.listeners.NetworkAdapter
NetworkComponent - Class in org.simbrain.network: Network component.
NetworkComponent(String) - Constructor for class org.simbrain.network.NetworkComponent: Create a new network component.
NetworkComponent(String, Network) - Constructor for class org.simbrain.network.NetworkComponent: Create a new network component.
networkCreationPanel - Variable in class org.simbrain.network.gui.dialogs.network.FeedForwardCreationDialog: Main network creation panel.
NetworkDesktopComponent - Class in org.simbrain.network.desktop: Network desktop component.
NetworkDesktopComponent(GenericFrame, NetworkComponent) - Constructor for class org.simbrain.network.desktop.NetworkDesktopComponent: Create a new network frame.
NetworkDialog - Class in org.simbrain.network.gui.dialogs: NetworkDialog is a dialog box for setting the properties of the Network GUI.
NetworkDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.NetworkDialog: This method is the default constructor.
NetworkEvent<T> - Class in org.simbrain.network.listeners: Network event which holds an old and new version of some type of object.
NetworkEvent(Network, T, T) - Constructor for class org.simbrain.network.listeners.NetworkEvent: Create a network event with a new and old object.
NetworkEvent(Network, T) - Constructor for class org.simbrain.network.listeners.NetworkEvent: Create a network event with one object only.
NetworkHierarchyPanel - Class in org.simbrain.network.gui: Displays the hierarchy of neurons, synapses and groups in a network in a Tree View.
NetworkHierarchyPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.NetworkHierarchyPanel: Construct the panel.
NetworkLayoutManager - Class in org.simbrain.network.util: A package for laying out neurons and groups with respect to each other.
NetworkLayoutManager() - Constructor for class org.simbrain.network.util.NetworkLayoutManager
NetworkLayoutManager.Direction - Enum in org.simbrain.network.util: Directions.
NetworkListener - Interface in org.simbrain.network.listeners: Listener interface for receiving general network events.
NetworkMenuBar - Class in org.simbrain.network.gui: Menu bar that appears inside of JPanel; for use in Applets.
NetworkMenuBar() - Constructor for class org.simbrain.network.gui.NetworkMenuBar
networkPanel - Variable in class org.simbrain.network.gui.actions.ConditionallyEnabledAction: Network panel.
networkPanel - Variable in class org.simbrain.network.gui.dialogs.network.FeedForwardCreationDialog: Network panel.
networkPanel - Variable in class org.simbrain.network.gui.dialogs.network.SupervisedTrainingDialog: Network panel.
networkPanel - Variable in class org.simbrain.network.gui.dialogs.NetworkDialog: Network panel.
networkPanel - Variable in class org.simbrain.network.gui.dialogs.NetworkPropertiesPanel: Network panel.
NetworkPanel - Class in org.simbrain.network.gui: Contains a piccolo PCanvas that maintains a visual representation of the network.
NetworkPanel(Network) - Constructor for class org.simbrain.network.gui.NetworkPanel: Create a new Network panel.
networkPanel - Variable in class org.simbrain.network.gui.nodes.SynapseGroupNode: Parent network panel.
NetworkPanelDesktop - Class in org.simbrain.network.desktop: Extension of Network Panel with functions used in a desktop setting.
NetworkPanelDesktop(NetworkDesktopComponent, Network) - Constructor for class org.simbrain.network.desktop.NetworkPanelDesktop: Construct the desktop extension of network panel.
networkPropertiesPanel - Variable in class org.simbrain.network.gui.dialogs.NetworkDialog: Main properties panel.
NetworkPropertiesPanel - Class in org.simbrain.network.gui.dialogs: NetworkPropertiesPanel is a panel for setting the properties of the neural network, mainly the GUI.
NetworkPropertiesPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.NetworkPropertiesPanel: This method is the default constructor.
NetworkScriptMenu - Class in org.simbrain.network.desktop: Creates a network script menu, which shows a menu item for each script in the relevant directory.
NetworkScriptMenu() - Constructor for class org.simbrain.network.desktop.NetworkScriptMenu
NetworkScriptMenu.ScriptAction - Class in org.simbrain.network.desktop: Create an action based on the name of a script.
NetworkSelectionEvent - Class in org.simbrain.network.gui: An event object representing a change in network selection.
NetworkSelectionEvent(NetworkPanel, Set<PNode>, Set<PNode>) - Constructor for class org.simbrain.network.gui.NetworkSelectionEvent: Create a new network selection event with the specified source.
NetworkSelectionListener - Interface in org.simbrain.network.gui: A listener that receives notification of changes in the selection for network panel.
NetworkSelectionModel - Class in org.simbrain.network.gui: Network selection model.
NetworkSelectionModel(NetworkPanel) - Constructor for class org.simbrain.network.gui.NetworkSelectionModel: Create a new network selection model for the specified source of selection events.
NetworkSettings - Class in org.simbrain.network: This class stores preferences for the logical network.
NetworkSettings() - Constructor for class org.simbrain.network.NetworkSettings
NetworkTextObject - Class in org.simbrain.network.core: NetworkTextObject is a string of text in a neural network, typically used to label elements of a neural network simulation.
NetworkTextObject(Network, double, double) - Constructor for class org.simbrain.network.core.NetworkTextObject: Construct the text object.
NetworkTextObject(Network, double, double, String) - Constructor for class org.simbrain.network.core.NetworkTextObject: Construct the text object with initial text.
NetworkTextObject(Network, NetworkTextObject) - Constructor for class org.simbrain.network.core.NetworkTextObject: Copy constructor.
NetworkUpdateAction - Interface in org.simbrain.network.core: Classes that implement this interface describe individual actions that together comprise a network update.
NetworkUpdateManager - Class in org.simbrain.network.core: Manage network updates.
NetworkUpdateManager(Network) - Constructor for class org.simbrain.network.core.NetworkUpdateManager: Construct a new update manager.
NetworkUpdateManager.UpdateManagerListener - Interface in org.simbrain.network.core: Listen from changes to update manager.
NetworkUpdateManagerPanel - Class in org.simbrain.network.gui: Panel for display the current network updates, and editing them (adding, removing, and changing their order).
NetworkUpdateManagerPanel(Network, StandardDialog) - Constructor for class org.simbrain.network.gui.NetworkUpdateManagerPanel: Creates a new update manager panel.
NetworkUtils - Class in org.simbrain.network.gui: NetworkUtils provides static utility methods for the Network class.
NetworkUtils() - Constructor for class org.simbrain.network.gui.NetworkUtils
Neuron - Class in org.simbrain.network.core: Neuron represents a node in the neural network.
Neuron(Network) - Constructor for class org.simbrain.network.core.Neuron: Construct a neuron with all default values in the specified network.
Neuron(Network, String) - Constructor for class org.simbrain.network.core.Neuron: Construct a specific type of neuron from a string description.
Neuron(Network, NeuronUpdateRule) - Constructor for class org.simbrain.network.core.Neuron: Construct a specific type of neuron.
Neuron(Network, Neuron) - Constructor for class org.simbrain.network.core.Neuron: Copy constructor.
neuron - Variable in class org.simbrain.network.gui.nodes.NeuronNode: The logical neuron this screen element represents.
NEURON_FONT - Static variable in class org.simbrain.network.gui.nodes.NeuronNode: Neuron Font.
NEURON_FONT_BOLD - Static variable in class org.simbrain.network.gui.nodes.NeuronNode: Neuron font bold.
NEURON_FONT_SMALL - Static variable in class org.simbrain.network.gui.nodes.NeuronNode: Neuron font small.
NEURON_FONT_VERYSMALL - Static variable in class org.simbrain.network.gui.nodes.NeuronNode: Neuron font very small.
NeuronAdapter - Class in org.simbrain.network.listeners: Adapter class for NeuronListener.
NeuronAdapter() - Constructor for class org.simbrain.network.listeners.NeuronAdapter
neuronAdded(NetworkEvent<Neuron>) - Method in class org.simbrain.network.listeners.NeuronAdapter
neuronAdded(NetworkEvent<Neuron>) - Method in interface org.simbrain.network.listeners.NeuronListener: Notify this listener of a Neuron added event.
neuronAdded(NetworkEvent<Neuron>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
neuronChanged(NetworkEvent<Neuron>) - Method in class org.simbrain.network.listeners.NeuronAdapter
neuronChanged(NetworkEvent<Neuron>) - Method in interface org.simbrain.network.listeners.NeuronListener: Notify this listener of a Neuron changed event.
neuronChanged(NetworkEvent<Neuron>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
neuronClampButton - Variable in class org.simbrain.network.gui.NetworkPanel: Toggle button for neuron clamping.
neuronClampMenuItem - Variable in class org.simbrain.network.gui.NetworkPanel: Menu item for neuron clamping.
NeuronComparator - Class in org.simbrain.network.gui: Comparator is used to compare positions of PNodes.
NeuronComparator(NeuronComparator.Type) - Constructor for class org.simbrain.network.gui.NeuronComparator: Constructor for Comparator.
NeuronComparator.Type - Enum in org.simbrain.network.gui: Whether to compare via x or y position.
NeuronDialog - Class in org.simbrain.network.gui.dialogs.neuron: NeuronDialog is a dialog box for setting the properties of a Neuron.
NeuronGroup - Class in org.simbrain.network.groups: A group of neurons.
NeuronGroup(Network, List<Neuron>) - Constructor for class org.simbrain.network.groups.NeuronGroup: Construct a new neuron group from a list of neurons.
NeuronGroup(Network, int) - Constructor for class org.simbrain.network.groups.NeuronGroup: Construct a new neuron group with a specified number of neurons.
NeuronGroup(Network, Point2D, int) - Constructor for class org.simbrain.network.groups.NeuronGroup: Construct a new neuron group with a specified number of neurons.
NeuronGroup(Network, Point2D) - Constructor for class org.simbrain.network.groups.NeuronGroup: Create a neuron group without any initial neurons and an initial position.
NeuronGroup(Network) - Constructor for class org.simbrain.network.groups.NeuronGroup: Create a neuron group without any initial neurons.
NeuronGroup(Network, NeuronGroup) - Constructor for class org.simbrain.network.groups.NeuronGroup: Copy constructor.
NeuronGroupCreationDialog - Class in org.simbrain.network.gui.dialogs.group: NeuronGroupCreationDialog is a dialog box for creating a bare neuron group.
NeuronGroupCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.group.NeuronGroupCreationDialog: This method is the default constructor.
NeuronGroupInteractionBox(NetworkPanel) - Constructor for class org.simbrain.network.gui.nodes.NeuronGroupNode.NeuronGroupInteractionBox
NeuronGroupNode - Class in org.simbrain.network.gui.nodes: PNode representation of a group of neurons.
NeuronGroupNode(NetworkPanel, NeuronGroup) - Constructor for class org.simbrain.network.gui.nodes.NeuronGroupNode: Create a Neuron Group PNode.
NeuronGroupNode.NeuronGroupInteractionBox - Class in org.simbrain.network.gui.nodes: Custom interaction box for Subnetwork node.
NeuronGroupNode.Port - Enum in org.simbrain.network.gui.nodes
NeuronGroupPanel - Class in org.simbrain.network.gui.dialogs.group: Main tabbed panel for editing neuron groups.
NeuronGroupSelectionPanel - Class in org.simbrain.network.gui
NeuronGroupSelectionPanel(JList) - Constructor for class org.simbrain.network.gui.NeuronGroupSelectionPanel
NeuronLayer - Class in org.simbrain.network.groups: Extend neuron group with layer information used in a layered network.
NeuronLayer(Network, List<Neuron>, NeuronLayer.LayerType) - Constructor for class org.simbrain.network.groups.NeuronLayer: Construct a neuron layer.
NeuronLayer.LayerType - Enum in org.simbrain.network.groups: Enumeration of layer types.
NeuronListener - Interface in org.simbrain.network.listeners: Listener interface for receiving events relating to neurons.
neuronMoved(NetworkEvent<Neuron>) - Method in class org.simbrain.network.listeners.NeuronAdapter
neuronMoved(NetworkEvent<Neuron>) - Method in interface org.simbrain.network.listeners.NeuronListener: Notify this listener of a Neuron moved event.
neuronMoved(NetworkEvent<Neuron>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
NeuronNode - Class in org.simbrain.network.gui.nodes: NeuronNode is a Piccolo PNode corresponding to a Neuron in the neural network model.
NeuronNode(NetworkPanel, Neuron) - Constructor for class org.simbrain.network.gui.nodes.NeuronNode: Create a new neuron node.
NeuronNoiseGenPanel - Class in org.simbrain.network.gui.dialogs.neuron: A panel specifically for the randomizers used by neurons...
NeuronNoiseGenPanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.NeuronNoiseGenPanel
NeuronPropertiesExtended - Class in org.simbrain.network.gui.dialogs.neuron: A panel containing more detailed generic information about neurons.
NeuronPropertiesExtended(List<Neuron>, Window) - Constructor for class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended: Construct the panel representing the provided neurons.
NeuronPropertiesPanel - Class in org.simbrain.network.gui.dialogs.neuron: The basic neuron info panel and neuron update settings panel are frequently used together and depend on each other.
NeuronPropertiesSimple - Class in org.simbrain.network.gui.dialogs.neuron: Panel showing activation and label properties of a neuron.
neuronRemoved(NetworkEvent<Neuron>) - Method in class org.simbrain.network.listeners.NeuronAdapter
neuronRemoved(NetworkEvent<Neuron>) - Method in interface org.simbrain.network.listeners.NeuronListener: Notify this listener of a Neuron removed event.
neuronRemoved(NetworkEvent<Neuron>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
neuronTypeChanged(NetworkEvent<NeuronUpdateRule>) - Method in class org.simbrain.network.listeners.NeuronAdapter
neuronTypeChanged(NetworkEvent<NeuronUpdateRule>) - Method in interface org.simbrain.network.listeners.NeuronListener: Notify this listener of a Neuron type changed event.
neuronTypeChanged(NetworkEvent<NeuronUpdateRule>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate
NeuronUpdateRule - Class in org.simbrain.network.core: A rule for updating a neuron.
NeuronUpdateRule() - Constructor for class org.simbrain.network.core.NeuronUpdateRule
NeuronUpdateRule.InputType - Enum in org.simbrain.network.core: An enum specifying how a neuron sums its inputs.
NeuronWithMemory - Class in org.simbrain.network.util: A neuron that stores a memory of its last activation.
NeuronWithMemory(Network, String) - Constructor for class org.simbrain.network.util.NeuronWithMemory
NewBarChartAction - Class in org.simbrain.workspace.actions.chart: Add bar chart component to workspace.
NewBarChartAction(Workspace) - Constructor for class org.simbrain.workspace.actions.chart.NewBarChartAction: Create a new bar chart component.
NewConsoleAction - Class in org.simbrain.workspace.actions: Add console to workspace.
NewConsoleAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewConsoleAction: Create a new console action with the specified workspace.
NewDataWorldAction - Class in org.simbrain.workspace.actions: Add data world to workspace.
NewDataWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewDataWorldAction: Create a new data world action with the specified workspace.
NewDisplayWorldAction - Class in org.simbrain.workspace.actions: Add display text world to workspace.
NewDisplayWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewDisplayWorldAction: Create a new text world action with the specified workspace.
NewDocViewerAction - Class in org.simbrain.workspace.actions: Add a document viewer to the workspace.
NewDocViewerAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewDocViewerAction: Create a new console action with the specified workspace.
NewGameWorldAction - Class in org.simbrain.workspace.actions: Add odor world to workspace.
NewGameWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewGameWorldAction: Create a new odor world action with the specified workspace.
NewHistogramAction - Class in org.simbrain.workspace.actions.chart: Add histogram chart component to workspace.
NewHistogramAction(Workspace) - Constructor for class org.simbrain.workspace.actions.chart.NewHistogramAction: Create a new histogram chart component.
NewMidiWorldAction - Class in org.simbrain.workspace.actions: Add MIDI world to workspace.
NewMidiWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewMidiWorldAction: Create a new MIDI world action with the specified workspace.
NewNetworkAction - Class in org.simbrain.workspace.actions: Add network to workspace.
NewNetworkAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewNetworkAction: Create a new network action with the specified workspace.
NewNeuronAction - Class in org.simbrain.network.gui.actions.neuron: New neuron action.
NewNeuronAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.neuron.NewNeuronAction: Create a new neuron action with the specified network panel.
NewNeuronGroupAction - Class in org.simbrain.network.gui.actions.modelgroups: Convert selected neurons to a neuron group.
NewNeuronGroupAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.modelgroups.NewNeuronGroupAction: Create a new new neuron group network action with the specified network panel.
NewOdorWorldAction - Class in org.simbrain.workspace.actions: Add odor world to workspace.
NewOdorWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewOdorWorldAction: Create a new odor world action with the specified workspace.
NewOscWorldAction - Class in org.simbrain.workspace.actions: Add OSC world to workspace.
NewOscWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewOscWorldAction: Create a new OSC world action with the specified workspace.
NewPieChartAction - Class in org.simbrain.workspace.actions.chart: Add pie chart component to workspace.
NewPieChartAction(Workspace) - Constructor for class org.simbrain.workspace.actions.chart.NewPieChartAction: Create a new pie chart component.
NewProjectionPlotAction - Class in org.simbrain.workspace.actions.chart: Add projection plot component to workspace.
NewProjectionPlotAction(Workspace) - Constructor for class org.simbrain.workspace.actions.chart.NewProjectionPlotAction: Create a new projection plot component.
NewRasterPlotAction - Class in org.simbrain.workspace.actions.chart: New raster plot action.
NewRasterPlotAction(Workspace) - Constructor for class org.simbrain.workspace.actions.chart.NewRasterPlotAction: Create a new histogram chart component.
NewReaderWorldAction - Class in org.simbrain.workspace.actions: Add display text world to workspace.
NewReaderWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewReaderWorldAction: Create a new text world action with the specified workspace.
NewScatterPlotAction - Class in org.simbrain.workspace.actions.chart: Add scatter plot component to workspace.
NewScatterPlotAction(Workspace) - Constructor for class org.simbrain.workspace.actions.chart.NewScatterPlotAction: Create a new scatter plot component.
NewThreeDeeWorldAction - Class in org.simbrain.workspace.actions: Add odor world to workspace.
NewThreeDeeWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewThreeDeeWorldAction: Create a new odor world action with the specified workspace.
NewTimeSeriesAction - Class in org.simbrain.workspace.actions.chart: Add Plot component to workspace.
NewTimeSeriesAction(Workspace) - Constructor for class org.simbrain.workspace.actions.chart.NewTimeSeriesAction: Create a new plot component.
NewtonianBouncer - Class in org.simbrain.world.odorworld.behaviors: Bounce off the walls...
NewtonianBouncer(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.behaviors.NewtonianBouncer: Construct the behavior.
NewVisionWorldAction - Class in org.simbrain.workspace.actions: Add vision world to workspace.
NewVisionWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.NewVisionWorldAction: Create a new vision world action with the specified workspace.
newWorkspaceOpened() - Method in class org.simbrain.workspace.gui.ComponentPanel: Called after a new workspace simulation file has been opened.
newWorkspaceOpened() - Method in class org.simbrain.workspace.gui.CouplingMenuComponent: Called after a new workspace simulation file has been opened.
newWorkspaceOpened() - Method in interface org.simbrain.workspace.WorkspaceListener: Called after a new workspace simulation file has been opened.
next - Variable in class org.simbrain.world.threedee.sensors.Sight
nextRand(double, double) - Method in enum org.simbrain.util.math.ProbDistribution
nextRandInt(int, int) - Method in enum org.simbrain.util.math.ProbDistribution
noiseGenerator - Variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Noise dialog.
NoisyUpdateRule - Interface in org.simbrain.network.neuron_update_rules.interfaces: An interface which should be implemented by any neuron update rule that uses a randomizer to provide noise.
normal - Static variable in class org.simbrain.console.CommandLineReader
normalize() - Method in class org.simbrain.util.table.SimbrainJTable: Normalize selected columns of selected cells.
normalizeAllIncomingWeights() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Normalize all weights coming in to this network.
normalizeColumn(int) - Method in class org.simbrain.util.table.NumericTable: Normalize data in selected column.
normalizeExcitatoryFanIn() - Method in class org.simbrain.network.core.Neuron: Normalizes the excitatory synaptic strengths impinging on this neuron, that is finds the sum of the exctiatory weights and divides each weight value by that sum;
normalizeFanIn() - Method in class org.simbrain.network.core.Neuron
normalizeIncomingWeights() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Normalize weights coming in to this network, separately for each neuron.
normalizeInhibitoryFanIn() - Method in class org.simbrain.network.core.Neuron
normalizeTable() - Method in class org.simbrain.util.table.NumericTable: Normalize the whole table.
normalizeVec(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: A normalized version of the vector, i.e.
normalView() - Method in class org.simbrain.world.visionworld.VisionWorld: Switch to the normal view.
NormalViewAction - Class in org.simbrain.world.visionworld.action: Normal view action.
NormalViewAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.NormalViewAction: Create a new normal view action.
notifyComponentUpdateFinished(WorkspaceComponent, int) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Called when a new component is finished updating.
notifyComponentUpdateStarted(WorkspaceComponent, int) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Called when a new component is starting to update.
notifyCouplingsUpdated() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Called when the couplings are updated.
NTree - Class in org.simbrain.util.projection: An n-dimensional generalization of a simple QuadTree structure.
NTree(int) - Constructor for class org.simbrain.util.projection.NTree: Constructs an NTree with the given number of dimensions.
nudge(int, int) - Method in class org.simbrain.network.gui.NetworkPanel: Nudge selected objects.
NULL_STRING - Static variable in class org.simbrain.network.gui.dialogs.neuron.NeuronDialog: Null string.
NULL_STRING - Static variable in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple: Null string.
NULL_STRING - Static variable in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: Null string.
NULL_STRING - Static variable in class org.simbrain.util.SimbrainConstants: Null string used in various parts of the GUI.
NumericMatrix - Interface in org.simbrain.util.math: Interface that indicates that a class holds a matrix of doubles.
NumericTable - Class in org.simbrain.util.table: Default implementation of a table of numerical data.
NumericTable(int, int) - Constructor for class org.simbrain.util.table.NumericTable: Construct a table with a specified number of rows and columns.
NumericTable(double[][]) - Constructor for class org.simbrain.util.table.NumericTable: Construct a table from an 2-d array of doubles.
NumericTable() - Constructor for class org.simbrain.util.table.NumericTable: Default constructor.

O

observationsToProbDist(double[][]) - Static method in enum org.simbrain.util.math.ProbDistribution: Normalizes a set of observations so they may be used as a discrete probability density function.
OdorWorld - Class in org.simbrain.world.odorworld: Core model class of Odor World, which contains a list of entities in the world.
OdorWorld() - Constructor for class org.simbrain.world.odorworld.OdorWorld: Default constructor.
OdorWorldComponent - Class in org.simbrain.world.odorworld: WorldPanel is the container for the world component.
OdorWorldComponent(String) - Constructor for class org.simbrain.world.odorworld.OdorWorldComponent: Default constructor.
OdorWorldComponent(String, OdorWorld) - Constructor for class org.simbrain.world.odorworld.OdorWorldComponent: Constructor used in deserializing.
OdorWorldDesktopComponent - Class in org.simbrain.world.odorworld: WorldPanel is the container for the world component.
OdorWorldDesktopComponent(GenericFrame, OdorWorldComponent) - Constructor for class org.simbrain.world.odorworld.OdorWorldDesktopComponent: Default constructor.
OdorWorldDialog - Class in org.simbrain.world.odorworld.dialogs: DialogOdorWorld is used to set the enivronment's parameters, in particular, the way stimuli are constructed to be sent the network, and the way outputs from the network are expressed in the world.
OdorWorldDialog(OdorWorldPanel) - Constructor for class org.simbrain.world.odorworld.dialogs.OdorWorldDialog: Constructor initializes a settings dialog for the odorworld from which it was called.
OdorWorldEntity - Class in org.simbrain.world.odorworld.entities: Parent class for all Odor World objects.
OdorWorldEntity(Animation, OdorWorld) - Constructor for class org.simbrain.world.odorworld.entities.OdorWorldEntity: Construct an entity from an animation.
OdorWorldEntity(String, OdorWorld) - Constructor for class org.simbrain.world.odorworld.entities.OdorWorldEntity: Construct an odor world entity from a single image location.
OdorWorldEntity(OdorWorld) - Constructor for class org.simbrain.world.odorworld.entities.OdorWorldEntity: Construct an entity.
OdorWorldFrameMenu - Class in org.simbrain.world.odorworld: OdorWorldFrameMenu.
OdorWorldFrameMenu(OdorWorldDesktopComponent, OdorWorld) - Constructor for class org.simbrain.world.odorworld.OdorWorldFrameMenu: Odor world frame menu constructor.
OdorWorldMenu - Class in org.simbrain.world.odorworld: OdorWorldMenu.
OdorWorldMenu(OdorWorldPanel) - Constructor for class org.simbrain.world.odorworld.OdorWorldMenu: Creates an instance of odor world menu.
OdorWorldPanel - Class in org.simbrain.world.odorworld: OdorWorldPanel represent the OdorWorld.
OdorWorldPanel(OdorWorld) - Constructor for class org.simbrain.world.odorworld.OdorWorldPanel: Construct a world, set its background color.
OdorWorldRenderer - Class in org.simbrain.world.odorworld: The OdorWorldRenderer class draws an odor world on the screen.
OdorWorldRenderer() - Constructor for class org.simbrain.world.odorworld.OdorWorldRenderer
OdorWorldResourceManager - Class in org.simbrain.world.odorworld.resources: OdorWorldResourceManager provides resources (stored in the same directory) to the rest of the program.
OdorWorldResourceManager() - Constructor for class org.simbrain.world.odorworld.resources.OdorWorldResourceManager
offset(double, double) - Method in class org.simbrain.network.core.Neuron: Translate the neuron by a specified amount.
offset(double, double) - Method in class org.simbrain.network.groups.NeuronGroup: Translate all neurons (the only objects with position information).
offset(double, double) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
offset(double, double) - Method in class org.simbrain.network.gui.nodes.NeuronNode
offset(double, double) - Method in class org.simbrain.network.gui.nodes.SubnetworkNode
offset(double, double) - Method in class org.simbrain.network.gui.nodes.TextNode
offsetNeuronGroup(NeuronGroup, NeuronGroup, NetworkLayoutManager.Direction, double) - Static method in class org.simbrain.network.util.NetworkLayoutManager: Group1 stays fixed.
OjaRule - Class in org.simbrain.network.synapse_update_rules: OjaSynapse is a synapse which asymptotically normalizes the sum of squares of the weights attaching to a neuron to a user-defined value.
OjaRule() - Constructor for class org.simbrain.network.synapse_update_rules.OjaRule
OjaRulePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: OjaSynapsePanel.
OjaRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel: This method is the default constructor.
OneToOne - Class in org.simbrain.network.connections: Connect each source neuron to a single target.
OneToOne() - Constructor for class org.simbrain.network.connections.OneToOne
OneToOnePanel - Class in org.simbrain.network.gui.dialogs.connect.connector_panels: OneToOnePanel creates a dialog for setting preferences of one to one neuron connections.
OneToOnePanel(OneToOne) - Constructor for class org.simbrain.network.gui.dialogs.connect.connector_panels.OneToOnePanel: Default constructor.
open(InputStream, String, String) - Static method in class org.simbrain.console.ConsoleComponent: Opens a saved component.
open(InputStream, String, String) - Static method in class org.simbrain.docviewer.DocViewerComponent: Opens a saved component.
open(InputStream, String, String) - Static method in class org.simbrain.network.NetworkComponent
open(InputStream, String, String) - Static method in class org.simbrain.plot.barchart.BarChartComponent: Opens a saved bar chart.
open(InputStream, String, String) - Static method in class org.simbrain.plot.histogram.HistogramComponent: Opens a saved bar chart.
open(InputStream, String, String) - Static method in class org.simbrain.plot.piechart.PieChartComponent: Streams file data for opening saved charts.
open(InputStream, String, String) - Static method in class org.simbrain.plot.projection.ProjectionComponent: Opens a saved projection component.
open(InputStream, String, String) - Static method in class org.simbrain.plot.rasterchart.RasterPlotComponent: Opens a saved raster plot.
open(InputStream, String, String) - Static method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
open(InputStream, String, String) - Static method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent: Opens a saved time series plot.
open(WorkspaceComponent, InputStream, String) - Static method in class org.simbrain.workspace.gui.GuiComponent: Creates a new desktop component from the provided stream.
open(Class<?>, File) - Static method in class org.simbrain.workspace.WorkspaceSerializer: Helper method for openings workspace components from a file.
open(InputStream, String, String) - Static method in class org.simbrain.world.dataworld.DataWorldComponent: Recreates an instance of this class from a saved component.
open(InputStream, String, String) - Static method in class org.simbrain.world.odorworld.OdorWorldComponent: Recreates an instance of this class from a saved component.
open(InputStream, String, String) - Static method in class org.simbrain.world.textworld.DisplayComponent
open(InputStream, String, String) - Static method in class org.simbrain.world.textworld.ReaderComponent
open(InputStream, String, String) - Static method in class org.simbrain.world.visionworld.VisionWorldComponent
OpenAction - Class in org.simbrain.workspace.component_actions: Open component action.
OpenAction(GuiComponent) - Constructor for class org.simbrain.workspace.component_actions.OpenAction: Create a new open component action with the specified.
OpenCouplingListAction - Class in org.simbrain.workspace.actions: Opens and displays a list of the current couplings.
OpenCouplingListAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.OpenCouplingListAction: Create a coupling list with the specified workspace.
OpenCouplingListAction.MyGlassPane - Class in org.simbrain.workspace.actions: Class for creating a glass pane.
OpenCouplingManagerAction - Class in org.simbrain.workspace.actions: Open data world in current workspace.
OpenCouplingManagerAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.OpenCouplingManagerAction: Create an open data world with the specified workspace.
OpenDataWorldAction - Class in org.simbrain.workspace.actions: Open data world in current workspace.
OpenDataWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.OpenDataWorldAction: Open a data world.
OpenNetworkAction - Class in org.simbrain.workspace.actions: Open a network within current workspace.
OpenNetworkAction(Workspace) - Constructor for class org.simbrain.workspace.actions.OpenNetworkAction: Create an open network action with the specified workspace.
OpenOdorWorldAction - Class in org.simbrain.workspace.actions: Open an odor world in current workspace.
OpenOdorWorldAction(Workspace) - Constructor for class org.simbrain.workspace.actions.OpenOdorWorldAction: Create an open odor world action with the specified workspace.
OpenPlotAction - Class in org.simbrain.plot.actions: Open plot action.
OpenPlotAction(GuiComponent) - Constructor for class org.simbrain.plot.actions.OpenPlotAction: Create a new open plot action.
OpenVisionWorldAction - Class in org.simbrain.world.visionworld.action: Create pixel matrix action.
OpenVisionWorldAction(VisionWorldDesktopComponent) - Constructor for class org.simbrain.world.visionworld.action.OpenVisionWorldAction: Create a new create pixel matrix action.
openWorkspace() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Shows the dialog for opening a workspace file.
openWorkspace(File) - Method in class org.simbrain.workspace.Workspace: Open a workspace from a file.
OpenWorkspaceAction - Class in org.simbrain.workspace.actions: Open a new workspace.
OpenWorkspaceAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.OpenWorkspaceAction: Create an open workspace action with the specified workspace.
OpenWorkspaceComponentListAction - Class in org.simbrain.workspace.actions: Opens and displays a list of the current workspace components.
OpenWorkspaceComponentListAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.OpenWorkspaceComponentListAction: Create a workspace component list of the specified workspace.
opposite(NeuronGroupNode.Port) - Static method in enum org.simbrain.network.gui.nodes.NeuronGroupNode.Port
org.simbrain.console - package org.simbrain.console: The console package contains commands that can be plugged in to the beanshell intepreter (http://www.beanshell.org/).
org.simbrain.docviewer - package org.simbrain.docviewer: The docviewer package contains classes for managing the document viewer.
org.simbrain.network - package org.simbrain.network: The network package contains representation of neural networks.
org.simbrain.network.connections - package org.simbrain.network.connections: The network.connections package contains classes for creating connecting groups of neurons.
org.simbrain.network.core - package org.simbrain.network.core: The network.core package contains all high level neural network classes, i.e.
org.simbrain.network.desktop - package org.simbrain.network.desktop: The network.desktop package contains code that is compiled for the Simbrain desktop app, but that is not compiled for non-desktop usage.
org.simbrain.network.groups - package org.simbrain.network.groups: The network.groups package contains classes for creating and managing groups of neurons in the network.
org.simbrain.network.gui - package org.simbrain.network.gui: The network.gui package contains the Piccolo-based zoomable GUI for designing, editing, and running neural networks.
org.simbrain.network.gui.actions - package org.simbrain.network.gui.actions: The network.action package contains the actions for responding to network events.
org.simbrain.network.gui.actions.connection - package org.simbrain.network.gui.actions.connection: The network.gui.actions.connection package contains action classes for creating and editing synapse connections.
org.simbrain.network.gui.actions.edit - package org.simbrain.network.gui.actions.edit: The network.gui.actions.edit package contains actions relating to the edit menu and other edit actions.
org.simbrain.network.gui.actions.modelgroups - package org.simbrain.network.gui.actions.modelgroups: The network.gui.actions.modelgroups package contains actions relating to neurongroups and synapsegroups.
org.simbrain.network.gui.actions.network - package org.simbrain.network.gui.actions.network: The network.gui.actions.network package contains general network actions (e.g.
org.simbrain.network.gui.actions.neuron - package org.simbrain.network.gui.actions.neuron: The network.gui.actions.neuron package contains actions relating to neurons (e.g.
org.simbrain.network.gui.actions.selection - package org.simbrain.network.gui.actions.selection: The network.gui.actions.selection package contains selection actions (e.g.
org.simbrain.network.gui.actions.synapse - package org.simbrain.network.gui.actions.synapse: The network.gui.actions.synapse package contains actions relating to synapses (e.g.
org.simbrain.network.gui.actions.toolbar - package org.simbrain.network.gui.actions.toolbar: The network.gui.actions.toolbar package contains actions relating to the toolbar (e.g.
org.simbrain.network.gui.dialogs - package org.simbrain.network.gui.dialogs: The network.gui.dialogs package contains all the dialog classes for graphical networks.
org.simbrain.network.gui.dialogs.connect - package org.simbrain.network.gui.dialogs.connect: The network.gui.dialogs.connect package contains panel classes for managing network connection types.
org.simbrain.network.gui.dialogs.connect.connector_panels - package org.simbrain.network.gui.dialogs.connect.connector_panels: The network.gui.dialogs.connect.connector_panels package contains dialogs and panels for editing, setting, and adjusting the preferences of a connection type.
org.simbrain.network.gui.dialogs.group - package org.simbrain.network.gui.dialogs.group: The network.gui.dialogs.group package contains dialogs for managing groups, mainly neuron groups and synapse groups
org.simbrain.network.gui.dialogs.layout - package org.simbrain.network.gui.dialogs.layout: The network.gui.dialogs.layout package contains dialogs for managing neuron layout objects.
org.simbrain.network.gui.dialogs.network - package org.simbrain.network.gui.dialogs.network: The network.gui.dialogs.network package contains dialog classes that manage the creation and editing of network-level dialog boxes.
org.simbrain.network.gui.dialogs.neuron - package org.simbrain.network.gui.dialogs.neuron: The network.gui.dialogs.neuron package contains dialog classes that manage the creation and editing of neuron-level dialog boxes.
org.simbrain.network.gui.dialogs.neuron.generator_panels - package org.simbrain.network.gui.dialogs.neuron.generator_panels: The network.gui.dialogs.neuron.generator_panels package contains dialogs for neuron generators (currently unused)
org.simbrain.network.gui.dialogs.neuron.rule_panels - package org.simbrain.network.gui.dialogs.neuron.rule_panels: The network.gui.dialogs.neuron.generator_panels package contains dialogs for neuron generators (currently unused)
org.simbrain.network.gui.dialogs.synapse - package org.simbrain.network.gui.dialogs.synapse: The network.gui.dialogs.synapse package contains dialog classes that manage the creation and editing of synapse-level dialog boxes.
org.simbrain.network.gui.dialogs.synapse.plasticity_panels - package org.simbrain.network.gui.dialogs.synapse.plasticity_panels: The network.gui.dialogs.synpase.plasticity_panels package contains the main panels for editing specific synapse update rules.
org.simbrain.network.gui.dialogs.synapse.spike_responders - package org.simbrain.network.gui.dialogs.synapse.spike_responders: The network.gui.dialogs.synpase.spike_responders package contains panel classes for setting the various types of response functions of spike repsonders.
org.simbrain.network.gui.dialogs.text - package org.simbrain.network.gui.dialogs.text: The network.gui.dialogs.text package contains classes for managing network text objects .
org.simbrain.network.gui.filters - package org.simbrain.network.gui.filters: The network.gui.filters package contains node filters.
org.simbrain.network.gui.nodes - package org.simbrain.network.gui.nodes: The simbrain.network.nodes package contains Piccolo nodes for various network elements.
org.simbrain.network.gui.nodes.neuronGroupNodes - package org.simbrain.network.gui.nodes.neuronGroupNodes: The network.gui.nodes.neuronGroupNodes package contains Piccolo Pnode classes corresponding to neuron group types.
org.simbrain.network.gui.nodes.subnetworkNodes - package org.simbrain.network.gui.nodes.subnetworkNodes: The network.gui.nodes.subnetworkNodes package contains Piccolo Pnode classes corresponding to subnetwork types.
org.simbrain.network.gui.trainer - package org.simbrain.network.gui.trainer: The network.gui.trainer package contains components that can be used to display trainer.
org.simbrain.network.gui.trainer.subnetworkTrainingPanels - package org.simbrain.network.gui.trainer.subnetworkTrainingPanels: The network.gui.trainer.subnetworkTrainingPanels package contains panel classes for training subnetwork types.
org.simbrain.network.layouts - package org.simbrain.network.layouts: The network.layouts package contains the neuron layouts.
org.simbrain.network.listeners - package org.simbrain.network.listeners: The network.listeners package contains all listener class for networks.
org.simbrain.network.neuron_update_rules - package org.simbrain.network.neuron_update_rules: The network.neuron_update_rules package contains code which describes all particular neuron update rules, which are used when neurons are updated.
org.simbrain.network.neuron_update_rules.activity_generators - package org.simbrain.network.neuron_update_rules.activity_generators: The network.neuron_update_rules.activity_generators package contains classes for network elements that generate activity but are not proper update rules
org.simbrain.network.neuron_update_rules.interfaces - package org.simbrain.network.neuron_update_rules.interfaces: The network.neuron_update_rules.interfaces package contains abstract classes and interfaces relating to neuron update.
org.simbrain.network.subnetworks - package org.simbrain.network.subnetworks: The network.subnetworks package contains all bottom-level subclasses of group.
org.simbrain.network.synapse_update_rules - package org.simbrain.network.synapse_update_rules: The network.synapse_update_rules package contains code which describes all particular synpase or weight types in Simbrain.
org.simbrain.network.synapse_update_rules.spikeresponders - package org.simbrain.network.synapse_update_rules.spikeresponders: The network.synpase_updaterules.spikeresponders package contains methods by which spikes are converted into activation post-synaptically.
org.simbrain.network.trainers - package org.simbrain.network.trainers: The network.trainers package contains supervised learning algorithms.
org.simbrain.network.update_actions - package org.simbrain.network.update_actions: The network.update_actions package contains all update action classes.
org.simbrain.network.update_actions.concurrency_tools - package org.simbrain.network.update_actions.concurrency_tools: The network.update_actions.concurrency_tools package contains utilities for parallel update actions.
org.simbrain.network.util - package org.simbrain.network.util: The util package contains utility classes for simnet.
org.simbrain.network.util.io_utilities - package org.simbrain.network.util.io_utilities: The network.util.io_utilities package contains classes for specialized serialization needs, e.g.
org.simbrain.plot - package org.simbrain.plot: The plot package contains classes for the implementation of Simbrain plots and charts.
org.simbrain.plot.actions - package org.simbrain.plot.actions: The plot.actions package contains common action classes for plot guis (e.g.
org.simbrain.plot.barchart - package org.simbrain.plot.barchart: The plot.barchart package contains classes for creating and editing barcharts.
org.simbrain.plot.histogram - package org.simbrain.plot.histogram: The plot.histogram package contains classes for creating and editing a histogram.
org.simbrain.plot.piechart - package org.simbrain.plot.piechart: The plot.piechart package contains classes for creating and editing a piechart.
org.simbrain.plot.projection - package org.simbrain.plot.projection: The plot.projection package contains classes for creating and editing a projection.
org.simbrain.plot.rasterchart - package org.simbrain.plot.rasterchart: The plot.rasterchart package contains classes for creating and editing a raster plot chart.
org.simbrain.plot.scatterplot - package org.simbrain.plot.scatterplot: The plot.scatterplot package contains classes for creating and plotting scatter plot (currently unused).
org.simbrain.plot.timeseries - package org.simbrain.plot.timeseries: The plot.timeseries package contains classes for creating and editing a time series plot.
org.simbrain.resource - package org.simbrain.resource: The resource package contains all the images used in Simbrain, as well as a class which provides access to to those images.
org.simbrain.util - package org.simbrain.util: The util package contains utilities classes used by multiple Simbrain packages.
org.simbrain.util.environment - package org.simbrain.util.environment: The util.environment package contains a simple 2-d environment model with smell sensors, simple motion, and very simple touch.
org.simbrain.util.genericframe - package org.simbrain.util.genericframe: The util.genericframe package contains an abstraction that is neutral between JFrames, JInternalFrames, and JDialogs, which is sometimes convenient when, for example, writing code that could be used both in a dialog or an internal desktop frame.
org.simbrain.util.math - package org.simbrain.util.math: The util.math package contains associated mathematical utility classes.
org.simbrain.util.projection - package org.simbrain.util.projection: The util.projection package contains the core api for dimensionality reduction, that is used in the projection plot (but which can also be used in scripts or just as a library).
org.simbrain.util.propertyeditor - package org.simbrain.util.propertyeditor: The util.propertyeditor package contains an api for creating quick and easy edit dialogs.
org.simbrain.util.propertyeditor.gui - package org.simbrain.util.propertyeditor.gui: The util.propertyeditory.gui package contains the main GUI classes for the property editor.
org.simbrain.util.randomizer - package org.simbrain.util.randomizer: The util.randomizer package contains classes for creating and managing randomizers, which handles cases where a number must be drawn from a probability distribution.
org.simbrain.util.randomizer.gui - package org.simbrain.util.randomizer.gui: The util.randomizer.gui package contains GUI classes for representing and setting properties of a randomizer.
org.simbrain.util.scripteditor - package org.simbrain.util.scripteditor: The util.scripteditor package contains the Simbrain script editor GUI code, which wraps around Robert Furtrell's RSyntaxTextArea
org.simbrain.util.table - package org.simbrain.util.table: The util.table package contains a simple table, and a GUI component for viewing this table.
org.simbrain.util.widgets - package org.simbrain.util.widgets: The simbrain.util.widgets package contains various custom GUI widgets, as well as other utility classes that rely on images and other graphics resources.
org.simbrain.workspace - package org.simbrain.workspace: The workspace package contains the top level container for the other components of Simbrain--the network, world, and gauge(s).
org.simbrain.workspace.actions - package org.simbrain.workspace.actions: The workspace.actions package contains common action classes for workspace components (e.g.
org.simbrain.workspace.actions.chart - package org.simbrain.workspace.actions.chart: The workspace.actions.chart package contains actions relating to adding charts.
org.simbrain.workspace.component_actions - package org.simbrain.workspace.component_actions: The workspace.component_actions package contains actions that can be used in specific workspace components.
org.simbrain.workspace.gui - package org.simbrain.workspace.gui: The workspace.gui package contains the main classes relating to the Simbrain desktop, a Piccolo-based zoomable GUI for designing, editing, and running workspace simulations.
org.simbrain.workspace.gui.couplingmanager - package org.simbrain.workspace.gui.couplingmanager: The workspace.gui.couplingmanager package contains the main classes relating to the workspace coupling manager.
org.simbrain.workspace.updater - package org.simbrain.workspace.updater: The workspace.updater package contains code for managing workspace update.
org.simbrain.world.dataworld - package org.simbrain.world.dataworld: The world.dataworld package contains the simplest world type, a "dataworld" which is simply a spreadsheet which sends data to worlds in the form of rows on a simple table.
org.simbrain.world.game - package org.simbrain.world.game: (Currently unused) Was going to hold different "game worlds", e.g.
org.simbrain.world.game.tictactoe - package org.simbrain.world.game.tictactoe: (Currently unused) The unfinished beginnings of a tic-tac-toe game.
org.simbrain.world.midiworld - package org.simbrain.world.midiworld: (Currently unused) A world which allows sounds to be produced using MIDI interface.
org.simbrain.world.odorworld - package org.simbrain.world.odorworld: The world.odorworld package describes a world in which an agent can move around and smell objects, which are coded as vectors of values which diminish in various ways as the agent is closer or farther from the agent.
org.simbrain.world.odorworld.actions - package org.simbrain.world.odorworld.actions: The odorworld.actions package contains classes of actions (mainly used in menus) for Odor World.
org.simbrain.world.odorworld.behaviors - package org.simbrain.world.odorworld.behaviors: The odorworld.behaviors package contains classes for the implementation of the behavior interface and related classes of the different types of behaviors.
org.simbrain.world.odorworld.dialogs - package org.simbrain.world.odorworld.dialogs: The odorworld.dialog package contains classes for creating and editing dialogs within Odor World.
org.simbrain.world.odorworld.effectors - package org.simbrain.world.odorworld.effectors: The world.odorworld.effectors package contains effects that can be added to objects to allow them to move in custom ways.
org.simbrain.world.odorworld.entities - package org.simbrain.world.odorworld.entities: The odorworld.entites package contains classes for managing and editing entities in Ordor World.
org.simbrain.world.odorworld.resources - package org.simbrain.world.odorworld.resources: The odorworld.resources package contains a resource manager class for retriving resources from the program.
org.simbrain.world.odorworld.sensors - package org.simbrain.world.odorworld.sensors: The odorworld.sensors package contains classes of different types of sensors for receiving information from the Odor World envirnoment.
org.simbrain.world.oscworld - package org.simbrain.world.oscworld: (Currently unused) A world which allows sounds to be produced using open sound control.
org.simbrain.world.textworld - package org.simbrain.world.textworld: The world.textworld package describes a world in which strings of text are converted into vectors.
org.simbrain.world.textworld.dictionary - package org.simbrain.world.textworld.dictionary: The textworld.dictionary package contains classes for managing and editing the dictionary in Text World.
org.simbrain.world.threedee - package org.simbrain.world.threedee: (Currently unused) The 3D world is a simple full three dimensional environment containing agents that can be controlled by and send information to external couplings.
org.simbrain.world.threedee.sensors - package org.simbrain.world.threedee.sensors: (Currently unused) This package contains the code for the 3-D world sensors.
org.simbrain.world.visionworld - package org.simbrain.world.visionworld: The vision world package contains classes for the implementation of Vision World.
org.simbrain.world.visionworld.action - package org.simbrain.world.visionworld.action: The visionworld.action package contain classes for creating, editing and managing actions within Vision World.
org.simbrain.world.visionworld.dialog - package org.simbrain.world.visionworld.dialog: The visionworld.dialog package contains classes for creating and editing dialogs within Vision World.
org.simbrain.world.visionworld.filter - package org.simbrain.world.visionworld.filter: The visionworld.filter package contains classes for the implementation of the filter interface.
org.simbrain.world.visionworld.filter.editor - package org.simbrain.world.visionworld.filter.editor: The visionworld.filter.editor package contains classes of the different types of filter editors.
org.simbrain.world.visionworld.node - package org.simbrain.world.visionworld.node: The visionworld.node package contains Vision World piccolo nodes and related classes.
org.simbrain.world.visionworld.node.editor - package org.simbrain.world.visionworld.node.editor: The visionworld.node.editor package contain the code for Vision World node editors.
org.simbrain.world.visionworld.pixelmatrix - package org.simbrain.world.visionworld.pixelmatrix: The visionworld.pixelmartix package contains classes for the implementation of the PixelMatrix interface.
org.simbrain.world.visionworld.pixelmatrix.editor - package org.simbrain.world.visionworld.pixelmatrix.editor: The visionworld.pixelmatrix.editor package contains classes of the different types of pixel matrix editors.
org.simbrain.world.visionworld.sensormatrix - package org.simbrain.world.visionworld.sensormatrix: The visionworld.sensormatrix package contains classes for the implementation of the SensorMatrix interface.
org.simbrain.world.visionworld.sensormatrix.editor - package org.simbrain.world.visionworld.sensormatrix.editor: The visionworld.sensormatrix.editor package contains classes of sensor matrix editors.
OrientationComparator - Enum in org.simbrain.network.util: Comparators for using in sorting various kinds of org.simbrain.network lists.
OscWorldComponent - Class in org.simbrain.world.oscworld: OSC world component.
OscWorldComponent(String) - Constructor for class org.simbrain.world.oscworld.OscWorldComponent: Create a new OSC world component with the specified name.
OscWorldDesktopComponent - Class in org.simbrain.world.oscworld: OSC world desktop component.
OscWorldDesktopComponent(GenericFrame, OscWorldComponent) - Constructor for class org.simbrain.world.oscworld.OscWorldDesktopComponent: Create a new OSC world desktop component with the specified OSC world component.
OutlinedObjects - Class in org.simbrain.network.gui.nodes: A node that draws an outline around its children nodes.
OutlinedObjects() - Constructor for class org.simbrain.network.gui.nodes.OutlinedObjects: Construct the outlined objects group.
outlinedObjects - Variable in class org.simbrain.network.gui.nodes.SynapseGroupNode: The outlined objects (synapses) for this node.
OverwritableHistogramDataset - Class in org.simbrain.plot.histogram: A modification of the JFreeChart class HistogramDataset that allows data to be overridden.
OverwritableHistogramDataset() - Constructor for class org.simbrain.plot.histogram.OverwritableHistogramDataset: Creates a new (empty) dataset with a default type of HistogramType.FREQUENCY.
OverwritableHistogramDataset.ColoredDataSeries - Class in org.simbrain.plot.histogram: A histogram data series associated with a color.
overwriteSeries(String, double[], int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Add new values to an existing series.

P

pack() - Method in interface org.simbrain.util.genericframe.GenericFrame
pack() - Method in class org.simbrain.world.dataworld.DataWorldDesktopComponent
paint(PPaintContext) - Method in class org.simbrain.network.gui.nodes.OutlinedObjects: Change the default paint to fill an expanded bounding box based on its children's bounds.
paint(PPaintContext) - Method in class org.simbrain.network.gui.nodes.SelectionMarquee
paint(Graphics, JComponent) - Method in class org.simbrain.util.MultiLineToolTipUI
paint(Graphics) - Method in class org.simbrain.workspace.actions.OpenCouplingListAction.MyGlassPane
paint(Graphics) - Method in class org.simbrain.workspace.gui.SplashWindow: Paints the image on the window.
paint(PPaintContext) - Method in class org.simbrain.world.visionworld.node.AbstractPixelMatrixNode
paint(PPaintContext) - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode
paint(PPaintContext) - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode
paintComponent(Graphics) - Method in class org.simbrain.util.ImagePreviewPanel
paintComponent(Graphics) - Method in class org.simbrain.util.widgets.LinkIcon
paintComponent(Graphics) - Method in class org.simbrain.util.widgets.StopLight
paintComponent(Graphics) - Method in class org.simbrain.world.odorworld.OdorWorldPanel
paintView() - Method in class org.simbrain.world.visionworld.VisionWorld: Switch to the paint view.
PaintViewAction - Class in org.simbrain.world.visionworld.action: Paint view action.
PaintViewAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.PaintViewAction: Create a new paint view action.
pan(PInputEvent) - Method in class org.simbrain.network.gui.DragEventHandler: Pans the camera in response to the pan event provided.
panel - Variable in class org.simbrain.network.gui.dialogs.text.TextDialog: Main panel.
panel - Variable in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: The panel containing the components.
param1 - Variable in class org.simbrain.util.randomizer.Randomizer: First parameter of the selected probability distribution.
param2 - Variable in class org.simbrain.util.randomizer.Randomizer: First parameter of the selected probability distribution.
ParameterGetter<T,V> - Interface in org.simbrain.network.gui
paramString() - Method in class org.simbrain.workspace.updater.SynchronizingInvocationEvent
parent - Variable in class org.simbrain.world.odorworld.effectors.Effector: Reference to parent entity.
parent - Variable in class org.simbrain.world.odorworld.LifeCycle: Parent entity.
parent - Variable in class org.simbrain.world.odorworld.sensors.Sensor: Reference to parent entity.
parentBoundsChanged() - Method in class org.simbrain.network.gui.nodes.SelectionHandle
parentBoundsChanged() - Method in class org.simbrain.network.gui.nodes.SourceHandle
parseInteger(JTextField) - Static method in class org.simbrain.util.Utils: Parses the given String in the text field into an integer.
parseInteger(String) - Static method in class org.simbrain.util.Utils: The same as Utils.parseInteger(JTextField) except using a String directly as an input.
parseVectorString(String) - Static method in class org.simbrain.util.Utils: Converts a String representation of a vector (e.g.
paste(NetworkPanel) - Static method in class org.simbrain.network.gui.Clipboard: Paste objects into the netPanel.
paste() - Method in class org.simbrain.network.gui.NetworkPanel: Paste from the clipboard.
PasteAction - Class in org.simbrain.network.gui.actions.edit: Paste action.
PasteAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.PasteAction: Create a new paste action with the specified network panel.
pasteItem(Point, OdorWorldPanel) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Paste an object to a world.
pdf - Variable in class org.simbrain.util.randomizer.Randomizer
perform() - Method in class org.simbrain.network.update_actions.concurrency_tools.BufferedUpdateTask: Updates the neurons (does not send their buffered value to their activation) then updates all afferent synapses to the neurons in question.
perform() - Method in class org.simbrain.network.update_actions.concurrency_tools.SynchronizationPoint
perform() - Method in interface org.simbrain.network.update_actions.concurrency_tools.Task
perturbationAmount - Variable in class org.simbrain.util.projection.ProjectSammon: Amount by which to perturb overlapping points.
perturbOverlappingPoints(double) - Method in class org.simbrain.util.projection.Dataset: Find repeated points and perturb them slightly so they don't overlap.
PieChartComponent - Class in org.simbrain.plot.piechart: Pie chart component.
PieChartComponent(String) - Constructor for class org.simbrain.plot.piechart.PieChartComponent: Create new PieChart Component.
PieChartComponent(String, PieChartModel) - Constructor for class org.simbrain.plot.piechart.PieChartComponent: Initializes a pie chart with a model.
PieChartGui - Class in org.simbrain.plot.piechart: Display a PieChart.
PieChartGui(GenericFrame, PieChartComponent) - Constructor for class org.simbrain.plot.piechart.PieChartGui: Construct the GUI Pie Chart.
PieChartModel - Class in org.simbrain.plot.piechart: Model data for pie charts.
PieChartModel() - Constructor for class org.simbrain.plot.piechart.PieChartModel: Default constructor.
pinv(Matrix) - Static method in class org.simbrain.util.math.Matrices: Computes the Moore-Penrose pseudoinverse using the SVD method.
PIXEL_ACCUMULATOR - Static variable in class org.simbrain.world.visionworld.filter.editor.FilterEditors: Pixel accumulator editor.
PixelAccumulator - Class in org.simbrain.world.visionworld.filter: Pixel accumulator.
PixelAccumulator() - Constructor for class org.simbrain.world.visionworld.filter.PixelAccumulator
PixelAccumulatorEditor - Class in org.simbrain.world.visionworld.filter.editor: Pixel accumulator editor.
PixelAccumulatorEditor() - Constructor for class org.simbrain.world.visionworld.filter.editor.PixelAccumulatorEditor: Create a new pixel accumulator editor.
PixelMatrix - Interface in org.simbrain.world.visionworld: Two-dimensional matrix of pixel data.
pixelMatrixChanged(VisionWorldModelEvent) - Method in class org.simbrain.world.visionworld.VisionWorldModelAdapter: Notify this listener the pixel matrix changed in a vision world model.
pixelMatrixChanged(VisionWorldModelEvent) - Method in interface org.simbrain.world.visionworld.VisionWorldModelListener: Notify this listener the pixel matrix changed in a vision world model.
PixelMatrixEditor - Interface in org.simbrain.world.visionworld.pixelmatrix.editor: Pixel matrix editor.
PixelMatrixEditorException - Exception in org.simbrain.world.visionworld.pixelmatrix.editor: Pixel matrix editor exception.
PixelMatrixEditorException() - Constructor for exception org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditorException: Create a new pixel matrix editor exception.
PixelMatrixEditorException(String) - Constructor for exception org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditorException: Create a new pixel matrix editor exception with the specified message.
PixelMatrixEditorException(Throwable) - Constructor for exception org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditorException: Create a new pixel matrix editor exception with the specified cause.
PixelMatrixEditorException(String, Throwable) - Constructor for exception org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditorException: Create a new pixel matrix editor exception with the specified message and cause.
PixelMatrixEditors - Class in org.simbrain.world.visionworld.pixelmatrix.editor: Pixel matrix editors.
PixelMatrixEditors() - Constructor for class org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditors
PixelMatrixImageNode - Class in org.simbrain.world.visionworld.node: Pixel matrix image node.
PixelMatrixImageNode(PixelMatrix) - Constructor for class org.simbrain.world.visionworld.node.PixelMatrixImageNode: Create a new pixel matrix image node with the specified pixel matrix.
PixelMatrixImageNodeEditor - Interface in org.simbrain.world.visionworld.node.editor: Pixel matrix image node editor.
PixelMatrixImageNodeTableEditor - Class in org.simbrain.world.visionworld.node.editor: Pixel matrix node table editor.
PixelMatrixImageNodeTableEditor() - Constructor for class org.simbrain.world.visionworld.node.editor.PixelMatrixImageNodeTableEditor: Create a new pixel matrix image node table editor.
PlotActionManager - Class in org.simbrain.plot.actions: Manages the actions for the plot components.
PlotActionManager(GuiComponent) - Constructor for class org.simbrain.plot.actions.PlotActionManager: Plot component action manager.
PointNeuronComparator() - Constructor for class org.simbrain.network.subnetworks.KWTA.PointNeuronComparator
PointNeuronRule - Class in org.simbrain.network.neuron_update_rules: PointNeuron from O'Reilley and Munakata, Computational Explorations in Cognitive Neuroscience, chapter 2.
PointNeuronRule() - Constructor for class org.simbrain.network.neuron_update_rules.PointNeuronRule
PointNeuronRule.OutputFunction - Enum in org.simbrain.network.neuron_update_rules: Output functions.
PointNeuronRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: PointNeuronPanel TODO: Check this class for consistency.
PointNeuronRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.PointNeuronRulePanel: Creates an instance of this panel.
polarity - Variable in class org.simbrain.util.randomizer.PolarizedRandomizer
PolarizedRandomizer - Class in org.simbrain.util.randomizer: A tentative solution to some of the issues involving randomizers....
PolarizedRandomizer() - Constructor for class org.simbrain.util.randomizer.PolarizedRandomizer: Default constructor.
PolarizedRandomizer(SimbrainConstants.Polarity) - Constructor for class org.simbrain.util.randomizer.PolarizedRandomizer
PolarizedRandomizer(SimbrainConstants.Polarity, ProbDistribution) - Constructor for class org.simbrain.util.randomizer.PolarizedRandomizer
PolarizedRandomizer(PolarizedRandomizer) - Constructor for class org.simbrain.util.randomizer.PolarizedRandomizer: Copy constructor.
polarizeSynapses(Collection<Synapse>, double) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Changes all the synapses in a given collection such that excitatoryRatio of them are excitatory and 1 - excitatoryRatio of them are inhibitory, assigning default strengths respectively to each.
positionChanged() - Method in interface org.simbrain.world.textworld.TextListener: The position of the caret has changed.
positionChanged() - Method in class org.simbrain.world.textworld.TextListener.TextAdapter
positionLayers() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: A helper method which positions the layers relative to each other in an aesthetically pleasing arrangement.
postAddInit() - Method in class org.simbrain.docviewer.DocViewerDesktopComponent
postAddInit() - Method in class org.simbrain.network.desktop.NetworkDesktopComponent
postAddInit() - Method in class org.simbrain.plot.barchart.BarChartGui: Initializes frame.
postAddInit() - Method in class org.simbrain.plot.piechart.PieChartGui: Initializes frame.
postAddInit() - Method in class org.simbrain.plot.projection.ProjectionGui: Initializes frame.
postAddInit() - Method in class org.simbrain.plot.rasterchart.RasterPlotGui: Initializes frame.
postAddInit() - Method in class org.simbrain.plot.scatterplot.ScatterPlotGui: Initializes frame.
postAddInit() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotGui: Initializes frame.
postAddInit() - Method in class org.simbrain.workspace.gui.GuiComponent: If any initialization is needed after adding this component to workspace.
postAddInit() - Method in class org.simbrain.workspace.updater.UpdateActionManager: Perform initialization after deserializing.
postAddInit() - Method in class org.simbrain.world.dataworld.DataWorldDesktopComponent
postAddInit() - Method in class org.simbrain.world.odorworld.OdorWorldDesktopComponent
postAddInit() - Method in class org.simbrain.world.textworld.DisplayComponentDesktopGui
postAddInit() - Method in class org.simbrain.world.textworld.ReaderComponentDesktopGui
postAddInit() - Method in class org.simbrain.world.visionworld.VisionWorldDesktopComponent: If any initialization is needed after adding this component to workspace.
postEvent(AWTEvent) - Method in class org.simbrain.workspace.updater.InterceptingEventQueue: Posts AWTEvents.
postOpenInit() - Method in class org.simbrain.util.projection.Dataset: Initializes Dataset from persistent data.
postOpenInit() - Method in class org.simbrain.util.projection.Projector: Updates datasets from persistent forms of data.
postOpenInit() - Method in class org.simbrain.world.textworld.DisplayWorld: Initializes Dataset from persistent data.
postSaveReInit() - Method in class org.simbrain.network.core.Network: Returns synapse groups to a usable state after a save is performed.
postSaveReInit() - Method in class org.simbrain.network.groups.SynapseGroup: A post initialization which must be done if the user wants to save the network, but continue using the network after saving (since the saving process sets the synapse sets to null.
postSerializationInit() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Initialize the animation from stored image location(s).
postSerializationInit() - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Initialize map animations using image location information.
postUnmarshallingInit() - Method in class org.simbrain.network.core.NetworkUpdateManager: Perform any initialization required after opening a network from xml.
postUnmarshallingInit() - Method in class org.simbrain.network.core.Neuron: Perform any initialization required when creating a neuron, but after the parent network has been added.
postUnmarshallingInit() - Method in class org.simbrain.network.core.Synapse: Called after a synapse is de-serialized, to repopulate fan-in and fan-out lists.
postUnmarshallingInit() - Method in class org.simbrain.network.groups.SynapseGroup: Perform operations required after opening a synapse group.
PotentialAttribute - Class in org.simbrain.workspace: Even though a Coupling consists of a Producer and a Consumer, these attributes are usually not directly created, but are created from a PotentialProducer or PotentialConsumer object (using creation methods in AttributeManager).
PotentialAttribute(WorkspaceComponent, Object, String, Class<?>, Class<?>[], Object[], String) - Constructor for class org.simbrain.workspace.PotentialAttribute: Construct a potential attribute.
PotentialAttributePanel - Class in org.simbrain.workspace.gui.couplingmanager: Displays a panel with a JComboBox, which the user uses to select a component, and a JList of attributes for that component.
PotentialAttributePanel(Workspace, PotentialAttributePanel.ProducerOrConsumer) - Constructor for class org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel: Creates a new attribute list panel.
PotentialAttributePanel.ProducerOrConsumer - Enum in org.simbrain.workspace.gui.couplingmanager
potentialAttributesChanged() - Method in interface org.simbrain.workspace.AttributeListener: Potential attributes have changed in some way, such that the list of potential attributes for a given workspace component is changed.
PotentialConsumer - Class in org.simbrain.workspace: A PotentialAttribute corresponding to a Consumer.
PotentialConsumer(WorkspaceComponent, Object, String, Class<?>[], Object[], String) - Constructor for class org.simbrain.workspace.PotentialConsumer: Construct a potential consumer for the case where the method has multiple arguments.
PotentialProducer - Class in org.simbrain.workspace: A PotentialAttribute corresponding to a Producer.
PotentialProducer(WorkspaceComponent, Object, String, Class<?>, Class<?>[], Object[], String) - Constructor for class org.simbrain.workspace.PotentialProducer: Construct a potential consumer.
PRE_ALLOCATED_NUM_SYNAPSES - Static variable in class org.simbrain.network.core.Neuron: Pre-allocates the number of bins in this neuron's fanIn/Out for efficiency.
preAllocateSynapses(int) - Method in class org.simbrain.network.groups.SynapseGroup: Pre-allocates, that is sets the initial capacity of the arraylist containing this synapse group's synapses.
Predicate - Interface in org.simbrain.util: Re-implementation of same interface from org.apache.commons.collections.
preferencesChanged() - Method in interface org.simbrain.world.textworld.TextListener: The current preferences have changed.
preferencesChanged() - Method in class org.simbrain.world.textworld.TextListener.TextAdapter
preSaveInit() - Method in class org.simbrain.network.core.Network: Perform operations required before saving a network.
preSaveInit() - Method in class org.simbrain.network.groups.SynapseGroup: Perform operations required before saving a synapse group.
preSaveInit() - Method in class org.simbrain.util.projection.Dataset: Initializes persistent data.
preSaveInit() - Method in class org.simbrain.world.textworld.DisplayWorld: Initializes persistent data.
preSaveInitFull() - Method in class org.simbrain.network.groups.SynapseGroup: The pre-save init to be used to save all relevant synapse parameters in the byte array.
preSerializationInit() - Method in class org.simbrain.workspace.Workspace: Actions required prior to proper serialization.
previewNextChar() - Method in class org.simbrain.world.textworld.TextWorld: Returns a "preview" of the next character in the world.
previewNextToken() - Method in class org.simbrain.world.textworld.ReaderWorld: Utility method to "preview" the next token after the current one.
printActivations() - Method in class org.simbrain.network.groups.NeuronGroup: Print activations as a vector.
printDataset() - Method in class org.simbrain.util.projection.Dataset: Print out all points in the dataset Useful for debugging.
printLayers(List<List<Neuron>>) - Static method in class org.simbrain.network.util.SimnetUtils: Prints a group of layers (a list of lists of neurons), typically for debugging.
printToTerminal(String) - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Print text to terminal.
printVector(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Prints out the vector list.
PRIORITY_FONT - Static variable in class org.simbrain.network.gui.nodes.NeuronNode: Priority Font.
PriorityComparator() - Constructor for class org.simbrain.network.core.Network.PriorityComparator
PriorityUpdate - Class in org.simbrain.network.update_actions: Loose neurons (neurons not in groups) are updated in accordance with an ordered priority list.
PriorityUpdate(Network) - Constructor for class org.simbrain.network.update_actions.PriorityUpdate
ProbabilisticResponder - Class in org.simbrain.network.synapse_update_rules.spikeresponders: Probabilistic spike responders produces a response with some probability.
ProbabilisticResponder() - Constructor for class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder
ProbabilisticSpikeResponderPanel - Class in org.simbrain.network.gui.dialogs.synapse.spike_responders: ProbabilisticSpikeResponderPanel.
ProbabilisticSpikeResponderPanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: This method is the default constructor.
ProbDistPanel - Class in org.simbrain.util.randomizer.gui: A panel representing a given probability distribution.
ProbDistPanel(ProbDistribution) - Constructor for class org.simbrain.util.randomizer.gui.ProbDistPanel: Creates a panel within this class that is globally accessible representing an editor for a randomizer with a specific probability distribution.
ProbDistPanel() - Constructor for class org.simbrain.util.randomizer.gui.ProbDistPanel
ProbDistribution - Enum in org.simbrain.util.math
producer - Variable in class org.simbrain.workspace.gui.CouplingMenuProducer: The base attribute for this menu.
Producer<E> - Interface in org.simbrain.workspace: A wrapper for a public getter in a Simbrain object.
progressUpdated(String, int) - Method in interface org.simbrain.network.trainers.TrainerListener: Called for updates on the progress of a trainer.
project() - Method in class org.simbrain.util.projection.ProjectCoordinate
project() - Method in class org.simbrain.util.projection.ProjectionMethod: Perform operations necessary to project the data.
project() - Method in class org.simbrain.util.projection.ProjectNNSubspace
project() - Method in class org.simbrain.util.projection.ProjectPCA
project() - Method in class org.simbrain.util.projection.ProjectSammon
project() - Method in class org.simbrain.util.projection.ProjectTriangulate
ProjectCoordinate - Class in org.simbrain.util.projection: Project Coordinate is perhaps the simplest possible projection algorithm; It simply takes two specified dimensions in the high dimensional space, and uses these as the basis for the low-dimensional space.
ProjectCoordinate(Projector) - Constructor for class org.simbrain.util.projection.ProjectCoordinate: Default projector coordinate constructor.
ProjectionComponent - Class in org.simbrain.plot.projection: Component for a projection plot.
ProjectionComponent(String) - Constructor for class org.simbrain.plot.projection.ProjectionComponent: Create new Projection Component.
ProjectionComponent(String, int) - Constructor for class org.simbrain.plot.projection.ProjectionComponent: Initializes a JFreeChart with specific number of data sources.
ProjectionComponent(ProjectionModel, String) - Constructor for class org.simbrain.plot.projection.ProjectionComponent: Create a projection component from an existing set of data.
ProjectionComponent.Dimension - Class in org.simbrain.plot.projection: Object which adds data to one dimension of a projection component.
ProjectionGui - Class in org.simbrain.plot.projection: Gui Component to display a high dimensional projection object.
ProjectionGui(GenericFrame, ProjectionComponent) - Constructor for class org.simbrain.plot.projection.ProjectionGui: Construct the Projection GUI.
ProjectionMethod - Class in org.simbrain.util.projection: ProjectionMethod is a superclass for all specific projection algorithms used.
ProjectionMethod(Projector) - Constructor for class org.simbrain.util.projection.ProjectionMethod: Superclass constructor which sets the projector instance.
projectionMethodChanged() - Method in interface org.simbrain.util.projection.ProjectorListener: Fired when the projection method is changed.
ProjectionModel - Class in org.simbrain.plot.projection: Main data for a projection chart.
ProjectionModel() - Constructor for class org.simbrain.plot.projection.ProjectionModel: Default constructor.
ProjectionModel(int) - Constructor for class org.simbrain.plot.projection.ProjectionModel: Construct a projection model with a specified number of dimensions.
ProjectionPlotActions - Class in org.simbrain.plot.projection: Actions for projection plot.
ProjectionPlotActions() - Constructor for class org.simbrain.plot.projection.ProjectionPlotActions
ProjectionPreferencesDialog - Class in org.simbrain.plot.projection: A dialog box for setting general projector preferences.
ProjectionPreferencesDialog(Projector) - Constructor for class org.simbrain.plot.projection.ProjectionPreferencesDialog: Construct the preference dialog.
ProjectionUpdater - Class in org.simbrain.plot.projection: Update iterable projection algorithms.
ProjectionUpdater(ProjectionComponent) - Constructor for class org.simbrain.plot.projection.ProjectionUpdater
ProjectNNSubspace - Class in org.simbrain.util.projection: ProjectNNSubspace is a Nearest Neighbor Subspace Method.
ProjectNNSubspace(Projector) - Constructor for class org.simbrain.util.projection.ProjectNNSubspace: Default PCA project.
projector - Variable in class org.simbrain.util.projection.ProjectionMethod: Reference to parent projector.
Projector - Class in org.simbrain.util.projection: Projector is a the main class of this package, which provides an interface for projecting high dimensional data to 2 dimensions (this is also known as "dimensionality reduction").
Projector() - Constructor for class org.simbrain.util.projection.Projector: Default constructor for projector.
Projector(int) - Constructor for class org.simbrain.util.projection.Projector: Default constructor for projector.
projectorColorsChanged() - Method in interface org.simbrain.util.projection.ProjectorListener: Fired when the colors of some datapoints have changed but nothing else.
projectorDataChanged() - Method in interface org.simbrain.util.projection.ProjectorListener: Fired when the the underlying data has been changed, e.g the projector has been reinitailzed, data reset, etc.
ProjectorListener - Interface in org.simbrain.util.projection: Classes with implement this interface fire events indicating changes in the status of a trainer.
ProjectPCA - Class in org.simbrain.util.projection: ProjectPCA Projects the high-dimensional dataset along its two principal components to the low-d dataset.
ProjectPCA(Projector) - Constructor for class org.simbrain.util.projection.ProjectPCA: Default PCA project.
ProjectSammon - Class in org.simbrain.util.projection: ProjectSammon.java implements gradient descent to compute image of Sammon projection.
ProjectSammon(Projector) - Constructor for class org.simbrain.util.projection.ProjectSammon: Default sammon projector constructor.
ProjectTriangulate - Class in org.simbrain.util.projection: ProjectTriangulate takes each new point and determines which two points in the current data set are closest to it.
ProjectTriangulate(Projector) - Constructor for class org.simbrain.util.projection.ProjectTriangulate: Default PCA project.
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.nodes.NeuronNode
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.nodes.SubnetworkNode
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNode
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.nodes.TextNode
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
propertyChange(PropertyChangeEvent) - Method in class org.simbrain.util.ImagePreviewPanel
propertyChanged() - Method in interface org.simbrain.world.odorworld.WorldListener: Some world parameter has changed.
propertyChanged() - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
PropertyNotFoundException(String) - Constructor for exception org.simbrain.util.SimbrainPreferences.PropertyNotFoundException: Construct the exception with an error message, indicating the property name that could not be found.
PropertyTabAction - Class in org.simbrain.workspace.actions: Open data world in current workspace.
PropertyTabAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.PropertyTabAction: Create an open data world with the specified workspace.
proposeMapping(List<Point2D>, Set<SynapseGroupArrow>, NeuronGroupNode.Port) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
PROTOTYPE_RESPONDER - Static variable in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel: The prototypical jump and decay responder.
PROTOTYPE_RESPONDER - Static variable in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: The prototypical jump and decay responder.
PROTOTYPE_RESPONDER - Static variable in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: The prototypical probabilistic responder rule.
PROTOTYPE_RESPONDER - Static variable in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: The prototypical rise and decay spike responder.
PROTOTYPE_RESPONDER - Static variable in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel: The prototypical rise and decay spike responder.
prune() - Method in class org.simbrain.network.groups.NeuronGroup: Removes all neurons with no incoming or outgoing synapses from the group.
prune() - Method in class org.simbrain.network.groups.SynapseGroup: Removes all synapses with weight 0 from the group.
PrunerPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.PrunerPanel: Construct the panel.
pullViewPositionFromModel() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Updates the position of the view neuron based on the position of the model neuron.
pushViewPositionToModel() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Update the position of the model neuron based on the global coordinates of this pnode.
pushViewPositionToModel() - Method in class org.simbrain.network.gui.nodes.TextNode: Update the position of the model text object based on the global coordinates of this pnode.
putDouble(String, double) - Static method in class org.simbrain.util.SimbrainPreferences: Set a property whose value is a double.
putFloat(String, float) - Static method in class org.simbrain.util.SimbrainPreferences: Set a property whose value is a float.
putInt(String, int) - Static method in class org.simbrain.util.SimbrainPreferences: Set a property whose value is a integer.
putString(String, String) - Static method in class org.simbrain.util.SimbrainPreferences: Set a property whose value is a String.

Q

queueTasks() - Method in class org.simbrain.workspace.updater.InterceptingEventQueue: Starts queuing tasks.
queueTasks() - Method in interface org.simbrain.workspace.updater.TaskSynchronizationManager: Tells the manager to queue tasks.
QuickConnectDialog(QuickConnectPreferencesPanel) - Constructor for class org.simbrain.network.gui.dialogs.connect.QuickConnectPreferencesPanel.QuickConnectDialog: Construct the dialog.
QuickConnectionManager - Class in org.simbrain.network.connections: Manage quick connection preferences, where a connection is applied using key commands.
QuickConnectionManager() - Constructor for class org.simbrain.network.connections.QuickConnectionManager: Construct the quick connection manager.
QuickConnectPreferencesPanel - Class in org.simbrain.network.gui.dialogs.connect: QuickConnectPreferencesPanel is a dialog box for setting the properties of the quick connection manager, which is used when creating connections on loose neurons using key commands.
QuickConnectPreferencesPanel(NetworkPanel, Window) - Constructor for class org.simbrain.network.gui.dialogs.connect.QuickConnectPreferencesPanel: Connection dialog default constructor.
QuickConnectPreferencesPanel.QuickConnectDialog - Class in org.simbrain.network.gui.dialogs.connect: Helper class for embedding this panel in a dialog.
quit(boolean) - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Quit application.
QuitWorkspaceAction - Class in org.simbrain.workspace.actions: Quit the application.
QuitWorkspaceAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.QuitWorkspaceAction: Create a clear workspace action with the specified workspace.

R

Radial - Class in org.simbrain.network.connections: This connection type makes four types of distance-based connection probabilistically.
Radial() - Constructor for class org.simbrain.network.connections.Radial: Default constructor
Radial(double) - Constructor for class org.simbrain.network.connections.Radial
Radial(double, double) - Constructor for class org.simbrain.network.connections.Radial
Radial(double, double, double, double, double) - Constructor for class org.simbrain.network.connections.Radial
Radial.DensityEstimator - Class in org.simbrain.network.connections
RadialPanel - Class in org.simbrain.network.gui.dialogs.connect.connector_panels: SparsePanel creates a dialog for setting preferences of Sparse neuron connections.
RadialPanel(Radial) - Constructor for class org.simbrain.network.gui.dialogs.connect.connector_panels.RadialPanel: This method is the default constructor.
RadialSimple - Class in org.simbrain.network.connections: For each neuron, consider every neuron in an excitatory and inhibitory radius from it, and make excitatory and inhibitory synapses with them according to some probability.
RadialSimple(Network, List<Neuron>) - Constructor for class org.simbrain.network.connections.RadialSimple
RadialSimpleConstrainedKIn - Class in org.simbrain.network.connections
RadialSimpleConstrainedKIn(int, int, int, int, int, int) - Constructor for class org.simbrain.network.connections.RadialSimpleConstrainedKIn
RadialSimpleConstrainedKIn(int, int) - Constructor for class org.simbrain.network.connections.RadialSimpleConstrainedKIn
RANDOM - Static variable in class org.simbrain.world.visionworld.filter.editor.FilterEditors: Random filter editor.
RandomFilter - Class in org.simbrain.world.visionworld.filter: Random filter.
RandomFilter(double, double) - Constructor for class org.simbrain.world.visionworld.filter.RandomFilter: Create a new random filter with the specified minimum and maximum values.
RandomFilterEditor - Class in org.simbrain.world.visionworld.filter.editor: Random filter editor.
RandomFilterEditor() - Constructor for class org.simbrain.world.visionworld.filter.editor.RandomFilterEditor: Create a new random filter editor.
RandomGeneratorPanel - Class in org.simbrain.network.gui.dialogs.neuron.generator_panels: RandomNeuronPanel Currently unimplemented pending decisions about changing random neurons into "input generators".
RandomGeneratorPanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.generator_panels.RandomGeneratorPanel: Creates an instance of this panel.
randomize() - Method in class org.simbrain.network.core.Neuron: Randomize this neuron to a value between upperBound and lowerBound.
randomize() - Method in class org.simbrain.network.core.Synapse: Randomize this weight to a value between its upper and lower bounds.
randomize() - Method in class org.simbrain.network.groups.NeuronGroup: Randomize all neurons in group.
randomize() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Randomize and normalize weights.
randomize() - Method in class org.simbrain.network.subnetworks.Hopfield: Randomize weights symmetrically.
randomize() - Method in class org.simbrain.network.trainers.BackpropTrainer: Randomize the network.
randomize(List<Neuron>) - Method in class org.simbrain.network.trainers.BackpropTrainer: Randomize the specified layer.
randomize() - Method in class org.simbrain.network.trainers.BPTTTrainer
randomize() - Method in class org.simbrain.network.trainers.IterableTrainer: Randomize the network being trained.
randomize() - Method in class org.simbrain.network.trainers.LMSIterative: A standard way of randomizing networks to which LMSIterative is applied, by randomizing bias on output nodes and the single layer of weights.
randomize() - Method in class org.simbrain.network.trainers.SRNTrainer
randomize() - Method in class org.simbrain.util.environment.SmellSource: Randomize values.
randomize(int) - Method in class org.simbrain.util.projection.Dataset: Randomize dataset to a value between 0 and upperBound.
randomize(int) - Method in class org.simbrain.util.projection.Projector: Randomize the low-dimensional data.
randomize(List<SimbrainJTable.CellIndex>) - Method in class org.simbrain.util.table.NumericTable: Randomize neurons within specified bounds.
randomize() - Method in class org.simbrain.util.table.SimbrainJTable: Randomize selected cells.
randomizeAndPolarizeSynapses(Collection<Synapse>, PolarizedRandomizer, PolarizedRandomizer, double) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Randomizes a collection of synapses based on excitatory and inhibitory (polarized appropriately) randomizers, which cannot be the same randomizer.
randomizeAndPolarizeSynapses(Collection<Synapse>, double) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Randomize and polarize synapses using default excitatory and inhibitory polarizers (uniform 0 to 1).
randomizeBias(double, double) - Method in class org.simbrain.network.core.Neuron: If this neuron has a bias field, randomize it within the specified bounds.
randomizeBiases(double, double) - Method in class org.simbrain.network.core.Network: Randomize all biased neurons.
randomizeBiases(double, double) - Method in class org.simbrain.network.groups.NeuronGroup: Randomize bias for all neurons in group.
randomizeBuffer() - Method in class org.simbrain.network.core.Neuron: Randomize this neuron to a value between upperBound and lowerBound.
randomizeConnectionWeights() - Method in class org.simbrain.network.groups.SynapseGroup: Randomizes all the synapses according to their corresponding randomizers.
randomizeExcitatoryConnections() - Method in class org.simbrain.network.groups.SynapseGroup: Randomizes the weights of the excitatory connections in this group based on the parameters of SynapseGroup.exciteRand.
randomizeExcitatorySynapses(Collection<Synapse>, PolarizedRandomizer) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Randomizes the excitatory synapses in the given list of synapses using the given excitatory randomizer.
randomizeExcitatorySynapsesUnsafe(Collection<Synapse>, PolarizedRandomizer) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Randomizes the given synapses using the given excitatory randomizer without checking first to make sure that the given synapses or their source neurons are not inhibitory.
randomizeFanIn() - Method in class org.simbrain.network.core.Neuron: Randomize all synapses that attach to this neuron.
randomizeFanOut() - Method in class org.simbrain.network.core.Neuron: Randomize all synapses that attach to this neuron.
randomizeIncomingWeights() - Method in class org.simbrain.network.groups.NeuronGroup: Randomize fan-in for all neurons in group.
randomizeIncomingWeights() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Randomize all weights coming in to this network.
randomizeIncomingWeights() - Method in class org.simbrain.network.subnetworks.SOMGroup: Randomize all weights coming in to this network.
randomizeInhibitoryConnections() - Method in class org.simbrain.network.groups.SynapseGroup: Randomizes the weights of the inhibitory connections in this group based on the parameters of SynapseGroup.inhibRand.
randomizeInhibitorySynapses(Collection<Synapse>, PolarizedRandomizer) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Randomizes the inhibitory synapses in the given list of synapses using the given inhibitory randomizer.
randomizeInhibitorySynapsesUnsafe(Collection<Synapse>, PolarizedRandomizer) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Randomizes the given synapses using the given inhibitory randomizer without checking first to make sure that the given synapses or their source neurons are not excitatory.
randomizeNeurons() - Method in class org.simbrain.network.core.Network: Randomizes all neurons.
RandomizeObjectsAction - Class in org.simbrain.network.gui.actions.edit: Randomize screen elements action.
RandomizeObjectsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.RandomizeObjectsAction: Create a new randomize screen elements action with the specified network panel.
randomizeOutgoingWeights() - Method in class org.simbrain.network.groups.NeuronGroup: Randomize fan-out for all neurons in group.
Randomizer - Class in org.simbrain.util.randomizer
Randomizer() - Constructor for class org.simbrain.util.randomizer.Randomizer: Default constructor.
Randomizer(ProbDistribution) - Constructor for class org.simbrain.util.randomizer.Randomizer
Randomizer(Randomizer) - Constructor for class org.simbrain.util.randomizer.Randomizer: Copy constructor.
RandomizerPanel - Class in org.simbrain.util.randomizer.gui: RandomizerPanel an interface for setting parameters of a randomizer object.
RandomizerPanel() - Constructor for class org.simbrain.util.randomizer.gui.RandomizerPanel: This method is the default constructor.
RandomizerPanel(Window) - Constructor for class org.simbrain.util.randomizer.gui.RandomizerPanel: A constructor specifying a parent window for auto-resizing.
randomizeSequence() - Method in class org.simbrain.network.subnetworks.Hopfield: Randomizes the update sequence by shuffling the neuron list associated with this Hopfield network.
randomizeSymmetric() - Method in class org.simbrain.network.core.Synapse: Randomizes this synapse and sets the symmetric analogue to the same value.
randomizeSynapses(Collection<Synapse>, PolarizedRandomizer, PolarizedRandomizer) - Static method in class org.simbrain.network.connections.ConnectionUtilities
randomizeWeights() - Method in class org.simbrain.network.core.Network: Randomizes all loose weights.
RandomNeuronRule - Class in org.simbrain.network.neuron_update_rules.activity_generators: RandomNeuron produces random activations within specified parameters.
RandomNeuronRule(Neuron) - Constructor for class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
RandomNeuronRule(RandomNeuronRule, Neuron) - Constructor for class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
RandomNeuronRule() - Constructor for class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
randomVector(int) - Static method in class org.simbrain.util.math.SimbrainMath: Create a random vector with i components.
randomVector(int, double, double) - Static method in class org.simbrain.util.math.SimbrainMath: Returns a vector of random values between min and max.
randPermute(int, int) - Static method in class org.simbrain.util.math.SimbrainMath: Returns a random permutation of all the integers between floor (inclusive) and ceil (exclusive).
randPermuteWithExclusion(int, int, int) - Static method in class org.simbrain.util.math.SimbrainMath: Returns a random permutation of all the integers between floor (inclusive) and ceil (exclusive) with the exception of one number (excluded) which is intentionally excluded.
randShuffleK(ArrayList<Integer>, int, Random) - Static method in class org.simbrain.network.connections.Sparse: Randomly shuffles k integers in a list.
randTab - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: Random tab.
RasterModel - Class in org.simbrain.plot.rasterchart: Data model for a raster plot.
RasterModel() - Constructor for class org.simbrain.plot.rasterchart.RasterModel: Raster series model constructor.
RasterModel(int) - Constructor for class org.simbrain.plot.rasterchart.RasterModel: Initialize model to specified number of data sources.
RasterPlotActions - Class in org.simbrain.plot.rasterchart: Contains actions for use in raster plot
RasterPlotActions() - Constructor for class org.simbrain.plot.rasterchart.RasterPlotActions
RasterPlotComponent - Class in org.simbrain.plot.rasterchart: Represents raster data.
RasterPlotComponent(String) - Constructor for class org.simbrain.plot.rasterchart.RasterPlotComponent: Create new raster plot component.
RasterPlotComponent(String, RasterModel) - Constructor for class org.simbrain.plot.rasterchart.RasterPlotComponent: Creates a new raster plot component from a specified model.
RasterPlotComponent(String, int) - Constructor for class org.simbrain.plot.rasterchart.RasterPlotComponent: Initializes a JFreeChart with specific number of data sources.
RasterPlotGui - Class in org.simbrain.plot.rasterchart: Display a raster plot.
RasterPlotGui(GenericFrame, RasterPlotComponent) - Constructor for class org.simbrain.plot.rasterchart.RasterPlotGui: Construct a raster plot gui.
RasterPlotPanel - Class in org.simbrain.plot.rasterchart: Display a raster plot.
RasterPlotPanel(RasterModel) - Constructor for class org.simbrain.plot.rasterchart.RasterPlotPanel: Construct a raster panel.
read() - Method in class org.simbrain.console.CommandLineReader
read(char[], int, int) - Method in class org.simbrain.console.CommandLineReader: This is a degenerate implementation.
readData(File, boolean, boolean) - Method in class org.simbrain.util.table.NumericTable: Load a .csv file.
readData(File, boolean, boolean) - Method in class org.simbrain.util.table.TextTable: Load a .csv file.
ReaderComponent - Class in org.simbrain.world.textworld: ReaderComponent is the container for the readerworld, which adds producers.
ReaderComponent(String) - Constructor for class org.simbrain.world.textworld.ReaderComponent: Creates a new frame of type TextWorld.
ReaderComponent(String, ReaderWorld) - Constructor for class org.simbrain.world.textworld.ReaderComponent: Construct a component from an existing world; used in deserializing.
ReaderComponentDesktopGui - Class in org.simbrain.world.textworld: ReaderComponentDesktopGui is the gui view for the reader world.
ReaderComponentDesktopGui(GenericFrame, ReaderComponent) - Constructor for class org.simbrain.world.textworld.ReaderComponentDesktopGui: Creates a new frame of type TextWorld.
ReaderPanel - Class in org.simbrain.world.textworld: Display panel for reading data from user and showing text world's state.
ReaderPanel.MyHighlightPainter - Class in org.simbrain.world.textworld: A private subclass of the default highlight painter.
ReaderWorld - Class in org.simbrain.world.textworld: ReaderWorld intuitively models "reading".
ReaderWorld.ParseStyle - Enum in org.simbrain.world.textworld: List of parsing style.
readFileContents(File) - Static method in class org.simbrain.util.Utils: Returns the contents of a file as a String.
readNextInputs() - Method in class org.simbrain.network.groups.NeuronGroup: A forwarding method surrounding NeuronGroup.readNextInputUnsafe() in the appropriate checks to make it safe.
readResolve() - Method in class org.simbrain.world.textworld.DisplayWorld: Standard method call made to objects after they are deserialized.
readResolve() - Method in class org.simbrain.world.textworld.TextWorld: Standard method call made to objects after they are deserialized.
recall() - Method in class org.simbrain.network.subnetworks.SOMGroup: Pushes the weight values of an SOM neuron onto the input neurons.
ReceptiveField - Class in org.simbrain.world.visionworld: Receptive field.
ReceptiveField(int, int, int, int) - Constructor for class org.simbrain.world.visionworld.ReceptiveField: Create a new receptive field.
reconstructCompressedSynapseStrengths(byte[], SynapseGroup) - Static method in class org.simbrain.network.util.io_utilities.GroupDeserializer
reconstructCompressedSynapseStrengths(String, SynapseGroup) - Static method in class org.simbrain.network.util.io_utilities.GroupDeserializer: Reads a file containing the relative position and strengths of synapses, in compressed row format and stored in compressed byte code and recreates those synapse positions and their strengths in the supplied synapse groups.
recursivelySetIds() - Method in class org.simbrain.network.groups.Group: Set the id for this group.
recursivelySetIds() - Method in class org.simbrain.network.groups.Subnetwork
red - Variable in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: The red threshold.
redo() - Method in class org.simbrain.network.gui.UndoManager: Redo the last undone action.
redo() - Method in interface org.simbrain.network.gui.UndoManager.UndoableAction: Redo this action.
redraw() - Method in class org.simbrain.plot.histogram.HistogramModel: Re-add the data.
ReflectivePropertyEditor - Class in org.simbrain.util.propertyeditor.gui: ReflectivePropertyEditor.
ReflectivePropertyEditor(Object) - Constructor for class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Construct a property editor panel only.
ReflectivePropertyEditor() - Constructor for class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Use this constructor to make an editor, adjust its settings, and then initialize it with an object.
refresh() - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel: Refreshes the panel's view.
registerComponentInstance(WorkspaceComponent, GuiComponent) - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Registers instance of guiComponents.
reinforce() - Method in class org.simbrain.network.core.Synapse: Increase the absolute value of this weight by increment amount.
RELATIVE - Static variable in class org.simbrain.network.neuron_update_rules.DecayRule: Relative.
releaseTasks() - Method in class org.simbrain.workspace.updater.InterceptingEventQueue: Releases the queuing flag.
releaseTasks() - Method in interface org.simbrain.workspace.updater.TaskSynchronizationManager: Tells the manager to stop queuing tasks.
remove(Object) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Remove the specified element from the selection.
remove(Sensor) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Remove the specified sensor from this sensor selection model.
removeAction(NetworkUpdateAction) - Method in class org.simbrain.network.core.NetworkUpdateManager: Completely remove an action.
removeAction - Variable in class org.simbrain.network.gui.nodes.NeuronGroupNode: Action for removing this group
removeAction - Variable in class org.simbrain.network.gui.nodes.SubnetworkNode: Action for removing this group
removeAction - Variable in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Action for removing this group
removeAction(UpdateAction) - Method in class org.simbrain.workspace.updater.UpdateActionManager: Completely remove an action.
removeAfferent(Synapse) - Method in class org.simbrain.network.core.Neuron: Remove this neuron from source neuron via a weight.
removeAll(Collection) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Remove all of the specified elements from the selection.
removeAll(Collection<Sensor>) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Remove all of the specified collection of sensors from this sensor selection model.
removeAllButtonsFromToolBar() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel: Remove all buttons from the button panel; used when customzing the buttons on this panel.
removeAllButtonsFromToolBar() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Remove all buttons from the button panel; used when customzing the buttons on this panel.
removeAllComponents() - Method in class org.simbrain.workspace.Workspace: Disposes all Simbrain Windows.
removeAttachedCouplings(Attribute) - Method in class org.simbrain.workspace.CouplingManager: Removes all couplings associated with a producer or consumer.
removeAttributeListener(AttributeListener) - Method in class org.simbrain.workspace.WorkspaceComponent: Removes an AttributeListener from this component.
removeColumn() - Method in class org.simbrain.plot.barchart.BarChartModel: Removes the last bar from the bar chart data.
removeColumn(int) - Method in class org.simbrain.plot.barchart.BarChartModel
removeColumn(int, boolean) - Method in class org.simbrain.util.table.MutableTable: Remove column with choice whether to fire an event or not.
removeColumn(int) - Method in class org.simbrain.util.table.MutableTable: Remove column at specified index.
removeComponentListener(ComponentUpdateListener) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Removes a component listener from this instance.
removeCoupling(Coupling<?>) - Method in class org.simbrain.workspace.CouplingManager: Removes a coupling from the manager.
removeCoupling(Coupling<?>) - Method in class org.simbrain.workspace.Workspace: Removes a coupling from the CouplingManager.
removeCouplingListener(CouplingListener) - Method in class org.simbrain.workspace.CouplingManager: Removes the listener from the list.
removeCouplings(WorkspaceComponent) - Method in class org.simbrain.workspace.CouplingManager: Remove all couplings associated with a WorkspaceComponent.
removeCouplings(ArrayList<Coupling<?>>) - Method in class org.simbrain.workspace.CouplingManager: Remove a specified list of couplings.
removeDataSource() - Method in class org.simbrain.plot.piechart.PieChartModel: Removes a data source from the plot.
removeDataSource() - Method in class org.simbrain.plot.rasterchart.RasterModel: Removes a data source from the chart.
removeDataSource() - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel: Removes a data source.
removeDataSource() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel: Removes a data source from the chart.
removeEffector(Effector) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel: Remove an effector from the table representation.
removeEffector(Effector) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Removes an effector.
removeEfferent(Synapse) - Method in class org.simbrain.network.core.Neuron: Remove this neuron from target neuron via a weight.
removeErrorListener(ErrorListener) - Method in class org.simbrain.network.trainers.IterableTrainer: Remove an error listener.
removeFromParent() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional: TODO: Not sure why below is needed.
removeFromParent() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeRecurrent
removeFromParent() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple: TODO: Not sure why below is needed.
removeGroup(Group) - Method in class org.simbrain.network.core.Network: Remove the specified group.
removeGroupListener(GroupListener) - Method in class org.simbrain.network.core.Network: Remove a group listener.
removeHighlights(JTextComponent) - Method in class org.simbrain.world.textworld.ReaderPanel: Removes highlights from specified component.
removeIncomingSg(SynapseGroup) - Method in class org.simbrain.network.groups.NeuronGroup
removeListener(NetworkUpdateManager.UpdateManagerListener) - Method in class org.simbrain.network.core.NetworkUpdateManager: Remove listener.
removeListener(TrainerListener) - Method in class org.simbrain.network.trainers.Trainer: Remove a trainer listener.
removeListener(UpdateActionManager.UpdateManagerListener) - Method in class org.simbrain.workspace.updater.UpdateActionManager: Remove listener.
removeListener(WorkspaceListener) - Method in class org.simbrain.workspace.Workspace: Removes the listener from the workspace.
removeListener(TextListener) - Method in class org.simbrain.world.textworld.TextWorld: Remove a listener.
removeMatchingCoupling(Coupling<?>) - Method in class org.simbrain.workspace.CouplingManager: Remove coupling (if any) that is essentially a copy of the supplied coupling.
removeModelListener(VisionWorldModelListener) - Method in interface org.simbrain.world.visionworld.VisionWorldModel: Remove the specified vision world model listener.
removeModelListener(VisionWorldModelListener) - Method in class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Remove the specified vision world model listener.
removeNetworkListener(NetworkListener) - Method in class org.simbrain.network.core.Network: Remove a network listener.
removeNeuron(Neuron) - Method in class org.simbrain.network.core.Network: Deletes a neuron from the network.
removeNeuron(Neuron) - Method in class org.simbrain.network.groups.NeuronGroup: Delete the provided neuron.
removeNeuronGroup(NeuronGroup) - Method in class org.simbrain.network.groups.Subnetwork: Remove a neuron group.
removeNeuronNode(NeuronNode) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Remove a neuron node from the group node.
removeOutgoingSg(SynapseGroup) - Method in class org.simbrain.network.groups.NeuronGroup
removePropertyChangeListener(PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Remove the specified property change listener.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Remove the specified property change listener for the specified property.
removePropertyChangeListener(PropertyChangeListener) - Method in interface org.simbrain.world.visionworld.PixelMatrix: Remove the specified property change listener.
removePropertyChangeListener(String, PropertyChangeListener) - Method in interface org.simbrain.world.visionworld.PixelMatrix: Remove the specified property change listener for the specified property.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Remove the specified property change listener.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Remove the specified property change listener for the specified property.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.simbrain.world.visionworld.Sensor: Remove the specified property change listener.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.simbrain.world.visionworld.Sensor: Remove the specified property change listener for the specified property.
removeRow(int, boolean) - Method in class org.simbrain.util.table.MutableTable: Remove row with choice whether to fire an event or not.
removeRow(int) - Method in class org.simbrain.util.table.MutableTable: Remove a specified row.
removeRow(WorkspaceComponent) - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel: Remove a component from the list.
removeRow(int) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel: Remove a row
removeRow(int) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel: Remove a row.
removeSelectionHandleFrom(PNode) - Static method in class org.simbrain.network.gui.nodes.SelectionHandle: Remove the selection handle(s) from the specified node, if any exist.
removeSelectionListener(NetworkSelectionListener) - Method in class org.simbrain.network.gui.NetworkPanel: Remove the specified Network selection listener.
removeSelectionListener(NetworkSelectionListener) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Remove the specified network selection listener.
removeSensor(Sensor) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel: Remove a sensor from the table representation.
removeSensor(Sensor) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Removes a sensor.
removeSensorSelectionListener(SensorSelectionListener) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Remove the specified sensor selection listener.
removeSourceHandleFrom(PNode) - Static method in class org.simbrain.network.gui.nodes.SourceHandle: Remove the selection handle(s) from the specified node, if any exist.
removeSprite(OdorWorldEntity) - Method in class org.simbrain.world.odorworld.TileMap: Removes a OdorWorldEntity object from this map.
removeSynapse(Synapse) - Method in class org.simbrain.network.core.Network: Delete a specified weight.
removeSynapse(Synapse) - Method in class org.simbrain.network.groups.SynapseGroup: Remove the provided synapse from the group, but not the network.
removeSynapseDock(NeuronGroupNode.Port, SynapseGroupArrow) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
removeSynapseGroup(SynapseGroup) - Method in class org.simbrain.network.groups.Subnetwork: Remove a synapse group.
removeSynapseListener(SynapseListener) - Method in class org.simbrain.network.core.Network: Remove a synapse listener.
removeSynapseNode(SynapseNode) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeVisible: Remove a synapse node from the group node.
removeToSparsity(double) - Method in class org.simbrain.network.connections.Sparse
removeUpdaterListener(WorkspaceUpdaterListener) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Removes an updater listener from this instance.
removeWorkspaceComponent(WorkspaceComponent) - Method in class org.simbrain.workspace.Workspace: Remove the specified component.
removeWorkspaceComponentListener(WorkspaceComponentListener) - Method in class org.simbrain.workspace.WorkspaceComponent: Adds a WorkspaceComponentListener to this component.
renameAction - Variable in class org.simbrain.network.gui.nodes.NeuronGroupNode: Action for editing the group name.
renameAction - Variable in class org.simbrain.network.gui.nodes.SubnetworkNode: Action for editing the group name.
renameAction - Variable in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Action for editing the group name.
rendererPane - Variable in class org.simbrain.util.MultiLineToolTipUI
repaint() - Method in class org.simbrain.network.gui.NetworkPanel
repaint() - Method in class org.simbrain.world.visionworld.VisionWorld
repaintPanel() - Method in class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Called to repaint the panel based on changes in the to the selected neuron type.
repaintPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesSimple: Called Externally to repaint this panel based on whether or not extra data is displayed.
repaintPanel() - Method in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: Called to repaint the panel based on changes in the to the selected neuron type.
repaintPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel: Called to repaint the panel based on changes in the to the selected synapse type.
repaintPanel() - Method in class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel: Called to repaint the panel based on changes in the to the selected synapse type.
replaceCouplings(Attribute, Attribute) - Method in class org.simbrain.workspace.CouplingManager: Replaces any couplings where the old attribute is the source or target with a new coupling with the new attribute in the source and/or target.
repopulateQueue(Collection<Neuron>) - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate.CyclicTaskQueue
reRender() - Method in class org.simbrain.plot.histogram.HistogramPanel
reset() - Method in class org.simbrain.network.subnetworks.SOMGroup: Resets SOM Network to initial values.
reset() - Method in class org.simbrain.network.update_actions.concurrency_tools.SynchronizationPoint
reset() - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate.CyclicTaskQueue
reset() - Method in class org.simbrain.util.projection.Projector: Reset the projector.
reset(int, int) - Method in class org.simbrain.util.table.MutableTable: Reset the table structure.
reset(int, int, T) - Method in class org.simbrain.util.table.MutableTable: Adds rows or columns.
resetActivation() - Method in class org.simbrain.util.projection.DataPointColored: Reset activation value.
resetColors() - Method in class org.simbrain.network.gui.NetworkPanel: Called by Network preferences as preferences are changed.
resetColors() - Method in class org.simbrain.network.gui.nodes.InteractionBox
resetColors() - Method in class org.simbrain.network.gui.nodes.NeuronNode
resetColors() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Reset colors when default colors have been changed in NetworkPreferences.
resetColors() - Method in class org.simbrain.network.gui.nodes.SynapseNode
resetColors() - Method in class org.simbrain.network.gui.nodes.TextNode
resetColors() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
resetColors() - Method in class org.simbrain.util.projection.Projector: Reset the colors of all colored data points.
resetData(List<double[]>, List<String>) - Method in class org.simbrain.plot.histogram.HistogramModel: Reset the data in the model.
resetData() - Method in class org.simbrain.plot.histogram.HistogramModel: Clears the data.
resetData(List<String>, List<double[]>, int) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Reset the data in the data map field.
resetData() - Method in class org.simbrain.plot.projection.ProjectionModel: Resets the JFreeChart data and re-adds all the datapoints.
resetElapsedTime() - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
resetSubsamplingIndices() - Method in class org.simbrain.network.groups.NeuronGroup: Reset the indices used for subsampling
resetSynapseDiameters() - Method in class org.simbrain.network.gui.NetworkPanel: Called by Network preferences as preferences are changed.
resetTime() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Reset time to 0.
resetTime() - Method in class org.simbrain.workspace.Workspace: Reset time.
resetWandCursor() - Method in class org.simbrain.network.gui.EditMode: Reset the wand cursor (must happen when its size is reset).
resize() - Method in class org.simbrain.util.table.SimbrainJTableScrollPanel: Resize the panel based on the data.
resortPriorities() - Method in class org.simbrain.network.core.Network: Resort the neurons according to their update priorities.
ResourceManager - Class in org.simbrain.resource: ResourceManager provides resources (stored in the same directory) to the rest of the program.
ResourceManager() - Constructor for class org.simbrain.resource.ResourceManager
RESPONDER_MAP - Static variable in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: A mapping of available spike responders to their respective panels.
restoreDefaults() - Method in class org.simbrain.network.desktop.DesktopNetworkDialog: Restores all values to their default settings.
restoreDefaultSetting(String) - Static method in class org.simbrain.util.SimbrainPreferences: Reverts a setting to its default value.
resultsToMaple(PrintStream) - Method in class org.simbrain.util.projection.Dataset: Print out low dimensional points so maple can plot them Just does low dimension = 2.
revalidateSynapseGroups() - Method in class org.simbrain.network.trainers.Trainer: Helper function to update synapse groups whose synapses may have changed based on training.
revalidateSynapseSets() - Method in class org.simbrain.network.groups.SynapseGroup: If an algorithm (like training) extensively changes the polarity of the synapses in this group, it's impractical to check every time a change is made.
RGB - Static variable in class org.simbrain.world.visionworld.filter.editor.FilterEditors: Pixel accumulator editor.
RgbFilter - Class in org.simbrain.world.visionworld.filter: Filters pixels against the provided thresholds and provides the fraction of those meeting the threshold against the provided lower and upper bound.
RgbFilter(int, int, int, int, int) - Constructor for class org.simbrain.world.visionworld.filter.RgbFilter: Creates a new filter.
RgbFilter(int, int, int) - Constructor for class org.simbrain.world.visionworld.filter.RgbFilter: Creates a new filter.
RgbFilterEditor - Class in org.simbrain.world.visionworld.filter.editor: FilterEditor that creates RgbFilters.
RgbFilterEditor() - Constructor for class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: Creates a new instance.
RIGHT - Static variable in class org.simbrain.world.odorworld.effectors.Turning: Direction value to turn right.
RiseAndDecay - Class in org.simbrain.network.synapse_update_rules.spikeresponders: RiseAndDecay.
RiseAndDecay() - Constructor for class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay
RiseAndDecayPanel - Class in org.simbrain.network.gui.dialogs.synapse.spike_responders: RiseAndDecayPanel.
RiseAndDecayPanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: This method is the default constructor.
RotatingEntity - Class in org.simbrain.world.odorworld.entities: Represents an entity that can rotate.
RotatingEntity(OdorWorld) - Constructor for class org.simbrain.world.odorworld.entities.RotatingEntity: Create a rotating entity using default map.
RotatingEntityManager - Class in org.simbrain.world.odorworld.entities: Manages the creation of treemaps for rotating entities.
RotatingEntityManager() - Constructor for class org.simbrain.world.odorworld.entities.RotatingEntityManager
round(double, int) - Static method in class org.simbrain.util.Utils: Returns a string rounded to the desired precision.
roundDouble(double, int) - Static method in class org.simbrain.util.math.SimbrainMath: Round a double value to a specified number of places.
ROUNDING_WIDTH_HEIGHT - Static variable in class org.simbrain.network.gui.nodes.OutlinedObjects: The width and height of the arc in the rounded rectangle that surrounds the outlined objects.
row - Variable in class org.simbrain.util.table.SimbrainJTable.CellIndex: Row index.
rowCompMat2CompByteArray(long[], GroupSerializer.Precision) - Static method in class org.simbrain.network.util.io_utilities.GroupSerializer: Converts a complete row compressed represenation of a matrix into a byte array.
rowData - Variable in class org.simbrain.util.table.SimbrainDataTable: The data.
rows() - Method in class org.simbrain.world.visionworld.sensormatrix.DenseSensorMatrix: Return the number of rows of this sensor matrix.
rows() - Method in interface org.simbrain.world.visionworld.SensorMatrix: Return the number of rows of this sensor matrix.
rows() - Method in class org.simbrain.world.visionworld.sensormatrix.SparseSensorMatrix: Return the number of rows of this sensor matrix.
RULE_MAP - Static variable in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Associations between names of rules and panels for editing them.
RULE_MAP - Static variable in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: A mapping of available update rules to their respective panels.
run() - Method in class org.simbrain.network.connections.Radial.DensityEstimator
run() - Method in class org.simbrain.network.update_actions.concurrency_tools.Consumer: Executes tasks or waits on a cyclic barrier until a poison task is consumed which kills this consumer (sets Consumer.live to false).
run() - Method in class org.simbrain.plot.projection.ProjectionUpdater
run() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Starts the update thread.
run() - Method in class org.simbrain.workspace.Workspace: Iterates all couplings on all components until halted by user.
RunNetworkAction - Class in org.simbrain.network.gui.actions.network: Run network action.
RunNetworkAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.network.RunNetworkAction: Create a new run network action with the specified network panel.
RunningAverageRule - Class in org.simbrain.network.neuron_update_rules: RunningAverageNeuron keeps a running average of current and past activity.
RunningAverageRule() - Constructor for class org.simbrain.network.neuron_update_rules.RunningAverageRule
RunningAverageRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: RunningAverageNeuronPanel Unimplemented: Scheduled for deletion pending discussion because rule model does not work.
RunningAverageRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.RunningAverageRulePanel: This method is the default constructor.
runOnce(CountDownLatch) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Submits a single task to the queue, and counts down a latch when done.
runOnce() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Submits a single task to the queue.
RunScriptAction - Class in org.simbrain.network.desktop: Run network script.
RunScriptAction(NetworkPanel) - Constructor for class org.simbrain.network.desktop.RunScriptAction: Create a new script action for the workspace.
runTasks() - Method in class org.simbrain.workspace.updater.InterceptingEventQueue: Executes all queued invocation events.
runTasks() - Method in interface org.simbrain.workspace.updater.TaskSynchronizationManager: Tells the managers to run all queued tasks.
runTrainer() - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel: Run the trainer.

S

sample(PixelMatrix) - Method in class org.simbrain.world.visionworld.Sensor: Sample the specified pixel matrix, reducing a view of the pixel matrix through the receptive field of this sensor to a single numerical value with the filter for this sensor.
save(OutputStream, String) - Method in class org.simbrain.console.ConsoleComponent
save(OutputStream, String) - Method in class org.simbrain.docviewer.DocViewerComponent
save() - Method in class org.simbrain.network.desktop.NetworkDesktopComponent
save(OutputStream, String) - Method in class org.simbrain.network.NetworkComponent
save(OutputStream, String) - Method in class org.simbrain.plot.barchart.BarChartComponent
save(OutputStream, String) - Method in class org.simbrain.plot.histogram.HistogramComponent
save(OutputStream, String) - Method in class org.simbrain.plot.piechart.PieChartComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.plot.projection.ProjectionComponent
save(OutputStream, String) - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent: Used when saving a workspace.
save() - Method in class org.simbrain.workspace.gui.GuiComponent: Save vs.
save(OutputStream) - Method in class org.simbrain.workspace.gui.GuiComponent: Writes the bounds of this desktop component to the provided stream.
save() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: If changes exist, show a change dialog, otherwise just save the current file.
save(OutputStream, String) - Method in class org.simbrain.workspace.WorkspaceComponent: Used when saving a workspace.
save(File, Workspace) - Static method in class org.simbrain.workspace.WorkspaceSerializer: Helper method to save a specified file.
save(OutputStream, String) - Method in class org.simbrain.world.dataworld.DataWorldComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.world.game.GameComponent: Saves the component to the given stream.
save(OutputStream, String) - Method in class org.simbrain.world.odorworld.OdorWorldComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.world.oscworld.OscWorldComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.world.textworld.DisplayComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.world.textworld.ReaderComponent: Used when saving a workspace.
save(OutputStream, String) - Method in class org.simbrain.world.visionworld.VisionWorldComponent
SaveAction - Class in org.simbrain.workspace.component_actions: Save component action.
SaveAction(GuiComponent) - Constructor for class org.simbrain.workspace.component_actions.SaveAction: Create a new save component action with the specified.
saveAs() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Show a save-as dialog.
SaveAsAction - Class in org.simbrain.workspace.component_actions: Save as action.
SaveAsAction(GuiComponent) - Constructor for class org.simbrain.workspace.component_actions.SaveAsAction: Create a new save component action with the specified.
SavePlotAction - Class in org.simbrain.plot.actions: Save plot action.
SavePlotAction(GuiComponent) - Constructor for class org.simbrain.plot.actions.SavePlotAction: Create a new save plot action.
SavePlotAsAction - Class in org.simbrain.plot.actions: Save plot As Action.
SavePlotAsAction(GuiComponent) - Constructor for class org.simbrain.plot.actions.SavePlotAsAction: Create a new save plot as action.
saveToFileAsLinkedList(String) - Method in class org.simbrain.network.groups.SynapseGroup: Saves the synapse group to a file in linked list format which can be read by most graph analysis software, in particular as of 6/27/2015 the author is aware of both OSLOM and Infomap which can interpret the linked list format.
saveToFileAsLinkedList() - Method in class org.simbrain.network.groups.SynapseGroup: See: SynapseGroup.saveToFileAsLinkedList(String) Uses the default name which is: label + date & time
saveToFileAsMatrix(String) - Method in class org.simbrain.network.groups.SynapseGroup: Saves the weight matrix represented by this synapse group to a file.
SaveVisionWorldAction - Class in org.simbrain.world.visionworld.action: Create pixel matrix action.
SaveVisionWorldAction(VisionWorldDesktopComponent) - Constructor for class org.simbrain.world.visionworld.action.SaveVisionWorldAction: Create a new create pixel matrix action.
SaveVisionWorldAsAction - Class in org.simbrain.world.visionworld.action: Create pixel matrix action.
SaveVisionWorldAsAction(VisionWorldDesktopComponent) - Constructor for class org.simbrain.world.visionworld.action.SaveVisionWorldAsAction: Create a new create pixel matrix action.
SaveWorkspaceAction - Class in org.simbrain.workspace.actions: Save current workspace.
SaveWorkspaceAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.SaveWorkspaceAction: Create a save workspace action with the specified workspace.
SaveWorkspaceAsAction - Class in org.simbrain.workspace.actions: Save current workspace to specified file.
SaveWorkspaceAsAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.SaveWorkspaceAsAction: Create a save workspace as action with the specified workspace.
scale(int, int) - Method in class org.simbrain.world.visionworld.filter.RgbFilter: Scales the percentage of bytes that meet the threshold to the provided upper and lower bound.
scaleEigenvalue(List<Neuron>, List<Neuron>, double) - Static method in class org.simbrain.network.util.SimnetUtils
ScalerPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.ScalerPanel: Construct the scaler panel.
scaleWeights(List<Neuron>, List<Neuron>, double) - Static method in class org.simbrain.network.util.SimnetUtils: Scales weights connecting source and target lists.
ScatterPlotComponent - Class in org.simbrain.plot.scatterplot: Data for a JFreeChart ScatterPlot.
ScatterPlotComponent(String) - Constructor for class org.simbrain.plot.scatterplot.ScatterPlotComponent: Create new ScatterChart Component.
ScatterPlotComponent(String, ScatterPlotModel) - Constructor for class org.simbrain.plot.scatterplot.ScatterPlotComponent: Create new Scatter Plot Component from a specified model.
ScatterPlotComponent(String, int) - Constructor for class org.simbrain.plot.scatterplot.ScatterPlotComponent: Initializes a jfreechart with specific number of data sources.
ScatterPlotComponent.ScatterPlotSetter - Class in org.simbrain.plot.scatterplot: Object which sets a value of one slice of a scatter chart.
ScatterPlotDialog - Class in org.simbrain.plot.scatterplot: Displays a dialog for setting of available plot parameters.
ScatterPlotDialog(JFreeChart, ScatterPlotModel) - Constructor for class org.simbrain.plot.scatterplot.ScatterPlotDialog: Dialog for displaying chart options.
ScatterPlotGui - Class in org.simbrain.plot.scatterplot: Display a Scatter Plot.
ScatterPlotGui(GenericFrame, ScatterPlotComponent) - Constructor for class org.simbrain.plot.scatterplot.ScatterPlotGui: Construct the ScatterPlot.
ScatterPlotModel - Class in org.simbrain.plot.scatterplot: Model for a JFreeChart Scatter plot.
ScatterPlotModel() - Constructor for class org.simbrain.plot.scatterplot.ScatterPlotModel: Scatter plot model constructor.
ScatterPlotSetter(Integer) - Constructor for class org.simbrain.plot.scatterplot.ScatterPlotComponent.ScatterPlotSetter: Construct a setter object.
SceneGraphBrowser - Class in org.simbrain.util: Piccolo scene graph browser component.
SceneGraphBrowser(PRoot) - Constructor for class org.simbrain.util.SceneGraphBrowser: Create a new scene graph browser component with the specified root node.
SCREEN_CAPTURE - Static variable in class org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditors: Screen capture pixel matrix editor.
ScreenCapturePixelMatrix - Class in org.simbrain.world.visionworld.pixelmatrix: Screen capture pixel matrix.
ScreenCapturePixelMatrix(int, int, int, int) - Constructor for class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Create a new screen capture pixel matrix at the specified dimensions.
ScreenCapturePixelMatrixEditor - Class in org.simbrain.world.visionworld.pixelmatrix.editor: Screen capture pixel matrix editor.
ScreenCapturePixelMatrixEditor() - Constructor for class org.simbrain.world.visionworld.pixelmatrix.editor.ScreenCapturePixelMatrixEditor: Create a new screen capture pixel matrix editor.
ScreenElement - Class in org.simbrain.network.gui.nodes: ScreenElement extends a Piccolo node with property change, tool tip, and property dialog, and support.
ScreenElement(NetworkPanel) - Constructor for class org.simbrain.network.gui.nodes.ScreenElement: Create a new abstract screen element with the specified network panel.
ScriptAction(String, NetworkPanel) - Constructor for class org.simbrain.network.desktop.NetworkScriptMenu.ScriptAction: Construct a network script action.
ScriptAction(SimbrainDesktop, String) - Constructor for class org.simbrain.workspace.gui.WorkspaceActionManager.ScriptAction: Create a new add gauge action with the specified workspace.
ScriptEditor - Class in org.simbrain.util.scripteditor: An editor for beanshell scripts with syntax highlighting.
ScriptEditor() - Constructor for class org.simbrain.util.scripteditor.ScriptEditor: Construct the main frame.
ScriptEditor(String) - Constructor for class org.simbrain.util.scripteditor.ScriptEditor: Initialize the script editor panel with some initial text.
ScriptEditor(String, String) - Constructor for class org.simbrain.util.scripteditor.ScriptEditor: Initialize with initial text and a default directory.
ScriptEditorAction - Class in org.simbrain.workspace.actions: Open a script editor.
ScriptEditorAction(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.ScriptEditorAction: Open a script editor.
scroller - Variable in class org.simbrain.network.gui.trainer.DataPanel: Scrollpane.
scrollPane - Variable in class org.simbrain.workspace.gui.ThreadViewerPanel: Thread viewer scroll pane.
sectionSeparator(String, GridBagConstraints, int) - Method in class org.simbrain.network.gui.dialogs.network.SRNCreationDialog: Creates a new dialog section given a title and using a JSeparator.
select(Collection, Predicate) - Static method in class org.simbrain.util.Utils: Reimplementation of same method from org.apache.commons.collections.CollectionUtils.
selectAll() - Method in class org.simbrain.network.gui.NetworkPanel: Select all elements.
selectAll() - Method in class org.simbrain.world.visionworld.VisionWorld: Selects all of the sensor nodes.
SelectAllAction - Class in org.simbrain.network.gui.actions.selection: Select all action.
SelectAllAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.selection.SelectAllAction: Create a new select all action with the specified network panel.
SelectAllAction - Class in org.simbrain.world.visionworld.action: Create pixel matrix action.
SelectAllAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.SelectAllAction: Create a new create pixel matrix action.
SelectAllNeuronsAction - Class in org.simbrain.network.gui.actions.selection: Select all neurons.
SelectAllNeuronsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.selection.SelectAllNeuronsAction: Create a new select all neurons action with the specified network panel.
SelectAllWeightsAction - Class in org.simbrain.network.gui.actions.selection: Select all weights.
SelectAllWeightsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.selection.SelectAllWeightsAction: Create a new select all weights action with the specified network panel.
SelectIncomingWeightsAction - Class in org.simbrain.network.gui.actions.selection: Select incoming weights action weights action.
SelectIncomingWeightsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.selection.SelectIncomingWeightsAction: Create select incoming weights action with the specified network panel.
SELECTION - Static variable in class org.simbrain.network.gui.EditMode: Selection edit mode.
selectionChanged(NetworkSelectionEvent) - Method in interface org.simbrain.network.gui.NetworkSelectionListener: Notify this listener that the selection has changed.
selectionChanged(SensorSelectionEvent) - Method in interface org.simbrain.world.visionworld.SensorSelectionListener: Notify this listener that the sensor selection changed.
SelectionEditModeAction - Class in org.simbrain.network.gui.actions.edit: Selection edit mode action.
SelectionEditModeAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.SelectionEditModeAction: Create a new selection edit mode action with the specified network panel.
SelectionEventHandler - Class in org.simbrain.world.visionworld: Sensor selection event handler.
SelectionEventHandler(VisionWorld) - Constructor for class org.simbrain.world.visionworld.SelectionEventHandler: Create a new selection event handler for the specified vision world.
SelectionHandle - Class in org.simbrain.network.gui.nodes: The graphical handle drawn around selected PNodes.
SelectionMarquee - Class in org.simbrain.network.gui.nodes: Selection marquee node.
SelectionMarquee(float, float) - Constructor for class org.simbrain.network.gui.nodes.SelectionMarquee: Create a new selection marquee at the specified point (x, y).
selectNone() - Method in class org.simbrain.world.visionworld.VisionWorld: Selects none of the sensor nodes.
SelectNoneAction - Class in org.simbrain.world.visionworld.action: Select none action.
SelectNoneAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.SelectNoneAction: Create a new select none action.
SelectOutgoingWeightsAction - Class in org.simbrain.network.gui.actions.selection: Clamps weights action.
SelectOutgoingWeightsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.selection.SelectOutgoingWeightsAction: Create a new clamp weights action with the specified network panel.
selfConnectionAllowed - Variable in class org.simbrain.network.connections.Sparse: Whether or not connections where the source and target are the same neuron are allowed.
Sensor - Class in org.simbrain.world.odorworld.sensors: Interface for 2d world sensors.
Sensor(OdorWorldEntity, String) - Constructor for class org.simbrain.world.odorworld.sensors.Sensor: Construct the sensor.
Sensor - Interface in org.simbrain.world.threedee: Base class for implementing sensors in 3D world.
Sensor - Class in org.simbrain.world.visionworld: Sensor.
Sensor(int, int, ReceptiveField) - Constructor for class org.simbrain.world.visionworld.Sensor: Create a new sensor with the specified receptive field and no filter.
Sensor(int, int, Filter, ReceptiveField) - Constructor for class org.simbrain.world.visionworld.Sensor: Create a new sensor with the specified filter and receptive field.
sensorAdded(Sensor) - Method in interface org.simbrain.world.odorworld.WorldListener: A sensor was added.
sensorAdded(Sensor) - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
SensorMatrix - Interface in org.simbrain.world.visionworld: Two-dimensional matrix of sensors with uniformly sized receptive fields.
sensorMatrixChanged(VisionWorldModelEvent) - Method in class org.simbrain.world.visionworld.VisionWorldModelAdapter: Notify this listener the sensor matrix changed in a vision world model.
sensorMatrixChanged(VisionWorldModelEvent) - Method in interface org.simbrain.world.visionworld.VisionWorldModelListener: Notify this listener the sensor matrix changed in a vision world model.
SensorMatrixEditor - Interface in org.simbrain.world.visionworld.sensormatrix.editor: Sensor matrix editor.
SensorMatrixEditorException - Exception in org.simbrain.world.visionworld.sensormatrix.editor: Sensor matrix editor exception.
SensorMatrixEditorException() - Constructor for exception org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditorException: Create a new sensor matrix editor exception.
SensorMatrixEditorException(String) - Constructor for exception org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditorException: Create a new sensor matrix editor exception with the specified message.
SensorMatrixEditorException(Throwable) - Constructor for exception org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditorException: Create a new sensor matrix editor exception with the specified cause.
SensorMatrixEditorException(String, Throwable) - Constructor for exception org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditorException: Create a new sensor matrix editor exception with the specified message and cause.
SensorMatrixEditors - Class in org.simbrain.world.visionworld.sensormatrix.editor: Sensor matrix editors.
SensorMatrixEditors() - Constructor for class org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditors
SensorMatrixNode - Class in org.simbrain.world.visionworld.node: Sensor matrix node.
SensorMatrixNode(VisionWorld, SensorMatrix) - Constructor for class org.simbrain.world.visionworld.node.SensorMatrixNode: Create a new sensor matrix node with the specified sensor matrix.
SensorModel() - Constructor for class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
SensorNode - Class in org.simbrain.world.visionworld.node: Sensor node.
SensorNode(VisionWorld, Sensor) - Constructor for class org.simbrain.world.visionworld.node.SensorNode: Create a new sensor node for the specified sensor.
SensorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel showing an agent's sensors.
SensorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.SensorPanel: Construct the sensor panel.
SensorPanel.SensorModel - Class in org.simbrain.world.odorworld.dialogs: Table model which represents sensors.
sensorRemoved(Sensor) - Method in interface org.simbrain.world.odorworld.WorldListener: A sensor was removed.
sensorRemoved(Sensor) - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
SensorSelectionEvent - Class in org.simbrain.world.visionworld: Sensor selection event.
SensorSelectionEvent(VisionWorld, Set<Sensor>, Set<Sensor>) - Constructor for class org.simbrain.world.visionworld.SensorSelectionEvent: Create a new sensor selection event with the specified source.
SensorSelectionListener - Interface in org.simbrain.world.visionworld: Sensor selection listener.
SensorSelectionModel - Class in org.simbrain.world.visionworld: Sensor selection model.
SensorSelectionModel(VisionWorld) - Constructor for class org.simbrain.world.visionworld.SensorSelectionModel: Create a new sensor selection model with the specified vision world.
sentSemi - Static variable in class org.simbrain.console.CommandLineReader
serialize(OutputStream) - Method in class org.simbrain.workspace.WorkspaceSerializer: Serializes the workspace to a zip compressed stream.
serializeComponent(WorkspaceComponent) - Method in class org.simbrain.workspace.WorkspaceComponentSerializer: Serializes a component and returns the id for that component.
serializeCompressedSynGroup(SynapseGroup, GroupSerializer.Precision, String) - Static method in class org.simbrain.network.util.io_utilities.GroupSerializer: Saves a synapse group with a given precision representing its weights to a file with the given filename.
set(int, DataPoint) - Method in class org.simbrain.util.projection.NTree: replaces the point at the given index with the one provided.
set(int, int, double) - Method in class org.simbrain.world.game.GameModel: Sets the value of the cell at the given coordinates.
set(int, int, double) - Method in class org.simbrain.world.game.tictactoe.TicTacToeModel: Sets the value of the cell at the given coordinates.
set_vClampValue(float) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setA(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setA(double) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setActivated(boolean) - Method in class org.simbrain.world.odorworld.effectors.Speech
setActivation(double) - Method in class org.simbrain.network.core.Neuron: Sets the activation of the neuron if it is not clamped.
setActivation(double) - Method in class org.simbrain.network.util.NeuronWithMemory
setActivationAmount(double) - Method in class org.simbrain.world.odorworld.sensors.TileSensor
setActivationLevels(double) - Method in class org.simbrain.network.groups.NeuronGroup: Set all activations to a specified value.
setActivationProbability(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder
setActivations(double) - Method in class org.simbrain.network.core.Network: Sets all neurons to a specified value.
setActivations(double[]) - Method in class org.simbrain.network.core.Network: Sets neuron activations using values in an array of doubles.
setActivations(double[]) - Method in class org.simbrain.network.groups.NeuronGroup: Set activations of neurons using an array of doubles.
setAdaptationParameter(double) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Sets the adaptation parameter.
setAdaptationTimeConstant(double) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Sets the adaptation time constant.
setAddAgentItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.IACRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setAddNoise(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setAddNoise(boolean) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.NoisyUpdateRule: Set whether noise should be used.
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.LinearRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
setAddNoise(boolean) - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
setAddNoise(boolean) - Method in class org.simbrain.util.environment.SmellSource: Sets the add noise.
setAdjusting(boolean) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Set to true if this model will be adjusting over a series of rapid changes.
setAllowSelfConnect(boolean) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
setAllowSelfConnections(boolean) - Method in class org.simbrain.network.connections.RadialSimple
setAlpha(double) - Method in class org.simbrain.network.trainers.LMSOffline
setAlpha(int, int) - Static method in class org.simbrain.util.Utils: Sets the alpha of the color represented by rgBInt to the value specified in alpha and returns the resulting color.
setAlphaDecayRate(double) - Method in class org.simbrain.network.subnetworks.SOMGroup: Set alphaDecayRate.
setAmount(double) - Method in class org.simbrain.world.odorworld.effectors.Speech
setAmount(double) - Method in class org.simbrain.world.odorworld.effectors.StraightMovement
setAmount(double) - Method in class org.simbrain.world.odorworld.effectors.Turning
setAndConformToTemplate(Synapse, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setAnimation(Animation) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setArgumentDataTypes(Class<?>[]) - Method in class org.simbrain.workspace.PotentialAttribute
setArgumentValues(Object[]) - Method in class org.simbrain.workspace.PotentialAttribute
setAsDoneDialog() - Method in class org.simbrain.util.StandardDialog: If called then this becomes a "Done" dialog.
setAutoDomain(boolean) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setAutoFind(boolean) - Method in class org.simbrain.util.projection.ProjectCoordinate
setAutoRange(boolean) - Method in class org.simbrain.plot.barchart.BarChartModel
setAutoRange(boolean) - Method in class org.simbrain.plot.rasterchart.RasterModel
setAutoRange(boolean) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setAutoRange(boolean) - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
SetAutoZoomAction - Class in org.simbrain.network.gui.actions.edit: Set auto zoom.
SetAutoZoomAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.SetAutoZoomAction: Create a new set auto zoom action with the specified network panel.
setAutoZoomMode(boolean) - Method in class org.simbrain.network.gui.NetworkPanel
setAuxiliaryObject(Object) - Method in class org.simbrain.network.listeners.NetworkEvent
setAuxValue(double) - Method in class org.simbrain.network.core.Neuron
setB(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setB(double) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setB(double) - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
setBackground(Image) - Method in class org.simbrain.world.odorworld.OdorWorldRenderer: Sets the background to draw.
setBackgroundColor(Color) - Static method in class org.simbrain.network.gui.NetworkPanel
setBackgroundColor(Color) - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
setBackgroundColor(int) - Method in class org.simbrain.world.odorworld.OdorWorldPanel: Sets the background color of the world.
setBackgroundCurrent(double) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setBackWeights(boolean) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Set to true for weights from output to reservoir.
setBarColor(Color) - Method in class org.simbrain.plot.barchart.BarChartModel
setBars(double[]) - Method in class org.simbrain.plot.barchart.BarChartModel: Set the values for all the bars using an array.
setBaseColor(Color) - Method in class org.simbrain.util.projection.DataColoringManager
setBaseExcitatorySynapse(Synapse) - Method in class org.simbrain.network.connections.RadialSimple
setBaseInhibitorySynapse(Synapse) - Method in class org.simbrain.network.connections.RadialSimple
setBaseLine(double) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setBaseLine(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
setBaseLine(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
setBaseLineStrength(double) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
setBaseProb(double) - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
setBatchSize(int) - Method in class org.simbrain.network.subnetworks.SOMGroup: Set the Batch Size.
setBeginPosition(Point2D) - Method in class org.simbrain.network.gui.NetworkPanel: Beginning position used in calculating offsets for multiple pastes.
setBetweenLayerInterval(int) - Method in class org.simbrain.network.subnetworks.FeedForward
setBetweenNeuronInterval(int) - Method in class org.simbrain.network.groups.NeuronGroup
setBezier_1(Point2D.Float) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setBezier_2(Point2D.Float) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setBias(double) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
setBias(double) - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
setBias(double) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
setBias(double) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.BiasedUpdateRule
setBias(double) - Method in class org.simbrain.network.neuron_update_rules.LinearRule
setBias(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setBias(double) - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
setBins(int) - Method in class org.simbrain.plot.histogram.HistogramModel: Sets the number of bins.
setBites(int) - Method in class org.simbrain.world.odorworld.LifeCycle: Number of times bitten.
setBitesToDie(int) - Method in class org.simbrain.world.odorworld.LifeCycle
setBlue(int, int) - Static method in class org.simbrain.util.Utils: Sets the blue value of the color represented by rgbIntColor to the value specified by blue and returns the resulting color.
setBold(boolean) - Method in class org.simbrain.network.core.NetworkTextObject
setBothTexts(String, String) - Method in class org.simbrain.util.widgets.DropDownTriangle: Changes the text displayed next to the triangle.
setBounds(int, int, int, int) - Method in interface org.simbrain.util.genericframe.GenericFrame
setBounds(Rectangle) - Method in interface org.simbrain.util.genericframe.GenericFrame
setBoundsEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended: Set the state of the clipping drop-down and upper / lower bound text fields to reflect whether bound are enabled or not.
setBoundsVisible(boolean) - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended: Whether or not to display the bounds sub-panel.
setBuffer(double) - Method in class org.simbrain.network.core.Neuron: Temporary buffer which can be used for algorithms which should not depend on the order in which neurons are updated.
setBuffer(double) - Method in class org.simbrain.network.util.NeuronWithMemory
setBuffer() - Method in class org.simbrain.workspace.Coupling: Set value of buffer.
setBumped(boolean) - Method in class org.simbrain.world.odorworld.sensors.BumpSensor
setBumpRate(double) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
setByPriority(boolean) - Method in class org.simbrain.network.subnetworks.Hopfield
setC(double) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setCeiling(double) - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
setCeiling(double) - Method in class org.simbrain.util.projection.DataColoringManager
setCenterLocation(float, float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Set the location of this entity.
setChangedSinceLastSave(boolean) - Method in class org.simbrain.workspace.WorkspaceComponent: Set to true when a component changes, set to false after a component is saved.
setChartSeriesPaint(List<Paint>) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setClamped(boolean) - Method in class org.simbrain.network.core.Neuron: Toggles whether this neuron is clamped.
setClamped(boolean) - Method in class org.simbrain.network.groups.NeuronGroup: Set clamping on all neurons in this group.
setClipboardEntity(OdorWorldEntity) - Static method in class org.simbrain.world.odorworld.WorldClipboard
setClipped(boolean) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
setClipped(boolean) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setClipped(boolean) - Method in class org.simbrain.network.neuron_update_rules.IACRule
setClipped(boolean) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.ClippableUpdateRule: Turn clipping on and off.
setClipped(boolean) - Method in class org.simbrain.network.neuron_update_rules.LinearRule
setClipped(boolean) - Method in class org.simbrain.network.synapse_update_rules.StaticSynapseRule
setClipping(boolean) - Method in class org.simbrain.util.randomizer.PolarizedRandomizer
setClipping(boolean) - Method in class org.simbrain.util.randomizer.Randomizer
setClippingVisible(boolean) - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended: Whether or not to display the clipping drop down.
setCm(double) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setcMembrane(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setColor(Color) - Method in class org.simbrain.util.projection.DataPointColored: Use this to manually set color.
setColor(Color) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setColorBasedOnVal(float) - Method in class org.simbrain.util.projection.DataPointColored: Set the color of this point based on the activation value.
setColoringMethod(String) - Method in class org.simbrain.util.projection.DataColoringManager: Set the coloring method.
setColumnHeadings(List<String>) - Method in class org.simbrain.util.table.SimbrainDataTable
setColumnHeadings(List<String>) - Method in class org.simbrain.util.table.SimbrainJTable
setColumns(int) - Method in class org.simbrain.util.JMultiLineToolTip
setComboBox(String) - Method in class org.simbrain.network.gui.dialogs.network.LayeredNetworkCreationPanel.LayerCreationPanel: Set selected item of the combo box.
setConnectionDensity(double) - Method in class org.simbrain.network.connections.Sparse: Set how dense the connections are between source and target neurons, generally speaking the connectionDensity parameter represents a probability reflecting how many possible connections between a given source neuron and all available target neurons will actually be made.
setConnectionManager(ConnectNeurons) - Method in class org.simbrain.network.groups.SynapseGroup: Sets the connection manager for this synapse group once and only once.
setConnectOrientation(OrientationComparator) - Method in class org.simbrain.network.connections.OneToOne
setContentPane(Container) - Method in interface org.simbrain.util.genericframe.GenericFrame
setContentPane(Container) - Method in class org.simbrain.util.StandardDialog: This method sets the content pane for adding components.
setContextMenu(JPopupMenu) - Method in class org.simbrain.network.gui.nodes.InteractionBox
setContextMenu(JPopupMenu) - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Set a custom context menu for the interaction box.
setCoolColor(float) - Static method in class org.simbrain.network.gui.nodes.NeuronNode
setCopyItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setCurrentConnector(ConnectNeurons) - Method in class org.simbrain.network.connections.QuickConnectionManager
setCurrentDirectory(String) - Method in class org.simbrain.workspace.Workspace
setCurrentDirectory(String) - Method in class org.simbrain.world.visionworld.pixelmatrix.editor.BufferedImagePixelMatrixEditor: Sets the current directory for class and persistence.
setCurrentFile(File) - Method in class org.simbrain.workspace.Workspace
setCurrentFile(File) - Method in class org.simbrain.workspace.WorkspaceComponent
setCurrentItem(TextWorld.TextItem) - Method in class org.simbrain.world.textworld.TextWorld
setCurrentLayout(Layout) - Method in class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Sets the neuron layout using a layout object.
setCurrentRow(int) - Method in interface org.simbrain.util.table.IterableRowsTable: Sets the current row.
setCurrentRow(int) - Method in class org.simbrain.util.table.NumericTable
setCurrentState(int) - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
setCurrentTask(ComponentUpdatePart) - Method in class org.simbrain.workspace.updater.UpdateThread: Sets the current component update that is being executed.
setCustomDescription(String) - Method in class org.simbrain.workspace.PotentialAttribute: Set a custom description, overriding the default description.
setCustomMenuItems() - Method in class org.simbrain.network.gui.nodes.neuronGroupNodes.SOMGroupNode: Sets custom menu for SOM node.
setCutItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setD(double) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setData(double[][]) - Method in class org.simbrain.network.gui.dialogs.TestInputPanel: Reset the data in this panel.
setData(double[][]) - Method in interface org.simbrain.util.math.NumericMatrix: Set the data.
setData(double[]) - Method in class org.simbrain.util.projection.DataPoint: Set the data vector.
setData(double[][]) - Method in class org.simbrain.util.table.NumericTable: Reset data using a 2-d array of doubles.
setDataDirectory(String) - Static method in class org.simbrain.network.gui.trainer.TrainerGuiActions: Sets the current data directory in user preferences (memory for file chooser).
setDead(boolean) - Method in class org.simbrain.world.odorworld.LifeCycle
setDecay(double) - Method in class org.simbrain.network.neuron_update_rules.IACRule
setDecayAmount(double) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setDecayFraction(double) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setDecayFunction(SmellSource.DecayFunction) - Method in class org.simbrain.util.environment.SmellSource
setDecayRate(double) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
setDecrementAmount(double) - Method in class org.simbrain.util.projection.DataColoringManager
setDefaults() - Method in class org.simbrain.network.desktop.DesktopNetworkDialog: Sets selected preferences as user defaults.
setDefaultUpdateActions() - Method in class org.simbrain.workspace.updater.UpdateActionManager: Puts the update in its default configuration, with Buffered update as the default action.
setDelay(int) - Method in class org.simbrain.network.core.Synapse: Delay manager.
setDelay(int, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setDeleteItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setDensity(double) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
setDesktop(SimbrainDesktop) - Method in class org.simbrain.workspace.gui.GuiComponent: TODO: This should really be set at construction time, but that would require deep changes so this should suffice for now.
setDictionaryDirectory(String) - Static method in class org.simbrain.world.textworld.TextWorldActions: Sets the current directory for the dictionary file (memory for file chooser).
setDimensions(int) - Method in class org.simbrain.plot.projection.ProjectionComponent: Set number of dimensions to specified amount.
setDirectInOutWeights(boolean) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Set to true for weights directly from input to output.
setDirection(double) - Method in class org.simbrain.world.odorworld.effectors.Turning
setDispersion(double) - Method in class org.simbrain.util.environment.SmellSource: Sets the dispersion.
setDisplayColumnHeadings(boolean) - Method in class org.simbrain.util.table.SimbrainDataTable: TODO: This only works for setting from true to false.
setDisplayColumnHeadings(boolean) - Method in class org.simbrain.util.table.SimbrainJTable: Forward setting to table model.
setDisplayNeuronGroups(boolean) - Method in class org.simbrain.network.groups.Subnetwork
setDisplayPopUpMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setDisplaySynapses(boolean) - Method in class org.simbrain.network.groups.SynapseGroup
setDisplayThreshold(double) - Method in class org.simbrain.world.textworld.DisplayWorld
setDistConst(double) - Method in class org.simbrain.network.connections.Radial
setDotSize(int) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setDoubleArray(double[]) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setDownLabelColor(Color) - Method in class org.simbrain.util.widgets.DropDownTriangle: Sets the color of the label when the triangle is in the down state.
setDownText(String) - Method in class org.simbrain.util.widgets.DropDownTriangle: Changes the text displayed when the triangle is in the down state
setDrawOutline(boolean) - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
setDt(double) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setDuration(int) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setEditable(boolean) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setEditMode(EditMode) - Method in class org.simbrain.network.gui.NetworkPanel: Set the current edit mode for this Network panel to editMode .
setEeDistConst(double) - Method in class org.simbrain.network.connections.Radial
setEffectors(List<Effector>) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setEffectorsEnabled(boolean) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setEiDistConst(double) - Method in class org.simbrain.network.connections.Radial
setEk(float) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setEna(float) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setEnabled(boolean) - Method in class org.simbrain.network.core.Synapse: A better name than setSendWeightedInput.
setEnabled(boolean) - Method in class org.simbrain.network.groups.Subnetwork
setEnabled(boolean, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
setEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel
setEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: Also enables/disables all UI sub-components
setEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: Also enables/disables all UI sub-components
setEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: Also enables/disables all UI sub-components
setEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel: Also enables/disables all UI sub-components
setEnabled(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel: Also enables/disables all UI sub-components
setEnabled(boolean) - Method in class org.simbrain.util.randomizer.gui.ProbDistPanel: Sets all the components of this panel to the desired enabled/disabled state.
setEnabled(boolean) - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
setEnabled(boolean) - Method in class org.simbrain.util.widgets.ApplyPanel
setEndPosition(Point2D) - Method in class org.simbrain.network.gui.NetworkPanel
setEndPt(Point2D.Float) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
setEndPt(Point2D.Float) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setEntityType(String) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity
setEnumeration(ComboBoxWrapper) - Method in class org.simbrain.util.propertyeditor.gui.TestObject: Sets the enumeration based on a boxable object.
setEpsilon(double) - Method in class org.simbrain.util.projection.ProjectSammon
setEqualizeEfferents(boolean) - Method in class org.simbrain.network.connections.Sparse
setError(double) - Method in class org.simbrain.util.projection.IterableProjectionMethod
setErrorThreshold(double) - Method in class org.simbrain.network.trainers.IterableTrainer
setExcitatoryColor(Color) - Static method in class org.simbrain.network.gui.nodes.SynapseNode
setExcitatoryConductance(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setExcitatoryCurrent(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setExcitatoryInputs(ArrayList<Synapse>) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setExcitatoryMaxConductance(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setExcitatoryProbability(double) - Method in class org.simbrain.network.connections.RadialSimple
setExcitatoryRadius(double) - Method in class org.simbrain.network.connections.RadialSimple
setExcitatoryRandomizer(PolarizedRandomizer) - Method in class org.simbrain.network.groups.SynapseGroup
setExcitatoryRatio(double) - Method in class org.simbrain.network.connections.QuickConnectionManager
setExcitatoryRatio(double) - Method in class org.simbrain.network.groups.SynapseGroup: Changes the ratio of synapses in this group that are excitatory subject to two constraints: 1) If neurons in the source neuron group have their own polarity ratio, the desired excitatoryRatio may not be possible.
setExcitatoryRatio(double) - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel: Set the ration of excitatory to inhibitory neurons, a value between 0 (no excitatory) and 1 (all excitatory).
setExcitatoryReversal(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setExcludeList(String[]) - Method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Set an exclude list.
setExRandomizer(PolarizedRandomizer) - Method in class org.simbrain.network.connections.QuickConnectionManager
setExReversal(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setFillBackground(boolean) - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
setFilter(Filter) - Method in class org.simbrain.world.visionworld.Sensor: Set the filter for this sensor to filter.
setFireUpdates(boolean) - Method in class org.simbrain.network.core.Network
setFiringProbability(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
setFiringThreshold(double) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
setFirstColumnWidth() - Method in class org.simbrain.util.table.SimbrainJTable: Special width for first column.
setFixedWidth(boolean) - Method in class org.simbrain.plot.rasterchart.RasterModel
setFixedWidth(boolean) - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
setFixedWidth(int) - Method in class org.simbrain.util.JMultiLineToolTip
setFloor(double) - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
setFloor(double) - Method in class org.simbrain.util.projection.DataColoringManager
setFocus(boolean) - Method in class org.simbrain.world.visionworld.node.PixelMatrixImageNode: Set to true to indicate this pixel matrix image node has focus and should enabled drawing via mouse clicks.
setFontName(String) - Method in class org.simbrain.network.core.NetworkTextObject
setFontSize(int) - Method in class org.simbrain.network.core.NetworkTextObject
setFrame(Window) - Method in class org.simbrain.network.gui.trainer.DataPanel: Set the frame.
setFrame(Window) - Method in class org.simbrain.network.gui.trainer.IterativeTrainingPanel
setFrame(Window) - Method in class org.simbrain.network.gui.trainer.TrainingSetPanel: Set the frame.
setFrequency(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
setFrozen(boolean) - Method in class org.simbrain.network.core.Synapse
setFrozen(boolean, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setG_Ca(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setG_e_bar(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setG_i_bar(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setG_K(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setG_L(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setG_L(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setGain(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setGenerator(boolean) - Method in class org.simbrain.network.core.Neuron: Mark this neuron as an input generator.
setGreen(int, int) - Static method in class org.simbrain.util.Utils: Sets the green value of the color represented by rgbIntColor to the value specified by green and returns the resulting color.
setGridPaint(Paint) - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Set the grid paint for this sensor matrix node to gridPaint.
setGridStroke(Stroke) - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Set the grid stroke for this sensor matrix node to gridStroke.
setGridThreshold(int) - Method in class org.simbrain.network.groups.NeuronGroup
setGroup(Group) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setGrouped(boolean) - Method in class org.simbrain.network.gui.nodes.NeuronNode
setGrouped(boolean) - Method in class org.simbrain.network.gui.nodes.ScreenElement
setGroupedObjects(ArrayList<ScreenElement>) - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
setGrowthRate(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
setGuiOn(boolean) - Method in class org.simbrain.network.gui.NetworkPanel
setGuiOn(Boolean) - Method in class org.simbrain.workspace.WorkspaceComponent
setHasChangedSinceLastSave(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setHasCollided(boolean) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setHasSpiked(boolean, Neuron) - Method in class org.simbrain.network.core.SpikingNeuronUpdateRule
setHeading(double) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Set the orientation of the creature.
setHebbian(boolean) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
setHeight(int, boolean) - Method in class org.simbrain.world.odorworld.OdorWorld: Set height.
setHeight(int) - Method in class org.simbrain.world.odorworld.OdorWorld
setHeight(int) - Method in class org.simbrain.world.odorworld.sensors.TileSensor
setHiD1(int) - Method in class org.simbrain.util.projection.ProjectCoordinate
setHiD2(int) - Method in class org.simbrain.util.projection.ProjectCoordinate
setHierarchyPanelVisible(boolean) - Method in class org.simbrain.network.gui.NetworkPanel: Set the visibility of the hiearchy panel.
setHighlightColor(Color) - Method in class org.simbrain.world.textworld.TextWorld
setHorizontalSpacing(double) - Method in class org.simbrain.network.util.CascadingNetworkBuilder
setHotColor(float) - Static method in class org.simbrain.network.gui.nodes.NeuronNode
setHotColor(Color) - Method in class org.simbrain.util.projection.DataColoringManager
setHotPointMode(boolean) - Method in class org.simbrain.util.projection.DataColoringManager: Set hot point coloring mode to on (true) or off (false).
setHSpacing(double) - Method in class org.simbrain.network.layouts.GridLayout
setHSpacing(double) - Method in class org.simbrain.network.layouts.HexagonalGridLayout
setI_bg(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setI_bg(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setiBg(double) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
setiBg(double) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setIcon(boolean) - Method in interface org.simbrain.util.genericframe.GenericFrame
setIcon(boolean) - Method in class org.simbrain.util.genericframe.GenericJDialog
setIcon(boolean) - Method in class org.simbrain.util.genericframe.GenericJFrame
setId(String) - Method in class org.simbrain.network.core.Neuron: Sets the id of the neuron.
setId(String) - Method in class org.simbrain.network.core.Synapse
setId(String) - Method in class org.simbrain.network.groups.Group
setId(String) - Method in class org.simbrain.world.odorworld.effectors.Effector
setId(String) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setId(String) - Method in class org.simbrain.world.odorworld.sensors.Sensor
setIdField(JLabel) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setIeDistConst(double) - Method in class org.simbrain.network.connections.Radial
setIiDistConst(double) - Method in class org.simbrain.network.connections.Radial
setImage(String) - Method in class org.simbrain.world.odorworld.entities.BasicEntity: Set type of object.
setImage(BufferedImage) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Set the image for this pixel matrix to image.
setImageMap(TreeMap<Double, Animation>) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity
setIncomingField(JLabel) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setIncrement(double) - Method in class org.simbrain.network.core.Neuron: Convenience method to set increment on the neuron's update rule.
setIncrement(double) - Method in class org.simbrain.network.core.NeuronUpdateRule
setIncrement(double) - Method in class org.simbrain.network.core.Synapse: Sets the amount to increment neuron.
setIncrement(double) - Method in class org.simbrain.network.groups.NeuronGroup: Set the increment on all neurons in this group.
setIncrement(double, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setIncrementAmount(double) - Method in class org.simbrain.util.projection.DataColoringManager
setIndexSets() - Method in class org.simbrain.network.trainers.TrainingSet: Populate the validation and main index sets.
setIndicatorColor() - Method in class org.simbrain.network.gui.dialogs.NetworkPropertiesPanel: Set the color indicator based on the current selection in the combo box.
setInhibitoryColor(Color) - Static method in class org.simbrain.network.gui.nodes.SynapseNode
setInhibitoryConductance(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setInhibitoryMaxConductance(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setInhibitoryProbability(double) - Method in class org.simbrain.network.connections.RadialSimple
setInhibitoryRadius(double) - Method in class org.simbrain.network.connections.RadialSimple
setInhibitoryRandomizer(PolarizedRandomizer) - Method in class org.simbrain.network.groups.SynapseGroup
setInhibitoryReversal(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setInitAlpha(double) - Method in class org.simbrain.network.subnetworks.SOMGroup: Set the initial value for alpha.
setInitialLocation(Point2D) - Method in class org.simbrain.network.layouts.GridLayout
setInitialLocation(Point2D) - Method in class org.simbrain.network.layouts.HexagonalGridLayout
setInitialLocation(Point2D) - Method in interface org.simbrain.network.layouts.Layout: Set the initial position.
setInitialLocation(Point2D) - Method in class org.simbrain.network.layouts.LineLayout
setInitialPosition(Point) - Method in class org.simbrain.network.util.CascadingNetworkBuilder
setInitNeighborhoodSize(double) - Method in class org.simbrain.network.subnetworks.SOMGroup: Set the initial neighborhood size.
setInputData(double[][]) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
setInputData(double[][]) - Method in class org.simbrain.network.trainers.TrainingSet: Set the input data.
setInputMode(boolean) - Method in class org.simbrain.network.groups.NeuronGroup: Sets whether or not this neuron group is in input mode.
setInputThreshold(double) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
setInputType(NeuronUpdateRule.InputType) - Method in class org.simbrain.network.core.NeuronUpdateRule
setInputValue(double) - Method in class org.simbrain.network.core.Neuron: Set the input value of the neuron.
setInputValues(double[]) - Method in class org.simbrain.network.groups.NeuronGroup: Set input values of neurons using an array of doubles.
setInRandomizer(PolarizedRandomizer) - Method in class org.simbrain.network.connections.QuickConnectionManager
setInReversal(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setInteractionBox(NeuronGroupNode.NeuronGroupInteractionBox) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Set a custom interaction box.
setItalic(boolean) - Method in class org.simbrain.network.core.NetworkTextObject
setIteration(int) - Method in class org.simbrain.network.trainers.CompetitiveTrainer
setIteration(int) - Method in class org.simbrain.network.trainers.IterableTrainer
setIteration(int) - Method in class org.simbrain.network.trainers.SOMTrainer
setIterationMode(boolean) - Method in class org.simbrain.util.table.NumericTable
setIterationsBeforeStopping(int) - Method in class org.simbrain.network.trainers.IterableTrainer
setJMenuBar(JMenuBar) - Method in interface org.simbrain.util.genericframe.GenericFrame
setJumpHeight(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
setJumpHeight(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
setK(int) - Method in class org.simbrain.network.subnetworks.KWTA
setKappa(double) - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
setLabel(String) - Method in class org.simbrain.network.core.Neuron
setLabel(String) - Method in class org.simbrain.network.groups.Group
setLabel(String) - Method in class org.simbrain.world.odorworld.effectors.Effector
setLabel(String) - Method in class org.simbrain.world.odorworld.sensors.Sensor
setLambda(double) - Method in class org.simbrain.network.connections.Radial
setLambda(double) - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
setLambda(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
setLastClickedPosition(Point2D) - Method in class org.simbrain.network.gui.NetworkPanel: Set the last position clicked on screen.
setLastReplaceString(String) - Method in class org.simbrain.util.scripteditor.ScriptEditor
setLastSearchString(String) - Method in class org.simbrain.util.scripteditor.ScriptEditor
setLastSelectedNeuron(NeuronNode) - Method in class org.simbrain.network.gui.NetworkPanel
setLastSpikeTime(double) - Method in class org.simbrain.network.core.SpikingNeuronUpdateRule
setLayout(Layout) - Method in class org.simbrain.network.groups.NeuronGroup: Set the layout.
setLayoutBasedOnSize() - Method in class org.simbrain.network.groups.NeuronGroup: If more than gridThreshold neurons use a grid layout, else a horizontal line layout.
setLayoutBasedOnSize(Point2D) - Method in class org.simbrain.network.groups.NeuronGroup: If more than gridThreshold neurons use a grid layout, else a horizontal line layout.
setLeakConductance(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setLeakConstant(double) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: ContinuousSigmoidalRule.leak
setLeakMaxConductance(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setLeakReversal(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setLeakReversal(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setLeakyLearningRate(double) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Sets the leaky learning rate.
setLearningRate(double) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Sets learning rate.
setLearningRate(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
setLearningRate(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianRule
setLearningRate(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
setLearningRate(double) - Method in class org.simbrain.network.synapse_update_rules.OjaRule
setLearningRate(double) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
setLearningRate(double) - Method in class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule
setLearningRate(double) - Method in class org.simbrain.network.trainers.BackpropTrainer
setLearningRate(double) - Method in class org.simbrain.network.trainers.BPTTTrainer
setLearningRate(double) - Method in class org.simbrain.network.trainers.LMSIterative
setLearningRule(SynapseUpdateRule) - Method in class org.simbrain.network.core.Synapse: Change this synapse's learning rule.
setLearningRule(SynapseUpdateRule, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setLineColor(Color) - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
setLineColor(Color) - Static method in class org.simbrain.network.gui.nodes.SynapseNode
setLocation(double, double) - Method in class org.simbrain.network.core.Neuron: Set x, y position of a neuron.
setLocation(double, double) - Method in class org.simbrain.network.groups.NeuronGroup
setLocation(double[]) - Method in class org.simbrain.util.environment.SmellSource: Set the location of this smell source.
setLocation(int, int) - Method in interface org.simbrain.util.genericframe.GenericFrame
setLocation(float, float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Set the location of this entity.
setLocationRelativeTo(Component) - Method in interface org.simbrain.util.genericframe.GenericFrame
setLocationRelativeTo(Component) - Method in class org.simbrain.util.genericframe.GenericJInternalFrame
setLogger(Logger) - Method in class org.simbrain.workspace.WorkspaceComponent
setLogicalValue(int, int, T, boolean) - Method in class org.simbrain.util.table.SimbrainDataTable: Set the value at specific position in the data underlying the table, and specify whether to fire a changed event (false useful when a lot of values need to be changed at once and it would waste time to update the GUI for every such change).
setLogSaturation(double) - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
setLoseValue(double) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Sets the loser value.
setLoseValue(double) - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
setLowerBound(double) - Method in class org.simbrain.network.core.Neuron: Convenience method to set lower bound on the neuron's update rule, if it is a bounded update rule.
setLowerBound(double) - Method in class org.simbrain.network.core.Synapse: Sets the lower synapse bound.
setLowerBound(double) - Method in class org.simbrain.network.groups.NeuronGroup: Set the lower bound on all neurons in this group.
setLowerBound(double, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Sets the lower bound of this neuron update rule's activation.
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Sets the lower bound of this neuron update rule's activation.
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.IACRule
setLowerBound(double) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.BoundedUpdateRule: Sets the lower bound of this neuron update rule's activation.
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.LinearRule
setLowerBound(double) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
setLowerBound(double) - Method in class org.simbrain.plot.barchart.BarChartModel
setLowerBound(double) - Method in class org.simbrain.util.randomizer.Randomizer
setLowerBound(int) - Method in class org.simbrain.util.table.NumericTable: Sets the lower bound .
setLowerDomainBoundary(double) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setLowerRangeBoundary(double) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setLowerThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
setLowerValue(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
setLowerValue(double) - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
setLtpMod(double) - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
setM(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
setMainPanel(LabelledItemPanel) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel
setManualColumns(boolean) - Method in class org.simbrain.network.layouts.GridLayout
setManualColumns(boolean) - Method in class org.simbrain.network.layouts.HexagonalGridLayout
setMarkedForDeletion(boolean) - Method in class org.simbrain.network.groups.Group
setMarqueeColor(Color) - Static method in class org.simbrain.network.gui.nodes.SelectionMarquee
setMaxDiameter(int) - Static method in class org.simbrain.network.gui.nodes.SynapseNode
setMaximizable(boolean) - Method in interface org.simbrain.util.genericframe.GenericFrame
setMaximizable(boolean) - Method in class org.simbrain.util.genericframe.GenericJDialog
setMaximizable(boolean) - Method in class org.simbrain.util.genericframe.GenericJFrame
setMaximumResponse(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay
setMaximumSize(Dimension) - Method in interface org.simbrain.util.genericframe.GenericFrame
setMaxState(int) - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
setMaxVisibleColumns(int) - Method in class org.simbrain.util.table.SimbrainJTableScrollPanel
setMaxVisibleRows(int) - Method in class org.simbrain.util.table.SimbrainJTableScrollPanel
setMembranePotential(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setMemCapacitance(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setMenu(OdorWorldFrameMenu) - Method in class org.simbrain.world.odorworld.OdorWorldDesktopComponent: Sets odor world frame menu.
setMiddleValue(double) - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
setMinDiameter(int) - Static method in class org.simbrain.network.gui.nodes.SynapseNode
setModel(DefaultListModel) - Method in class org.simbrain.network.gui.NeuronGroupSelectionPanel
setMomentum(double) - Method in class org.simbrain.network.trainers.BackpropTrainer
setMomentum(double) - Method in class org.simbrain.network.trainers.BPTTTrainer
setMouseover(boolean) - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Set to true if the mouse is over this sensor node.
setMouseoverPaint(Paint) - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Set the mouseover paint for this sensor node to mouseoverPaint.
setMyNextItemRow(int) - Method in class org.simbrain.util.LabelledItemPanel: Sets the current row where the next item will be placed.
setName(String) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setName(String) - Method in class org.simbrain.workspace.WorkspaceComponent
setName(String) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Set the entity's name.
setNameField(JTextField) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setNeedsReInit(boolean) - Method in class org.simbrain.util.projection.IterableProjectionMethod
setNeighborhoodDecayAmount(double) - Method in class org.simbrain.network.subnetworks.SOMGroup: Set neighborhoodDecayAmount.
setNetTimeConstant(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setNetwork(Network) - Method in class org.simbrain.network.gui.NetworkPanel: Set Root network.
setNetworkPanel(NetworkPanel) - Method in class org.simbrain.network.gui.nodes.ScreenElement: Set the network panel for this screen element to networkPanel.
setNeuron(Neuron) - Method in class org.simbrain.network.gui.nodes.NeuronNode: Set the neuron for this neuron node to neuron.
setNeuronGroups(JList) - Method in class org.simbrain.network.gui.NeuronGroupSelectionPanel
setNeuroninfoPanel(NeuronPropertiesSimple) - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel
setNeuronLayout(Layout) - Method in class org.simbrain.network.gui.dialogs.layout.AbstractLayoutPanel: Set the layout being edited by this panel.
setNeuronPanel(AbstractNeuronRulePanel) - Method in class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel
SetNeuronPropertiesAction - Class in org.simbrain.network.gui.actions.neuron: Set neuron properties.
SetNeuronPropertiesAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.neuron.SetNeuronPropertiesAction: Create a new set neuron properties action with the specified network panel.
setNeuronSet(HashSet<Neuron>) - Method in class org.simbrain.network.subnetworks.Hopfield
setNeuronType(NeuronUpdateRule) - Method in class org.simbrain.network.groups.NeuronGroup: Set the update rule for the neurons in this group.
setNeuronType(String) - Method in class org.simbrain.network.groups.NeuronGroup: Set the string update rule for the neurons in this group.
setNeuronType(String) - Method in class org.simbrain.network.util.CascadingNetworkBuilder
setNoise(boolean) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
setNoiseAdded(boolean) - Method in class org.simbrain.network.trainers.LMSOffline
setNoiseAmplitude(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.IACRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setNoiseGenerator(Randomizer) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.NoisyUpdateRule: Set the noise generator.
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.LinearRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
setNoiseGenerator(Randomizer) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
setNoiseLevel(double) - Method in class org.simbrain.util.environment.SmellSource: Sets the noise level.
setNoiseVar(double) - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
setNormalizationFactor(double) - Method in class org.simbrain.network.synapse_update_rules.OjaRule
setNormalizeInputs(boolean) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Sets the normalize inputs value.
setNudgeAmount(double) - Static method in class org.simbrain.network.gui.NetworkPanel
setNull() - Method in class org.simbrain.util.widgets.TristateDropDown: Sets the tristate drop down box to null.
setNumberOfPastes(double) - Method in class org.simbrain.network.gui.NetworkPanel
setNumBrachesPerNeuron(int) - Method in class org.simbrain.network.util.CascadingNetworkBuilder
setNumColumns(int) - Method in class org.simbrain.network.layouts.GridLayout
setNumColumns(int) - Method in class org.simbrain.network.layouts.HexagonalGridLayout
setNumLayers(int) - Method in class org.simbrain.network.util.CascadingNetworkBuilder
setNumNeurons(int) - Method in class org.simbrain.network.subnetworks.SOMGroup: Set the number of neurons.
setNumSubSamples(int) - Static method in class org.simbrain.network.groups.NeuronGroup
setNumTargs(int) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
setNumThreads(int) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Set number of threads in updater.
setObject(T) - Method in class org.simbrain.network.listeners.NetworkEvent
setObject(Object) - Method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor: Set object to edit.
setObjectPropsItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setObjectsBlockMovement(boolean) - Method in class org.simbrain.world.odorworld.OdorWorld
setOldObject(T) - Method in class org.simbrain.network.listeners.NetworkEvent
setOrientation(LineLayout.LineOrientation) - Method in class org.simbrain.network.layouts.LineLayout
setOutgoingField(JLabel) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setOutlinePadding(int) - Method in class org.simbrain.network.gui.nodes.OutlinedObjects
setOutlinePaint(Paint) - Method in class org.simbrain.world.visionworld.node.AbstractPixelMatrixNode: Set the outline paint for this pixel matrix node to outlinePaint.
setOutlinePaint(Paint) - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Set the outline paint for this sensor matrix node to outlinePaint.
setOutlinePaint(Paint) - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Set the outline paint for this sensor node to outlinePaint.
setOutlineStroke(Stroke) - Method in class org.simbrain.world.visionworld.node.AbstractPixelMatrixNode: Set the outline stroke for this pixel matrix node to outlineStroke.
setOutlineStroke(Stroke) - Method in class org.simbrain.world.visionworld.node.AbstractSensorMatrixNode: Set the outline stroke for this sensor matrix node to outlineStroke.
setOutlineStroke(Stroke) - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Set the outline stroke for this sensor node to outlineStroke .
setOutputAmount(double) - Method in class org.simbrain.world.odorworld.sensors.Hearing
setOutputFunction(PointNeuronRule.OutputFunction) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setOutputThreshold(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
setOutputThresholdMomentum(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
setParam1(double) - Method in class org.simbrain.util.randomizer.Randomizer
setParam1Consistent(String, double) - Method in class org.simbrain.util.randomizer.Randomizer
setParam2(double) - Method in class org.simbrain.util.randomizer.Randomizer
setParam2Consistent(String, double) - Method in class org.simbrain.util.randomizer.Randomizer
setParams(double, double) - Method in class org.simbrain.util.randomizer.Randomizer
setParamsConsistent(String, double, String, double) - Method in class org.simbrain.util.randomizer.Randomizer
setParentFrame(GenericFrame) - Method in class org.simbrain.workspace.gui.GuiComponent: Sets the parent frame of this view.
setParentGroup(Group) - Method in class org.simbrain.network.core.Neuron
setParentGroup(SynapseGroup) - Method in class org.simbrain.network.core.Synapse
setParentGroup(Group) - Method in class org.simbrain.network.groups.Group
setParentGroupField(JLabel) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setParseStyle(ComboBoxWrapper) - Method in class org.simbrain.world.textworld.ReaderWorld: Set the current parse style.
setParseStyle(ReaderWorld.ParseStyle) - Method in class org.simbrain.world.textworld.ReaderWorld
setPasteDelta() - Method in class org.simbrain.network.gui.NetworkPanel: Set the offset used in multiple pastes.
setPasteItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setPasteX(double) - Method in class org.simbrain.network.gui.NetworkPanel
setPasteY(double) - Method in class org.simbrain.network.gui.NetworkPanel
setPdf(ProbDistribution) - Method in class org.simbrain.util.randomizer.Randomizer
setPeak(double) - Method in class org.simbrain.util.environment.SmellSource
setPenBackground(Color) - Method in class org.simbrain.world.visionworld.node.PixelMatrixImageNode: Set the pen background color for this pixel matrix image node to penBackground.
setPenForeground(Color) - Method in class org.simbrain.world.visionworld.node.PixelMatrixImageNode: Set the pen foreground color for this pixel matrix image node to penForeground.
setPercentExcitatory(double) - Method in class org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel
setPercentValidation(double) - Method in class org.simbrain.network.trainers.TrainingSet
setPerKChannels(float) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setPermitDensityEditing(boolean) - Method in class org.simbrain.network.connections.Sparse
setPerNaChannels(float) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setPhase(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
setPhi(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setPhrase(String) - Method in class org.simbrain.world.odorworld.effectors.Speech
setPhrase(String) - Method in class org.simbrain.world.odorworld.sensors.Hearing
setPixel(int, int, Color) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: Set the pixel at the specified (x, y) coordinates to the RGB and alpha values in the specified color (optional operation).
setPixel(int, int, Color) - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: Set the pixel at the specified (x, y) coordinates to the RGB and alpha values in the specified color (optional operation).
setPixel(int, int, Color) - Method in interface org.simbrain.world.visionworld.PixelMatrix: Set the pixel at the specified (x, y) coordinates to the RGB and alpha values in the specified color (optional operation).
setPixelMatrix(PixelMatrix) - Method in class org.simbrain.world.visionworld.ImmutableVisionWorldModel: Set the pixel matrix for this vision world model to pixelMatrix (optional operation).
setPixelMatrix(PixelMatrix) - Method in class org.simbrain.world.visionworld.MutableVisionWorldModel: Set the pixel matrix for this vision world model to pixelMatrix (optional operation).
setPixelMatrix(PixelMatrix) - Method in interface org.simbrain.world.visionworld.VisionWorldModel: Set the pixel matrix for this vision world model to pixelMatrix (optional operation).
setPixelMatrixImageNode(PixelMatrixImageNode) - Method in interface org.simbrain.world.visionworld.node.editor.PixelMatrixImageNodeEditor: Set the pixel matrix image node to edit to pixelMatrixImageNode.
setPixelMatrixImageNode(PixelMatrixImageNode) - Method in class org.simbrain.world.visionworld.node.editor.PixelMatrixImageNodeTableEditor: Set the pixel matrix image node to edit to pixelMatrixImageNode.
setPlasticityType(int) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
setPoint(int, DataPoint) - Method in class org.simbrain.util.projection.Dataset: Set a specified point in the dataset.
setPolarity(SimbrainConstants.Polarity) - Method in class org.simbrain.network.core.Neuron
setPolarity(SimbrainConstants.Polarity) - Method in class org.simbrain.util.randomizer.PolarizedRandomizer
setPopField(JLabel) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setPosition(Point2D) - Method in class org.simbrain.network.core.Neuron: Set position of neuron using a point object.
setPosition(int) - Method in class org.simbrain.world.textworld.TextWorld
setPosition(int, boolean) - Method in class org.simbrain.world.textworld.TextWorld: Set position.
setPotentialTimeConstant(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setPreferredSize(Dimension) - Method in interface org.simbrain.util.genericframe.GenericFrame
setPrioritiesVisible(boolean) - Method in class org.simbrain.network.gui.NetworkPanel: Turns the displaying of neuron priorities on or off.
setPriority(int) - Method in class org.simbrain.workspace.CouplingManager: Set the priority.
setPriorityView(boolean) - Method in class org.simbrain.network.gui.nodes.NeuronNode: Toggles the visibility of the priority view text label.
setProjectionMethod(ProjectionMethod) - Method in class org.simbrain.util.projection.Projector: Change the current projection method and perform and other needed initialization.
setProjectionMethod(String) - Method in class org.simbrain.util.projection.Projector
setPropsItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setPsr(double) - Method in class org.simbrain.network.core.Synapse
setPSRDecayTimeConstant(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.UDF: Sets the time constant for the decay of the PSR which is always governed by a ConvolvedJumpAndDecay spike responder.
setRadius(double) - Method in class org.simbrain.world.odorworld.sensors.SmellSensor
setRandomizer(Randomizer) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
setRandomizers(PolarizedRandomizer, PolarizedRandomizer) - Method in class org.simbrain.network.groups.SynapseGroup
setRandomProb(double) - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
setRange(double, double) - Method in class org.simbrain.plot.barchart.BarChartModel
setRangeLowerBound(double) - Method in class org.simbrain.plot.rasterchart.RasterModel
setRangeLowerBound(double) - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
setRangeUpperBound(double) - Method in class org.simbrain.plot.rasterchart.RasterModel
setRangeUpperBound(double) - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
setRateConstant(double) - Method in class org.simbrain.network.neuron_update_rules.RunningAverageRule
setRecordAsSpikes(boolean) - Method in class org.simbrain.network.groups.NeuronGroup
setRecurrent(boolean) - Method in class org.simbrain.network.gui.dialogs.connect.connector_panels.SparseConnectionPanel
setRecurrentOutWeights(boolean) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Set to true for the output to receive input from itself from the previous time-step.
setRed(int, int) - Static method in class org.simbrain.util.Utils: Sets the red value of the color represented by rgbIntColor to the value specified by red and returns the resulting color.
setRefractoryPeriod(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setRefractoryPeriod(double) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
setRefractoryPeriod(double) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setRefractoryPotential(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setRegularExpression(String) - Method in class org.simbrain.world.textworld.ReaderWorld
setRelAbs(int) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setReplace(boolean) - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Tells this panel whether it is going to be editing neuron update rules, or creating new ones and replacing the update rule of each of the neurons being edited.
setReplace(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Tells this panel whether it is going to be editing spike responders, or creating new ones and replacing the spike responders of each of the synapses being edited.
setReplace(boolean) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Tells this panel whether it is going to be editing synapse update rules, or creating new ones and replacing the update rule of each of the synapses being edited.
setReservoirNeuronType(NeuronUpdateRule) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Set type of reservoir neurons.
setResetPotential(double) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setResistance(double) - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule
setResistance(double) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setResizable(boolean) - Method in interface org.simbrain.util.genericframe.GenericFrame
setResponseDuration(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.Step
setResponseHeight(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.Step
setResponseValue(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder
setRest(double) - Method in class org.simbrain.network.neuron_update_rules.IACRule
setRestingPotential(double) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setResurrectionProb(double) - Method in class org.simbrain.world.odorworld.LifeCycle
setRidgeRegression(boolean) - Method in class org.simbrain.network.trainers.LMSOffline
setRowHeadings(List<String>) - Method in class org.simbrain.util.table.SimbrainJTable
setRunning(boolean) - Method in class org.simbrain.network.gui.NetworkPanel
setRunning(boolean) - Method in class org.simbrain.plot.projection.ProjectionModel: This flag allows the user to start and stop iterative projection techniques.
setScalingFactor(double) - Method in class org.simbrain.world.odorworld.effectors.StraightMovement
setScriptFile(File) - Method in class org.simbrain.util.scripteditor.ScriptEditor
setScriptString(String) - Method in class org.simbrain.network.update_actions.CustomUpdate
setScriptString(String) - Method in class org.simbrain.workspace.updater.UpdateActionCustom
setSelected(boolean) - Method in class org.simbrain.util.widgets.TristateDropDown: Sets the selected item.
setSelected(boolean) - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Set to true if this sensor node is selected.
setSelectedItem(Object) - Method in class org.simbrain.workspace.gui.couplingmanager.GenericListModel: Sets the selected item(s).
setSelectedPaint(Paint) - Method in class org.simbrain.world.visionworld.node.AbstractSensorNode: Set the selected paint for this sensor node to selectedPaint .
setSelectedPoint(Point) - Method in class org.simbrain.util.table.SimbrainJTable: Sets the selected point.
setSelection(Collection) - Method in class org.simbrain.network.gui.NetworkPanel: Set the selection to the specified collection of elements.
setSelection(Collection) - Method in class org.simbrain.network.gui.NetworkSelectionModel: Set the selection to the specified collection of elements.
setSelection(Collection<Sensor>) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Set the selection for this sensor selection model to the specified collection of sensors.
setSelectionColor(Color) - Static method in class org.simbrain.network.gui.nodes.SelectionHandle
setSelfConnectionAllowed(boolean) - Method in class org.simbrain.network.connections.AllToAll: Set whether or not self connections are allowed.
setSelfConnectionAllowed(boolean) - Method in class org.simbrain.network.connections.Sparse: Set whether or not self connections (connections where the source and target neuron are the same neuron) are allowed.
setSemiSaturationConstant(double) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
setSensorMatrix(SensorMatrix) - Method in class org.simbrain.world.visionworld.ImmutableVisionWorldModel: Set the sensor matrix for this vision world model to sensorMatrix (optional operation).
setSensorMatrix(SensorMatrix) - Method in class org.simbrain.world.visionworld.MutableVisionWorldModel: Set the sensor matrix for this vision world model to sensorMatrix (optional operation).
setSensorMatrix(SensorMatrix) - Method in interface org.simbrain.world.visionworld.VisionWorldModel: Set the sensor matrix for this vision world model to sensorMatrix (optional operation).
setSensors(List<Sensor>) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setSensorsEnabled(boolean) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setSerializePriority(int) - Method in class org.simbrain.workspace.WorkspaceComponent
setSeriesColor(String, Color) - Method in class org.simbrain.plot.histogram.HistogramModel: Set the color of a data series.
setSeriesColor(String, Color) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Set the color of a data series.
setShowCSVInPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowDeleteColumnPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowDeleteRowPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowEditInPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowFillInPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowHistory(boolean) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel: Boolean show history.
setShowInsertColumnPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowInsertRowPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowNormalizeInPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowRandomizeInPopupMenu(boolean) - Method in class org.simbrain.util.table.SimbrainJTable
setShowSensors(boolean) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setShowSubnetOutline(boolean) - Method in class org.simbrain.network.gui.NetworkPanel
setShowTime(boolean) - Method in class org.simbrain.network.gui.NetworkPanel
setSimulationRunning(boolean) - Static method in class org.simbrain.util.StandardDialog
setSlope(double) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
setSlope(double) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
setSlope(double) - Method in class org.simbrain.network.neuron_update_rules.LinearRule
setSlopeFactor(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setSmallWtThreshold(double) - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
setSmellSource(SmellSource) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setSolutionType(LMSOffline.SolutionType) - Method in class org.simbrain.network.trainers.LMSOffline: Set solution type.
setSolutionType(ComboBoxWrapper) - Method in class org.simbrain.network.trainers.LMSOffline: Set the current parse style.
setSource(NeuronNode) - Method in class org.simbrain.network.gui.nodes.SynapseNode
setSource(VisionWorldModel) - Method in class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Set the source of vision world model events to source.
setSourceColor(Color) - Static method in class org.simbrain.network.gui.nodes.SourceHandle
setSourceElements() - Method in class org.simbrain.network.gui.NetworkPanel: Set selected elements to be source elements (with red rectangles around them).
SetSourceNeurons - Class in org.simbrain.network.gui.actions.connection: Set source neurons.
SetSourceNeurons(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.connection.SetSourceNeurons: Construct action.
setSpacing(double) - Method in class org.simbrain.network.layouts.LineLayout
setSpectralRadius(double) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Set spectral radius.
setSpike(boolean) - Method in class org.simbrain.network.core.Neuron
setSpikeResponder(SpikeResponder) - Method in class org.simbrain.network.core.Synapse
setSpikeResponder(SpikeResponder, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setSpikingColor(Color) - Static method in class org.simbrain.network.gui.nodes.NeuronNode
setSpikingNeuronGroup(boolean) - Method in class org.simbrain.network.groups.NeuronGroup
setSpkBuffer(boolean) - Method in class org.simbrain.network.core.Neuron
setSquashFunctionType(SquashingFunction) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule
setSquashFunctionType(SquashingFunction) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
setStartPort(NeuronGroupNode.Port) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
setStartPt(Point2D.Float) - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
setStartPt(Point2D.Float) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setState(boolean) - Method in class org.simbrain.util.widgets.LinkIcon: Sets the state of the link icon, linked or unlinked
setState(boolean) - Method in class org.simbrain.util.widgets.StopLight: Set the current state of the stoplight.
setState(int, int, TicTacToeModel.State) - Method in class org.simbrain.world.game.tictactoe.TicTacToeModel: Sets the state of the given square.
setStateInfo(String) - Method in class org.simbrain.network.groups.Group
setSteepness(double) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
setStepsPerSequences(int) - Method in class org.simbrain.network.subnetworks.BPTTNetwork
setStimulusS(String) - Method in class org.simbrain.util.environment.SmellSource: Sets the stimulus string.
setStimulusVector(double[]) - Method in class org.simbrain.util.environment.SmellSource: Sets the stimulus vector.
setStoppingCond(ComboBoxWrapper) - Method in class org.simbrain.network.trainers.IterableTrainer: Set the current stopping condition.
setStoppingCondition(IterableTrainer.StoppingCondition) - Method in class org.simbrain.network.trainers.IterableTrainer
setStrength(double) - Method in class org.simbrain.network.core.Synapse: Sets the strength of the synapse.
setStrength(double, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setStrokeWidth(float) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setSynapse(Synapse) - Method in class org.simbrain.network.gui.nodes.SynapseNode
setSynapsePanel(AbstractSynapseRulePanel) - Method in class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel
setSynapsePanel(AbstractSpikeResponsePanel) - Method in class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel
setSynapseParameter(Synapse, T) - Method in interface org.simbrain.network.connections.ConnectionUtilities.SynapseParameterSetter: A generic setter intended to be used to set some parameter of the synapse parameter to the given value.
SetSynapsePropertiesAction - Class in org.simbrain.network.gui.actions.synapse: Set synapse properties.
SetSynapsePropertiesAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.synapse.SetSynapsePropertiesAction: Create a new set synapse properties action with the specified network panel.
setSynapses(ConnectionUtilities.SynapseParameterSetter<T>, T, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup: A generic method that takes in a functional interface, a value and a polarity.
setSynapseStrength(Synapse, double) - Method in class org.simbrain.network.groups.SynapseGroup: Sets the strength of a single synapse in the group specified as a parameter.
setSynapseVisibilityThreshold(int) - Static method in class org.simbrain.network.core.Network
setSynpaseDecayPercent(double) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup
setTable(SimbrainJTable) - Method in class org.simbrain.network.gui.trainer.DataPanel
setTable(SimbrainJTable) - Method in class org.simbrain.util.table.SimbrainJTableScrollPanel: Sets the jtable.
setTarget(NeuronNode) - Method in class org.simbrain.network.gui.nodes.SynapseNode
setTargetData(double[][]) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
setTargetData(double[][]) - Method in class org.simbrain.network.trainers.TrainingSet: Set the target data.
setTargetValue(double) - Method in class org.simbrain.network.core.Neuron: Set target value.
setTaskSynchronizationManager(TaskSynchronizationManager) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Sets the manager.
setTaskSynchronizationManager(TaskSynchronizationManager) - Method in class org.simbrain.workspace.Workspace: Set the task synchronization manager.
setTau_minus(double) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
setTau_plus(double) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
setTauW(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setTemp(double) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setTemplate(DirectedCubicArrow.BezierTemplate) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setTestData(double[][]) - Method in class org.simbrain.network.groups.NeuronGroup
setText(String) - Method in class org.simbrain.docviewer.DocViewerComponent
setText(String) - Method in class org.simbrain.network.core.NetworkTextObject
setText(String) - Method in class org.simbrain.network.gui.nodes.InteractionBox: Set text for interaction box.
setText(String) - Method in class org.simbrain.util.scripteditor.ScriptEditor: Sets text of the underlying text area.
setText(String) - Method in class org.simbrain.world.textworld.TextWorld
setText(String, boolean) - Method in class org.simbrain.world.textworld.TextWorld: Set text, and fire an event if the fireEvent flag is set.
SetTextPropertiesAction - Class in org.simbrain.network.gui.actions: Set neuron properties.
SetTextPropertiesAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.SetTextPropertiesAction: Create a new set neuron properties action with the specified network panel.
setTheBool(boolean) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheBooleanObject(Boolean) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheColor(Color) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheDecayFunction(ComboBoxWrapper) - Method in class org.simbrain.util.environment.SmellSource
setTheDouble(double) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheDoubleObject(Double) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheFloat(float) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheFloatObject(Float) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheInt(int) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheIntObject(Integer) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheLong(long) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheLongObject(Long) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheShort(short) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheShortObject(Short) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheString(String) - Method in class org.simbrain.util.propertyeditor.gui.TestObject
setTheta(double) - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
setTheta(float) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setTheta(double) - Method in class org.simbrain.world.odorworld.sensors.SmellSensor
setThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.BinaryRule
setThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
setThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule
setThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
setThreshold(double) - Method in class org.simbrain.world.odorworld.effectors.Speech
setThresholdPotential(double) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule
setTile(int, int, Image) - Method in class org.simbrain.world.odorworld.TileMap: Sets the tile at the specified location.
setTime(double) - Method in class org.simbrain.network.core.Network: Set the current time.
setTime(int) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Sets the time.
setTimeConstant(double) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule
setTimeConstant(double) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule
setTimeConstant(double) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
setTimeConstant(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
setTimeConstant(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay
setTimeConstant(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay
setTimeStep(double) - Method in class org.simbrain.network.core.Network
setTimeType(Network.TimeType) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
setTitle(String) - Method in class org.simbrain.network.gui.NetworkPanel
setTitle(String) - Method in interface org.simbrain.util.genericframe.GenericFrame
setTitle(String) - Method in class org.simbrain.workspace.gui.GuiComponent
setToBufferVals() - Method in class org.simbrain.network.core.Neuron: A general purpose method that moves all relevant values from this neuron's buffer to its main values.
setTolerance(double) - Method in class org.simbrain.util.projection.Projector
setTrainer(IterableTrainer) - Method in class org.simbrain.network.gui.trainer.IterativeControlsPanel
setTrainer(LMSOffline) - Method in class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.LMSOfflineControlPanel: ESN must set the trainer because when the ESN training panel is opened the trainer has not been created yet.
setTransparency(float) - Method in class org.simbrain.util.widgets.DirectedCubicArrow
setType(HistogramType) - Method in class org.simbrain.plot.histogram.OverwritableHistogramDataset: Sets the histogram type and sends a DatasetChangeEvent to all registered listeners.
setType(ComboBoxWrapper) - Method in class org.simbrain.world.odorworld.entities.BasicEntity: Setter which takes the data from a combo box as an argument.
setType(ComboBoxWrapper) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Setter which takes the data from a combo box as an argument.
setTypeField(JLabel) - Method in class org.simbrain.network.gui.dialogs.group.SummaryPanel
setUpdateComplete(boolean) - Method in class org.simbrain.network.gui.NetworkPanel
setUpdateComplete(boolean) - Method in class org.simbrain.network.listeners.NetworkAdapter
setUpdateComplete(boolean) - Method in interface org.simbrain.network.listeners.NetworkListener: A way to tell listeners that their update is incomplete signaling that they should update.
setUpdateCompleted(boolean) - Method in class org.simbrain.network.core.Network: Used by Network thread to ensure that an update cycle is complete before updating again.
setUpdateCompleted(boolean) - Method in class org.simbrain.network.trainers.CompetitiveTrainer: Sets updated completed value.
setUpdateCompleted(boolean) - Method in class org.simbrain.network.trainers.IterableTrainer: Sets updated completed value.
setUpdateCompleted(boolean) - Method in class org.simbrain.network.trainers.SOMTrainer: Sets updated completed value.
setUpdateCompleted(boolean) - Method in class org.simbrain.plot.projection.ProjectionModel: Swing update flag.
setUpdateDelay(int) - Method in class org.simbrain.workspace.Workspace
setUpdateFunc(Hopfield.HopfieldUpdate) - Method in class org.simbrain.network.subnetworks.Hopfield
setUpdateInfoPanel(SpecificNeuronRulePanel) - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesPanel
setUpdateInfoPanel(SpecificSynapseRulePanel) - Method in class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesPanel
setUpdateMethod(CompetitiveGroup.UpdateMethod) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup
setUpdateOn(Boolean) - Method in class org.simbrain.workspace.WorkspaceComponent
setUpdatePriority(int) - Method in class org.simbrain.network.core.Neuron
setUpdateRule(String) - Method in class org.simbrain.network.core.Neuron: Sets the update rule using a String description.
setUpdateRule(NeuronUpdateRule) - Method in class org.simbrain.network.core.Neuron: Set a new update rule.
setUpEditMenu() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu: Sets up edit menu items.
setUpFileMenu() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu: Sets up file menu items.
setUpLabelColor(Color) - Method in class org.simbrain.util.widgets.DropDownTriangle: Sets the color of the label when the triangle is in the up state.
setUpMenus() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu: Sets up menus.
setUpperBound(double) - Method in class org.simbrain.network.core.Neuron: Convenience method to set upper bound on the neuron's update rule, if it is a bounded update rule.
setUpperBound(double) - Method in class org.simbrain.network.core.Synapse: Sets the upper synapse bound.
setUpperBound(double) - Method in class org.simbrain.network.groups.NeuronGroup: Set the upper bound on all neurons in this group.
setUpperBound(double, SimbrainConstants.Polarity) - Method in class org.simbrain.network.groups.SynapseGroup
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Sets the upper bound of this neuron update rule's activation.
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Sets the upper bound of this neuron update rule's activation.
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.DecayRule
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.IACRule
setUpperBound(double) - Method in interface org.simbrain.network.neuron_update_rules.interfaces.BoundedUpdateRule: Sets the upper bound of this neuron update rule's activation.
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.LinearRule
setUpperBound(double) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule
setUpperBound(double) - Method in class org.simbrain.plot.barchart.BarChartModel
setUpperBound(double) - Method in class org.simbrain.util.randomizer.Randomizer
setUpperBound(int) - Method in class org.simbrain.util.table.NumericTable: Sets the upper bound value.
setUpperDomainBoundary(double) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setUpperRangeBoundary(double) - Method in class org.simbrain.plot.scatterplot.ScatterPlotModel
setUpperThreshold(double) - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
setUpperValue(double) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
setUpperValue(double) - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule
setUpText(String) - Method in class org.simbrain.util.widgets.DropDownTriangle: Changes the text displayed when the triangle is in the "up" state
setUseAdaptation(boolean) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Sets the boolean use adaptation value.
setUseApplyButton(boolean, ActionListener) - Method in class org.simbrain.network.gui.dialogs.layout.MainLayoutPanel: Set whether to use the apply button.
setUseBidirectionalConnections(boolean) - Method in class org.simbrain.network.connections.OneToOne
setUseExcitatoryRandomization(boolean) - Method in class org.simbrain.network.connections.QuickConnectionManager
setUseFullRepOnSave(boolean) - Method in class org.simbrain.network.groups.SynapseGroup
setUseGroupLevelSettings(boolean) - Method in class org.simbrain.network.groups.SynapseGroup
setUseImagePreview(boolean) - Method in class org.simbrain.util.SFileChooser: Sets the file chooser to use image preview viewer.
setUseInhibitoryRandomization(boolean) - Method in class org.simbrain.network.connections.QuickConnectionManager
setUseLeakyLearning(boolean) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Sets the leaky learning value.
setUseNoise(boolean) - Method in class org.simbrain.network.subnetworks.EchoStateNetwork
setUseRandom(boolean) - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
setUseSlidingOutputThreshold(boolean) - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
setUseSubSampling(boolean) - Static method in class org.simbrain.network.groups.NeuronGroup
setUseSuperclass(boolean) - Method in class org.simbrain.util.propertyeditor.gui.ReflectivePropertyEditor
setV(double) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
setV_m1(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setV_m2(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setV_mem(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setV_Peak(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setV_Reset(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setV_Th(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setV_w1(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setV_w2(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setVal(int, E) - Method in class org.simbrain.workspace.AttributeList: Set the value of setter at the specified index.
setValue(double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder
setValue(double) - Method in class org.simbrain.plot.barchart.BarChartComponent.BarChartSetter: Set the value.
setValue(double, Integer) - Method in class org.simbrain.plot.barchart.BarChartModel: Set value of a specified bar.
setValue(double, Integer) - Method in class org.simbrain.plot.piechart.PieChartModel: Set the value of a specified "slice".
setValue(double) - Method in class org.simbrain.plot.projection.ProjectionComponent.Dimension: Set the value.
setValue(double, Integer) - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent: Set the value of a specified data source (one curve in the time series plot).
setValue(int, int, T) - Method in class org.simbrain.util.table.SimbrainDataTable: Set the value at specific position in the table.
setValue(int, int, T, boolean) - Method in class org.simbrain.util.table.SimbrainDataTable: Set the value at specific position in the table, and specify whether to fire a changed event (false useful when a lot of values need to be changed at once and it would waste time to update the GUI for every such change).
setValue(E) - Method in class org.simbrain.workspace.AttributeList.GetterSetter
setValue(E) - Method in interface org.simbrain.workspace.Consumer: Set the value for this consuming attribute to value.
setValue(double) - Method in class org.simbrain.world.dataworld.DataWorldComponent.ColumnAttribute: Set the value.
setValue(double) - Method in class org.simbrain.world.odorworld.sensors.TileSensor
setValueAt(Object, int, int) - Method in class org.simbrain.util.table.SimbrainDataTable
setValueAt(Object, int, int) - Method in class org.simbrain.workspace.gui.ComponentPanel.ComponentTableModel
setValueAt(Object, int, int) - Method in class org.simbrain.workspace.gui.couplingmanager.AttributeTypePanel.AttributeTypeModel
setValueAt(Object, int, int) - Method in class org.simbrain.world.odorworld.dialogs.EffectorPanel.EffectorModel
setValueAt(Object, int, int) - Method in class org.simbrain.world.odorworld.dialogs.SensorPanel.SensorModel
setValueCurrentRow(int, double) - Method in class org.simbrain.util.table.NumericTable: Set the values of the specified column in the current row.
setValues(double[]) - Method in class org.simbrain.plot.piechart.PieChartModel: Set the values for all the "slices" using an array.
setValues(double[], Integer) - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent: Set the value of a specified data source (one curve in the raster plot).
setValues() - Method in class org.simbrain.world.odorworld.dialogs.OdorWorldDialog: Set world values based on fields.
setVClampOn(boolean) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
setVectorCurrentRow(double[]) - Method in class org.simbrain.util.table.NumericTable: Set the current row using an array of doubles.
setVelocityX(float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Sets the horizontal velocity of this OdorWorldEntity in pixels per millisecond.
setVelocityY(float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Sets the vertical velocity of this OdorWorldEntity in pixels per millisecond.
setVerticalSpacing(double) - Method in class org.simbrain.network.util.CascadingNetworkBuilder
setVisible(boolean) - Method in interface org.simbrain.util.genericframe.GenericFrame
setVisible(boolean) - Method in class org.simbrain.util.randomizer.gui.RandomizerPanel
setVisible(boolean) - Method in class org.simbrain.workspace.AttributeType
setVisionWorldDesktopComponent(VisionWorldDesktopComponent) - Method in class org.simbrain.world.visionworld.VisionWorld: Sets the desktop component.
setvRest_Ca(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setvRest_k(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setvRest_L(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setVSpacing(double) - Method in class org.simbrain.network.layouts.GridLayout
setVSpacing(double) - Method in class org.simbrain.network.layouts.HexagonalGridLayout
setW(double) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
setW(double) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo
setW_K(double) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
setW_minus(double) - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
setW_minus(double) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
setW_plus(double) - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule
setW_plus(double) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
setWallItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setWallPropsItem(JMenuItem) - Method in class org.simbrain.world.odorworld.OdorWorldMenu
setWandRadius(int) - Static method in class org.simbrain.network.gui.EditMode: Set the new wand radius.
setWeights(double) - Method in class org.simbrain.network.core.Network: Sets all weights to a specified value.
setWeights(List<Neuron>, List<Neuron>, double[][]) - Static method in class org.simbrain.network.util.SimnetUtils: Set the weights connecting two lists of neurons using a weight matrix.
setWeightsToZero() - Method in class org.simbrain.network.core.Network: Sets all weight values to zero, effectively eliminating them.
setWeightsVisible(boolean) - Method in class org.simbrain.network.gui.NetworkPanel: Turns the displaying of loose synapses on and off (for performance increase or visual clarity).
setWidth(int, boolean) - Method in class org.simbrain.world.odorworld.OdorWorld: Set width.
setWidth(int) - Method in class org.simbrain.world.odorworld.OdorWorld
setWidth(int) - Method in class org.simbrain.world.odorworld.sensors.TileSensor
setWindowSize(int) - Method in class org.simbrain.plot.rasterchart.RasterModel
setWindowSize(int) - Method in class org.simbrain.plot.timeseries.TimeSeriesModel
setWinValue(double) - Method in class org.simbrain.network.subnetworks.CompetitiveGroup: Sets the winner value.
setWinValue(double) - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
setWorkAvailable(boolean) - Method in class org.simbrain.network.update_actions.concurrency_tools.SynchronizationPoint
setWorkspace(Workspace) - Method in class org.simbrain.workspace.WorkspaceComponent: Sets the workspace for this component.
setWorkspaceChanged(boolean) - Method in class org.simbrain.workspace.Workspace: Sets whether the workspace has been changed.
setWorld(OdorWorld) - Method in class org.simbrain.world.odorworld.OdorWorldPanel
setWrapAround(boolean) - Method in class org.simbrain.world.odorworld.OdorWorld
setX(double) - Method in class org.simbrain.network.core.NetworkTextObject
setX(double) - Method in class org.simbrain.network.core.Neuron
setX(double) - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent.ScatterPlotSetter
setX(float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Sets this OdorWorldEntity's current x position.
setX(double) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setX(int) - Method in class org.simbrain.world.odorworld.sensors.TileSensor
setxAxisName(String) - Method in class org.simbrain.plot.histogram.HistogramPanel
setXpos(double) - Method in class org.simbrain.network.gui.nodes.NeuronNode
setXYZCoordinatesFromFile(String) - Method in class org.simbrain.network.groups.NeuronGroup
setY(double) - Method in class org.simbrain.network.core.NetworkTextObject
setY(double) - Method in class org.simbrain.network.core.Neuron
setY(double) - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent.ScatterPlotSetter
setY(float) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Sets this OdorWorldEntity's current y position.
setY(double) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity
setY(int) - Method in class org.simbrain.world.odorworld.sensors.TileSensor
setyAxisName(String) - Method in class org.simbrain.plot.histogram.HistogramPanel
setYpos(double) - Method in class org.simbrain.network.gui.nodes.NeuronNode
setZ(double) - Method in class org.simbrain.network.core.Neuron
setZeroWeightColor(Color) - Static method in class org.simbrain.network.gui.nodes.SynapseNode
SFileChooser - Class in org.simbrain.util: SFileChooser extends java's JFileChooser, providing for automatic adding of file extensions, memory of file-locations, and checks to prevent file-overwrites.
SFileChooser(String, String) - Constructor for class org.simbrain.util.SFileChooser: Creates file chooser dialog.
SFileChooser(String, String, String) - Constructor for class org.simbrain.util.SFileChooser: Creates the file chooser dialog.
sFunction - Variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Current implementation.
ShortTermPlasticityRule - Class in org.simbrain.network.synapse_update_rules: ShortTermPlasticitySynapse.
ShortTermPlasticityRule() - Constructor for class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
ShortTermPlasticityRulePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: ShortTermPlasticitySynapsePanel.
ShortTermPlasticityRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel: Creates a short term plasticity synapse panel.
ShowAdjustConnectivityDialog - Class in org.simbrain.network.gui.actions.synapse: Show dialog for adjusting connectivity.
ShowAdjustConnectivityDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.synapse.ShowAdjustConnectivityDialog: Construct action.
ShowAdjustSynapsesDialog - Class in org.simbrain.network.gui.actions.synapse: Show synapse adjustment dialog.
ShowAdjustSynapsesDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.synapse.ShowAdjustSynapsesDialog: Construct the action.
ShowClampToolBarAction - Class in org.simbrain.network.gui.actions.toolbar: Clamps neurons action.
ShowClampToolBarAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.toolbar.ShowClampToolBarAction: Create a new clamp neurons action with the specified network panel.
showColorChooser() - Method in class org.simbrain.network.gui.dialogs.NetworkPropertiesPanel: Show the color palette and get a color.
ShowDebugAction - Class in org.simbrain.network.gui.actions: Prints debug information to standard output.
ShowDebugAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.ShowDebugAction: Create a new show help action with the specified network panel.
showDictionaryEditor(TextWorld) - Static method in class org.simbrain.world.textworld.TextWorldActions: Action for showing the vector dictionary editor, either the token-to-vector dictionary used in readerworld or the vector-to-token dictionary used in display world.
ShowEditToolBarAction - Class in org.simbrain.network.gui.actions.toolbar: Clamps neurons action.
ShowEditToolBarAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.toolbar.ShowEditToolBarAction: Create a new clamp neurons action with the specified network panel.
ShowEntityDialogAction - Class in org.simbrain.world.odorworld.actions: Action for showing an entity dialog.
ShowEntityDialogAction(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.actions.ShowEntityDialogAction: Construct a show entity action.
showHasChangedDialog() - Method in class org.simbrain.workspace.gui.GuiComponent: Checks to see if anything has changed and then offers to save if true.
ShowHelpAction - Class in org.simbrain.util.widgets: An action that opens a help file in an external web browser.
ShowHelpAction(String, String) - Constructor for class org.simbrain.util.widgets.ShowHelpAction: Create a help action that opens the specified URL (relative to Simbrain/docs).
ShowHelpAction(String) - Constructor for class org.simbrain.util.widgets.ShowHelpAction: Create a help action that opens the specified URL (relative to the "Pages" directory in Simbrain/docs).
showHelpPage(String) - Static method in class org.simbrain.util.Utils: Display a documentation page under {simbrainhome}/docs/...
showJFrame(WorkspaceComponent) - Static method in class org.simbrain.workspace.gui.SimbrainDesktop: Show Gui View of a workspace component.
ShowLayoutDialogAction - Class in org.simbrain.network.gui.actions: Show layout dialog action.
ShowLayoutDialogAction(Layout, NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.ShowLayoutDialogAction: Show layout dialog action.
ShowMainToolBarAction - Class in org.simbrain.network.gui.actions.toolbar: Clamps neurons action.
ShowMainToolBarAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.toolbar.ShowMainToolBarAction: Create a new main tool bar action with the specified network panel.
ShowNetworkHierarchyPanel - Class in org.simbrain.network.gui.actions.network: Show Network Hierarchy Panel
ShowNetworkHierarchyPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.network.ShowNetworkHierarchyPanel: Shows the property inspector.
ShowNetworkPreferencesAction - Class in org.simbrain.network.gui.actions.network: Show network preferences action.
ShowNetworkPreferencesAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.network.ShowNetworkPreferencesAction: Create a new show network preferences action with the specified network panel.
ShowNetworkUpdaterDialog - Class in org.simbrain.network.gui.actions.network: Show network updater panel.
ShowNetworkUpdaterDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.network.ShowNetworkUpdaterDialog: Construct the action.
showOpenDialog() - Method in class org.simbrain.util.SFileChooser: Shows dialog for opening files.
showOpenFileDialog() - Method in class org.simbrain.workspace.gui.GuiComponent: Calls up a dialog for opening a workspace component.
ShowPrioritiesAction - Class in org.simbrain.network.gui.actions.neuron: Show Priorities action.
ShowPrioritiesAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.neuron.ShowPrioritiesAction: Shows and updates the GUI with the specified network panel.
showPropertiesDialog() - Method in class org.simbrain.plot.rasterchart.RasterPlotPanel: Show properties dialog.
showPropertiesDialog() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Show properties dialog.
ShowPropertyDialogAction - Class in org.simbrain.workspace.actions: Opens a workspace property dialog.
ShowPropertyDialogAction(Workspace) - Constructor for class org.simbrain.workspace.actions.ShowPropertyDialogAction: Create a workspace component list of the specified workspace.
ShowRunToolBarAction - Class in org.simbrain.network.gui.actions.toolbar: Show / hide run toolbar
ShowRunToolBarAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.toolbar.ShowRunToolBarAction: Create a new clamp neurons action with the specified network panel.
showSaveDialog(File) - Method in class org.simbrain.util.SFileChooser: Shows dialog for saving files.
showSaveDialog(String) - Method in class org.simbrain.util.SFileChooser: Shows the save dialog for the given string name.
showSaveDialog() - Method in class org.simbrain.util.SFileChooser: Shows the save dialog.
showSaveFileDialog() - Method in class org.simbrain.network.desktop.NetworkDesktopComponent
showSaveFileDialog() - Method in class org.simbrain.workspace.gui.GuiComponent: Show the dialog for saving a workspace component.
showSelectedNeuronProperties() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Creates and displays the neuron properties dialog.
showSelectedNeuronProperties() - Method in class org.simbrain.network.gui.NetworkPanel: Creates and displays the neuron properties dialog.
showSelectedSynapseProperties() - Method in class org.simbrain.network.desktop.NetworkPanelDesktop: Creates and displays the synapse properties dialog.
showSelectedSynapseProperties() - Method in class org.simbrain.network.gui.NetworkPanel: Creates and displays the synapse properties dialog.
showSelectionHandle() - Method in class org.simbrain.network.gui.nodes.InteractionBox
showSelectionHandle() - Method in class org.simbrain.network.gui.nodes.NeuronNode
showSelectionHandle() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Return true if this screen element should show a selection handle.
showSelectionHandle() - Method in class org.simbrain.network.gui.nodes.SynapseNode
showSelectionHandle() - Method in class org.simbrain.network.gui.nodes.TextNode
showSelectionHandle() - Method in class org.simbrain.network.gui.nodes.ViewGroupNode
showTextPropertyDialog() - Method in class org.simbrain.network.gui.NetworkPanel: Creates and displays the text properties dialog.
ShowTrainerAction - Class in org.simbrain.network.gui.actions: Show Trainer object for training selected source and target neurons.
ShowTrainerAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.ShowTrainerAction: Construct action.
ShowWeightMatrixAction - Class in org.simbrain.network.gui.actions.synapse: Show weight matrix connecting selected source and target neurons.
ShowWeightMatrixAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.synapse.ShowWeightMatrixAction: Construct action.
showWeightMatrixAction - Variable in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Action for showing the weight matrix for this neuron group.
ShowWeightsAction - Class in org.simbrain.network.gui.actions.synapse: Show GUI weights action.
ShowWeightsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.synapse.ShowWeightsAction: Shows and updates the GUI with the specified network panel.
ShowWorkspaceUpdaterDialog - Class in org.simbrain.workspace.actions: Show workspace updater panel.
ShowWorkspaceUpdaterDialog(SimbrainDesktop) - Constructor for class org.simbrain.workspace.actions.ShowWorkspaceUpdaterDialog: Construct the show dialog action.
ShowWorldPrefsAction - Class in org.simbrain.world.odorworld.actions: Action for showing world preferences.
ShowWorldPrefsAction(OdorWorldPanel) - Constructor for class org.simbrain.world.odorworld.actions.ShowWorldPrefsAction: Construct a show prefs action
shuffle() - Method in class org.simbrain.util.table.SimbrainDataTable: Shuffle the rows of the dataset.
shutdown() - Method in class org.simbrain.network.update_actions.concurrency_tools.Consumer
sideBySideView() - Method in class org.simbrain.world.visionworld.VisionWorld: Switch to the side by side view.
SideBySideViewAction - Class in org.simbrain.world.visionworld.action: Side-by-side view action.
SideBySideViewAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.SideBySideViewAction: Create a new side-by-side view action.
Sight - Class in org.simbrain.world.threedee.sensors
Sight() - Constructor for class org.simbrain.world.threedee.sensors.Sight
Sight.SightSensor - Class in org.simbrain.world.threedee.sensors
SightSensor(Sensor) - Constructor for class org.simbrain.world.threedee.sensors.Sight.SightSensor
SigmoidalRule - Class in org.simbrain.network.neuron_update_rules: SigmoidalRule provides various implementations of a standard sigmoidal neuron.
SigmoidalRule() - Constructor for class org.simbrain.network.neuron_update_rules.SigmoidalRule: Default sigmoidal.
SigmoidalRule(SquashingFunction) - Constructor for class org.simbrain.network.neuron_update_rules.SigmoidalRule: Construct a sigmoid update with a specified implementation.
SigmoidalRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: SigmoidalRulePanel.
SimbrainButton - Class in org.simbrain.workspace.gui: A JButton which is automatically disabled when the workspace is running.
SimbrainButton(String, Workspace) - Constructor for class org.simbrain.workspace.gui.SimbrainButton: Construct a button with a reference the workspace which, when running, will disable the button.
SimbrainConstants - Class in org.simbrain.util: A class solely for storing constants used throughout simbrain.
SimbrainConstants() - Constructor for class org.simbrain.util.SimbrainConstants
SimbrainConstants.Polarity - Enum in org.simbrain.util: Used to indicate if an object (in particular neurons) have a polarity, i.e.
SimbrainDataTable<T> - Class in org.simbrain.util.table: Superclass for tables that can be viewed by a SimbrainJTable, and saved in a reasonable, readable way with XStream.
SimbrainDataTable() - Constructor for class org.simbrain.util.table.SimbrainDataTable
SimbrainDesktop - Class in org.simbrain.workspace.gui: Creates a Swing-based environment for working with a workspace.
SimbrainDesktop(Workspace) - Constructor for class org.simbrain.workspace.gui.SimbrainDesktop: Default constructor.
SimbrainJTable - Class in org.simbrain.util.table: SimbrainJTable is a version of a JXTable (itself an improved JTable from SwingLabs) which provides GUI access to a SimbrainDataTable.
SimbrainJTable(SimbrainDataTable) - Constructor for class org.simbrain.util.table.SimbrainJTable: Construct the jtable.
SimbrainJTable.CellIndex - Class in org.simbrain.util.table: Holds reference to row / column index.
SimbrainJTableScrollPanel - Class in org.simbrain.util.table: A scroll panel for a jtable, which sizes itself to fit whatever data it shows.
SimbrainJTableScrollPanel() - Constructor for class org.simbrain.util.table.SimbrainJTableScrollPanel: Default constructor.
SimbrainJTableScrollPanel(SimbrainJTable) - Constructor for class org.simbrain.util.table.SimbrainJTableScrollPanel
SimbrainMath - Class in org.simbrain.util.math: SimbrainMath is the math functions used in simbrain.
SimbrainMath() - Constructor for class org.simbrain.util.math.SimbrainMath
SimbrainPreferences - Class in org.simbrain.util: A wrapper for Java's preference framework, which encapsulates the main needs of preferences in Simbrain: Getting a preference value for a property Setting a preference value for a property Restoring a property's value to its default setting Setting default values for a property To do the last item 4 use the static initializer here.
SimbrainPreferences() - Constructor for class org.simbrain.util.SimbrainPreferences
SimbrainPreferences.PropertyNotFoundException - Exception in org.simbrain.util: Thrown when a property cannot be found.
SimbrainScriptEditor - Class in org.simbrain.workspace.gui: Extension of script editor configured to be able to run and edit Simbrain scripts.
SimbrainScriptEditor(SimbrainDesktop, String) - Constructor for class org.simbrain.workspace.gui.SimbrainScriptEditor: Initialize the script editor panel with some initial text.
SimnetUtils - Class in org.simbrain.network.util: SimnetUtils provides utility classes relating to Simbrain networks.
SimnetUtils() - Constructor for class org.simbrain.network.util.SimnetUtils
SimpleFrame - Class in org.simbrain.util: Displays a simple JFrame, centers it, packs it, and makes it visible.
SimpleFrame() - Constructor for class org.simbrain.util.SimpleFrame
SimpleId - Class in org.simbrain.util: SimpleId provides an id based on a base name and an integer index.
SimpleId(String, int) - Constructor for class org.simbrain.util.SimpleId: Construct simpleId.
SimpleRecurrentNetwork - Class in org.simbrain.network.subnetworks: Implements a simple recurrent network (See, e.g, Elman 1991).
SimpleRecurrentNetwork(Network, int, int, int) - Constructor for class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Build an SRN with default activation rules and initial position.
SimpleRecurrentNetwork(Network, int, int, int, NeuronUpdateRule, NeuronUpdateRule, Point2D) - Constructor for class org.simbrain.network.subnetworks.SimpleRecurrentNetwork: Constructor specifying root network, and number of nodes in each layer.
SimpleTrainerControlPanel - Class in org.simbrain.network.gui.trainer: Simple trainer control panel for cases where the trainer just involves an apply and randomize button.
SimpleTrainerControlPanel(NetworkPanel, Trainer) - Constructor for class org.simbrain.network.gui.trainer.SimpleTrainerControlPanel: Construct the panel with a trainer specified.
singleClickEvent() - Method in class org.simbrain.network.gui.nodes.InteractionBox
singleClickEvent() - Method in class org.simbrain.network.gui.nodes.ScreenElement: Called when element is single clicked on.
SingleStepPanel - Class in org.simbrain.network.gui.trainer: Component for training a network using current data only.
SingleStepPanel(Trainer) - Constructor for class org.simbrain.network.gui.trainer.SingleStepPanel: Construct panel.
SinusoidalGeneratorPanel - Class in org.simbrain.network.gui.dialogs.neuron.generator_panels: SinusoidalNeuronPanel.
SinusoidalGeneratorPanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.generator_panels.SinusoidalGeneratorPanel: Creates an instance of this panel.
SinusoidalRule - Class in org.simbrain.network.neuron_update_rules.activity_generators: SinusoidalNeuron produces a sine wave; inputs are ignored.
SinusoidalRule() - Constructor for class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule
size() - Method in class org.simbrain.network.groups.Group
size() - Method in class org.simbrain.network.groups.NeuronGroup
size() - Method in class org.simbrain.network.groups.Subnetwork
size() - Method in class org.simbrain.network.groups.SynapseGroup
size() - Method in class org.simbrain.network.gui.NetworkSelectionModel: Return the size of the selection.
size() - Method in class org.simbrain.util.projection.NTree: Returns the number of points in the tree.
size() - Method in class org.simbrain.world.game.GameModel: Returns the size of the board.
size() - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Return the number of selected sensors for this sensor selection model.
slope - Variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: Slope.
smellPanel - Variable in class org.simbrain.world.odorworld.dialogs.EntityDialog: Editor panel for smell source.
SmellSensor - Class in org.simbrain.world.odorworld.sensors: A sensor which is updated based on the presence of SmellSources near it.
SmellSensor(OdorWorldEntity, String, double, double) - Constructor for class org.simbrain.world.odorworld.sensors.SmellSensor: Construct a smell sensor.
SmellSensorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel to add a smell sensor to an entity.
SmellSensorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.SmellSensorPanel: Constructor for the case where a sensor is being created.
SmellSensorPanel(OdorWorldEntity, SmellSensor) - Constructor for class org.simbrain.world.odorworld.dialogs.SmellSensorPanel: Constructor for the case where a sensor is being edited.
smellSensorScalars - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
smellSensorVectors - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
SmellSource - Class in org.simbrain.util.environment: Stimulus represent a distal stimulus in the form of a vector.
SmellSource(double[], SmellSource.DecayFunction, double, boolean, double) - Constructor for class org.simbrain.util.environment.SmellSource: Construct smell source from specified parameters.
SmellSource(double[], SmellSource.DecayFunction, double, double[]) - Constructor for class org.simbrain.util.environment.SmellSource: Construct smell source from specified parameters.
SmellSource(double[], SmellSource.DecayFunction, double[]) - Constructor for class org.simbrain.util.environment.SmellSource: Construct smell source from specified parameters.
SmellSource(double[]) - Constructor for class org.simbrain.util.environment.SmellSource: Construct a smell source from a specified stimulus vector, using defaults otherwise.
SmellSource(int) - Constructor for class org.simbrain.util.environment.SmellSource: Construct a smell source with a specified number of dimensions, randomly initialized.
SmellSource() - Constructor for class org.simbrain.util.environment.SmellSource: Default constructor.
SmellSource.DecayFunction - Enum in org.simbrain.util.environment: Decay Functions.
SmellSourcePanel - Class in org.simbrain.util.environment: PanelStimulus is a panel used to adjust the "smell signatures" (arrays of doubles representing the effect an object has on the input nodes of the network of non-creature entities in the world.
SmellSourcePanel(SmellSource) - Constructor for class org.simbrain.util.environment.SmellSourcePanel: Create and populate the stimulus panel.
softMax(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: The soft-max of the vector.
SOMGroup - Class in org.simbrain.network.subnetworks: SOM implements a Self-Organizing Map network.
SOMGroup(Network, int) - Constructor for class org.simbrain.network.subnetworks.SOMGroup: Constructs an SOM network with specified number of neurons.
SOMGroup(Network, SOMGroup) - Constructor for class org.simbrain.network.subnetworks.SOMGroup: Copy constructor
SOMGroupCreationDialog - Class in org.simbrain.network.gui.dialogs.network: SOMDialog is used as an assistant to create SOM networks.
SOMGroupCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.SOMGroupCreationDialog: This method is the default constructor.
SOMGroupNode - Class in org.simbrain.network.gui.nodes.neuronGroupNodes: PNode representation of Self-Organizing Map.
SOMGroupNode(NetworkPanel, SOMGroup) - Constructor for class org.simbrain.network.gui.nodes.neuronGroupNodes.SOMGroupNode: Create a SOM Network PNode.
SOMNetwork - Class in org.simbrain.network.subnetworks: SOMNetwork is a small network encompassing an SOM group.
SOMNetwork(Network, int, int, Point2D) - Constructor for class org.simbrain.network.subnetworks.SOMNetwork: Construct an SOM Network.
SOMNetworkCreationDialog - Class in org.simbrain.network.gui.dialogs.network: SOMDialog is used as an assistant to create SOM networks.
SOMNetworkCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.SOMNetworkCreationDialog: This method is the default constructor.
SOMNetworkNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of SOM Network.
SOMNetworkNode(NetworkPanel, SOMNetwork) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.SOMNetworkNode: Create a SOM Network PNode.
SOMPropertiesPanel - Class in org.simbrain.network.gui.dialogs.network: SOMPropertiesDialog is a dialog box for setting the properties of a Self organizing map.
SOMPropertiesPanel(NetworkPanel, SOMPropertiesPanel.SOMPropsPanelType) - Constructor for class org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel: Constructor for the case where an som group is being created.
SOMPropertiesPanel(NetworkPanel, SOMGroup) - Constructor for class org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel: Constructor for case where an existing som group is being edited.
SOMPropertiesPanel.SOMPropsPanelType - Enum in org.simbrain.network.gui.dialogs.network: Whether the panel is for creating an SOM group, network, or editing a group.
SOMTrainer - Class in org.simbrain.network.trainers: A trainer for SOM Networks.
SOMTrainer(SOMNetwork) - Constructor for class org.simbrain.network.trainers.SOMTrainer: Construct the UnsupervisedNeuronGroupTrainer trainer.
SOMTrainerControlsPanel - Class in org.simbrain.network.gui.trainer.subnetworkTrainingPanels: Training panel for SOM Network.
SOMTrainerControlsPanel(NetworkPanel, SOMTrainer, SOMNetwork) - Constructor for class org.simbrain.network.gui.trainer.subnetworkTrainingPanels.SOMTrainerControlsPanel: Construct the SOM Training Controls Panel.
SOMTrainingDialog - Class in org.simbrain.network.gui.dialogs.network: Dialog for training a SOM network.
SOMTrainingDialog(NetworkPanel, SOMNetwork) - Constructor for class org.simbrain.network.gui.dialogs.network.SOMTrainingDialog: Construct the dialog.
sourceAndTargetNeuronGroupsSelected(NetworkPanel) - Static method in class org.simbrain.network.gui.actions.ConditionallyEnabledAction: True if at least one source and one target neuron group are selected.
sourceAndTargetNeuronSelected(NetworkPanel) - Static method in class org.simbrain.network.gui.actions.ConditionallyEnabledAction: True if at least one source and one target neuron are selected.
SourceHandle - Class in org.simbrain.network.gui.nodes: Selection handle.
spaceHorizontal() - Method in class org.simbrain.network.gui.NetworkPanel: TODO: Push this and related methods to model? Spaces neurons horizontally.
SpaceHorizontalAction - Class in org.simbrain.network.gui.actions.edit: Space horizontal.
SpaceHorizontalAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.SpaceHorizontalAction: Create a new space horizontal action with the specified network panel.
spaceVertical() - Method in class org.simbrain.network.gui.NetworkPanel: Spaces neurons vertically.
SpaceVerticalAction - Class in org.simbrain.network.gui.actions.edit: Space vertical.
SpaceVerticalAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.SpaceVerticalAction: Create a new space vertical action with the specified network panel.
Sparse - Class in org.simbrain.network.connections: A superclass for all connectors whose primary parameter is related to base connection density, taking no other major factors into account insofar as selecting which neurons should be connected goes.
Sparse() - Constructor for class org.simbrain.network.connections.Sparse: Default constructor.
Sparse(double, boolean, boolean) - Constructor for class org.simbrain.network.connections.Sparse: Construct a sparse object from main arguments.
SPARSE - Static variable in class org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditors: Sparse sensor matrix editor.
SparseConnectionPanel - Class in org.simbrain.network.gui.dialogs.connect.connector_panels: The SparsityAdjustmentPanel is a sub-panel for other connection panels which adjusts the sparsity of the connection.
SparseSensorMatrix - Class in org.simbrain.world.visionworld.sensormatrix: Sparse sensor matrix.
SparseSensorMatrix(int, int, int, int, Filter) - Constructor for class org.simbrain.world.visionworld.sensormatrix.SparseSensorMatrix: Create a new sparse sensor matrix with the specified filter.
SparseSensorMatrixEditor - Class in org.simbrain.world.visionworld.sensormatrix.editor: Sparse sensor matrix editor.
SparseSensorMatrixEditor() - Constructor for class org.simbrain.world.visionworld.sensormatrix.editor.SparseSensorMatrixEditor: Create a new sparse sensor matrix editor.
speakToEntity(String) - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Add a phrase to the list of things currently being said.
SpecificNeuronRulePanel - Class in org.simbrain.network.gui.dialogs.neuron: A panel for setting the neuron type and changing the parameters of the selected update rule.
SpecificNeuronRulePanel(List<Neuron>, Window) - Constructor for class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: Create a the panel with the default starting visibility (visible) for the neuron panel.
SpecificNeuronRulePanel(List<Neuron>, Window, boolean) - Constructor for class org.simbrain.network.gui.dialogs.neuron.SpecificNeuronRulePanel: Create the panel with specified starting visibility.
SpecificSynapseRulePanel - Class in org.simbrain.network.gui.dialogs.synapse: A panel for setting the synapse type and changing the parameters of the selected update rule.
SpecificSynapseRulePanel(Collection<Synapse>, Window) - Constructor for class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel: Constructs a synapse update settings panel for a given synapse list and within a specified parent window.
SpecificSynapseRulePanel(Collection<Synapse>, Window, boolean) - Constructor for class org.simbrain.network.gui.dialogs.synapse.SpecificSynapseRulePanel: Constructs a synapse update settings panel for a given synapse list and within a specified parent window, and with the starting display state of the neuron update panel specified.
Speech - Class in org.simbrain.world.odorworld.effectors: Model simple speech behaviors.
Speech(OdorWorldEntity, String, double) - Constructor for class org.simbrain.world.odorworld.effectors.Speech: Construct the speech effector.
SpeechEffectorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel to add a speech effector to an entity.
SpeechEffectorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.SpeechEffectorPanel: Constructor for the case where an effector is being created.
SpeechEffectorPanel(OdorWorldEntity, Speech) - Constructor for class org.simbrain.world.odorworld.dialogs.SpeechEffectorPanel: Constructor for the case where an effector is being edited.
speechEffectorType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
spikeActivation(double) - Method in class org.simbrain.util.projection.DataPointColored: Max out the activation of this point (for decay trail coloring).
SpikeResponder - Class in org.simbrain.network.synapse_update_rules.spikeresponders: SpikeResponder.
SpikeResponder() - Constructor for class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder
SpikeResponderSettingsPanel - Class in org.simbrain.network.gui.dialogs.synapse: Panel to display spike responder settings.
SpikeResponderSettingsPanel(Collection<Synapse>, Window) - Constructor for class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel: A constructor that sets up the panel in its default display state.
SpikeResponderSettingsPanel(Collection<Synapse>, boolean, Window) - Constructor for class org.simbrain.network.gui.dialogs.synapse.SpikeResponderSettingsPanel: A constructor that sets up the panel with the spike response panel either hidden or displayed.
SpikingNeuronUpdateRule - Class in org.simbrain.network.core: SpikingNeuron is the superclass for spiking neuron types (e.g.
SpikingNeuronUpdateRule() - Constructor for class org.simbrain.network.core.SpikingNeuronUpdateRule
SpikingThresholdRule - Class in org.simbrain.network.neuron_update_rules: A simple spiking neuron that fires when weighted inputs exceed a threshold.
SpikingThresholdRule() - Constructor for class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
SpikingThresholdRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: ProbabilisticSpikingNeuronPanel.
SpikingThresholdRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.SpikingThresholdRulePanel: Creates a new instance of the probabilistic spiking neuron panel.
splash(Image) - Static method in class org.simbrain.workspace.gui.SplashWindow: Open's a splash window using the specified image.
Splasher - Class in org.simbrain.workspace.gui: Splasher displays the simbrain splash screen an initializes the workspace.
Splasher() - Constructor for class org.simbrain.workspace.gui.Splasher
SplashWindow - Class in org.simbrain.workspace.gui: SplashWindow
SquashingFunction - Enum in org.simbrain.util.math: An enumerated type containing methods for calculating values of different squashing functions, their inverses, and their derivatives.
SRNCreationDialog - Class in org.simbrain.network.gui.dialogs.network: Creates a GUI dialog to set the parameters for and then build a simple recurrent network.
SRNCreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.SRNCreationDialog: Constructs a labeled item panel dialog for the creation of a simple recurrent network.
SRNEditorDialog - Class in org.simbrain.network.gui.dialogs.network: Creates a GUI dialog to set the parameters for and then build a simple recurrent network.
SRNEditorDialog(NetworkPanel, SimpleRecurrentNetwork) - Constructor for class org.simbrain.network.gui.dialogs.network.SRNEditorDialog: Constructs a labeled item panel dialog for the creation of a simple recurrent network.
SRNNetworkNode - Class in org.simbrain.network.gui.nodes.subnetworkNodes: PNode representation of a group of a srn network.
SRNNetworkNode(NetworkPanel, SimpleRecurrentNetwork) - Constructor for class org.simbrain.network.gui.nodes.subnetworkNodes.SRNNetworkNode: Create a layered network.
SRNTrainer - Class in org.simbrain.network.trainers: Trainer for SRN Networks.
SRNTrainer(SimpleRecurrentNetwork) - Constructor for class org.simbrain.network.trainers.SRNTrainer: Construct the SRN trainer.
stackedView() - Method in class org.simbrain.world.visionworld.VisionWorld: Switch to the stacked view.
StackedViewAction - Class in org.simbrain.world.visionworld.action: Stacked view action.
StackedViewAction(VisionWorld) - Constructor for class org.simbrain.world.visionworld.action.StackedViewAction: Create a new stacked view action.
StandardDialog - Class in org.simbrain.util: StandardDialog implements a standard data entry dialog with "Ok" and "Cancel" buttons.
StandardDialog() - Constructor for class org.simbrain.util.StandardDialog: This method is the default constructor.
StandardDialog(Frame, String) - Constructor for class org.simbrain.util.StandardDialog: This method creates a StandardDialog with the given parent frame and title.
start() - Method in class org.simbrain.world.odorworld.entities.Animation: Starts this animation over from the beginning.
startDrag(PInputEvent) - Method in class org.simbrain.network.gui.DragEventHandler
startDrag(PInputEvent) - Method in class org.simbrain.network.gui.WandEventHandler
startDrag(PInputEvent) - Method in class org.simbrain.world.visionworld.SelectionEventHandler
startingComponentUpdate(WorkspaceComponent, int, int) - Method in interface org.simbrain.workspace.updater.ComponentUpdateListener: Called when a component update begins.
startRecording(File) - Method in class org.simbrain.network.groups.NeuronGroup: Creates a file which activations will be written to and activates the necessary output streams.
statCalculator - Variable in class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel: Calculates some basic statistics about the private final StatisticsBlock
state - Variable in class org.simbrain.console.CommandLineReader
StaticSynapsePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: ClampedSynapsePanel.
StaticSynapsePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel: This method is the default constructor.
StaticSynapseRule - Class in org.simbrain.network.synapse_update_rules: ClampedSynapse.
StaticSynapseRule() - Constructor for class org.simbrain.network.synapse_update_rules.StaticSynapseRule
StationaryBehavior - Class in org.simbrain.world.odorworld.behaviors: Null behavior; do nothing.
StationaryBehavior() - Constructor for class org.simbrain.world.odorworld.behaviors.StationaryBehavior
StatisticsBlock() - Constructor for class org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.StatisticsBlock
Stats() - Constructor for class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
stdDev - Variable in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
STDPRule - Class in org.simbrain.network.synapse_update_rules: STDPSynapse models spike time dependent plasticity.
STDPRule() - Constructor for class org.simbrain.network.synapse_update_rules.STDPRule
STDPRulePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: ShortTermPlasticitySynapsePanel allows users to edit STDP synapses.
STDPRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel: Creates a short term plasticity synapse panel.
Step - Class in org.simbrain.network.synapse_update_rules.spikeresponders: Step.
Step() - Constructor for class org.simbrain.network.synapse_update_rules.spikeresponders.Step
StepSpikerPanel - Class in org.simbrain.network.gui.dialogs.synapse.spike_responders: StepSpikerPanel.
StepSpikerPanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel: This method is the default constructor.
StochasticGeneratorPanel - Class in org.simbrain.network.gui.dialogs.neuron.generator_panels: StochasticNeuronPanel.
StochasticGeneratorPanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.generator_panels.StochasticGeneratorPanel: Creates an instance of this panel.
StochasticRule - Class in org.simbrain.network.neuron_update_rules.activity_generators: StochasticNeuron is a simple type of random neuron which takes the value of the upper bound if a random variable is above a specified firing probability, and the lower bound otherwise.
StochasticRule() - Constructor for class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule
stop() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Stops the update thread.
stop() - Method in class org.simbrain.workspace.Workspace: Stops iteration of all couplings on all components.
stopEditing() - Method in class org.simbrain.network.gui.TextEventHandler: Removes empty text objects.
StopLight - Class in org.simbrain.util.widgets: A custom status light component for use in GUI dialogs.
StopLight() - Constructor for class org.simbrain.util.widgets.StopLight: Default Constructor, by default current status is redlight: image is RedX and greenlight is false.
StopLight(boolean) - Constructor for class org.simbrain.util.widgets.StopLight: Constructor which fully paints and prepares stoplight as a JPanel for integration into another panel/dialog/etc.
StopNetworkAction - Class in org.simbrain.network.gui.actions.network: Stop network action.
StopNetworkAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.network.StopNetworkAction: Create a new stop network action with the specified network panel.
stopped() - Method in class org.simbrain.workspace.WorkspaceComponent: Called by Workspace to notify that updates have stopped.
stopRecording() - Method in class org.simbrain.network.groups.NeuronGroup: Halts recording of activations.
stopTrainer() - Method in class org.simbrain.network.gui.dialogs.network.BackpropEditorDialog
stopTrainer() - Method in class org.simbrain.network.gui.dialogs.network.LMSEditorDialog
stopTrainer() - Method in class org.simbrain.network.gui.dialogs.network.SRNEditorDialog
stopTrainer() - Method in class org.simbrain.network.gui.dialogs.network.SupervisedTrainingDialog: Method to stop the trainer from running.
StraightEffectorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel to add a straight movement effector to an entity or to modify and existing one.
StraightEffectorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.StraightEffectorPanel: Constructor for the case where an effector is being created.
StraightEffectorPanel(OdorWorldEntity, StraightMovement) - Constructor for class org.simbrain.world.odorworld.dialogs.StraightEffectorPanel: Constructor for the case where an effector is being edited.
StraightMovement - Class in org.simbrain.world.odorworld.effectors: Effector for straight ahead movement.
StraightMovement(RotatingEntity, String) - Constructor for class org.simbrain.world.odorworld.effectors.StraightMovement: Construct the straight movement effector.
straightMovementType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
stringArrayToDoubleArray(String[]) - Static method in class org.simbrain.util.Utils: Converts an array of strings containing doubles into an array of doubles.
StringDataPoint(double[], String) - Constructor for class org.simbrain.world.textworld.DisplayWorld.StringDataPoint: Construct the string data point.
Subnetwork - Class in org.simbrain.network.groups: A collection of neuron groups and synapse groups which functions as a subnetwork within the main root network, with its own update rules.
Subnetwork(Network) - Constructor for class org.simbrain.network.groups.Subnetwork: Create subnetwork group.
SubnetworkNode - Class in org.simbrain.network.gui.nodes: PNode representation of a subnetwork.
SubnetworkNode(NetworkPanel, Subnetwork) - Constructor for class org.simbrain.network.gui.nodes.SubnetworkNode: Create a subnetwork node.
SubnetworkPanel - Class in org.simbrain.network.gui.dialogs.network: Default subnetwork panel that displays basic info.
SubnetworkPanel(NetworkPanel, Subnetwork, StandardDialog) - Constructor for class org.simbrain.network.gui.dialogs.network.SubnetworkPanel: Constructor for case where an existing subnetwork is being edited.
SubtractiveNormalizationRule - Class in org.simbrain.network.synapse_update_rules: SubtractiveNormalizationSynapse.
SubtractiveNormalizationRule() - Constructor for class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule
SubtractiveNormalizationRulePanel - Class in org.simbrain.network.gui.dialogs.synapse.plasticity_panels: SubtractiveNormalizationSynapsePanel.
SubtractiveNormalizationRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel: This method is the default constructor.
suggestedMinPoints() - Method in class org.simbrain.util.projection.ProjectionMethod: Some projection methods require a certain number of datapoints to be added before they work well.
suggestedMinPoints() - Method in class org.simbrain.util.projection.ProjectNNSubspace
suggestedMinPoints() - Method in class org.simbrain.util.projection.ProjectTriangulate
sum(double[]) - Static method in class org.simbrain.util.math.SimbrainMath: Sums all the values in an array.
SummaryPanel - Class in org.simbrain.network.gui.dialogs.group: A panel which provides a high level summary of certain groups in Simbrain.
SummaryPanel(NeuronGroup, boolean) - Constructor for class org.simbrain.network.gui.dialogs.group.SummaryPanel: Constructs the summary panel based on a neuron group.
SummaryPanel(SynapseGroup) - Constructor for class org.simbrain.network.gui.dialogs.group.SummaryPanel: Constructs the summary panel based on a synapse group.
SupervisedTrainingDialog - Class in org.simbrain.network.gui.dialogs.network: SupervisedTrainingDialog is the superclass of edit dialogs associated with most supervised learning networks.
SupervisedTrainingDialog(NetworkPanel, Trainable) - Constructor for class org.simbrain.network.gui.dialogs.network.SupervisedTrainingDialog: Default constructor.
swapElements(int, int) - Method in class org.simbrain.network.core.NetworkUpdateManager: Swap elements at the specified location.
swapElements(int, int) - Method in class org.simbrain.workspace.updater.UpdateActionManager: Swap elements at the specified location.
SwitchableActionListener - Class in org.simbrain.util: A custom action listener which can be turned off and on.
SwitchableActionListener() - Constructor for class org.simbrain.util.SwitchableActionListener
SwitchableChangeListener - Class in org.simbrain.util
SwitchableChangeListener() - Constructor for class org.simbrain.util.SwitchableChangeListener
SwitchablePropertyChangeListener - Class in org.simbrain.util
SwitchablePropertyChangeListener() - Constructor for class org.simbrain.util.SwitchablePropertyChangeListener
Synapse - Class in org.simbrain.network.core: Synapse objects represent "connections" between neurons, which learn (grow or weaken) based on various factors, including the activation level of connected neurons.
Synapse(Neuron, Neuron) - Constructor for class org.simbrain.network.core.Synapse: Construct a synapse using a source and target neuron, defaulting to ClampedSynapse and assuming the parent of the source neuron is the parent of this synapse.
Synapse(Neuron, Neuron, double) - Constructor for class org.simbrain.network.core.Synapse: Construct a synapse with a specified initial strength.
Synapse(Network, Neuron, Neuron, SynapseUpdateRule) - Constructor for class org.simbrain.network.core.Synapse: Construct a synapse using a source and target neuron, and a specified learning rule and parent network
Synapse(Neuron, Neuron, SynapseUpdateRule) - Constructor for class org.simbrain.network.core.Synapse: Construct a synapse using a source and target neuron, and a specified learning rule.
Synapse(Network, Neuron, Neuron, SynapseUpdateRule, Synapse) - Constructor for class org.simbrain.network.core.Synapse: Construct a synapse using a source and target neuron, and a specified learning rule.
Synapse(Neuron, Neuron, SynapseUpdateRule, Network) - Constructor for class org.simbrain.network.core.Synapse: Construct a synapse using a source and target neuron, and a specified learning rule.
Synapse(Network, Synapse) - Constructor for class org.simbrain.network.core.Synapse: Copy a synapse with a specified new parent.
Synapse(Synapse) - Constructor for class org.simbrain.network.core.Synapse: Copy constructor.
SYNAPSE_VISIBILITY_CHANGED - Static variable in class org.simbrain.network.gui.nodes.SynapseGroupNode: Constant for use in group changed events, indicating that the visibility of synpases in a synapse group has changed.
SynapseAdapter - Class in org.simbrain.network.listeners: Adapter class for SynapseListener.
SynapseAdapter() - Constructor for class org.simbrain.network.listeners.SynapseAdapter
synapseAdded(NetworkEvent<Synapse>) - Method in class org.simbrain.network.listeners.SynapseAdapter
synapseAdded(NetworkEvent<Synapse>) - Method in interface org.simbrain.network.listeners.SynapseListener: Notify this listener of a synapse added event.
synapseAdded(NetworkEvent<Synapse>) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Notify this listener of a synapse added event.
SynapseAdjustmentPanel - Class in org.simbrain.network.gui.dialogs.synapse: Panel for editing collections of synapses.
SynapseAdjustmentPanel.PrunerPanel - Class in org.simbrain.network.gui.dialogs.synapse: Panel for pruning synapses.
SynapseAdjustmentPanel.ScalerPanel - Class in org.simbrain.network.gui.dialogs.synapse: Panel for scaling synapses.
SynapseAdjustmentPanel.StatisticsBlock - Class in org.simbrain.network.gui.dialogs.synapse
SynapseAdjustmentPanel.SynapseView - Enum in org.simbrain.network.gui.dialogs.synapse
synapseChanged(NetworkEvent<Synapse>) - Method in class org.simbrain.network.listeners.SynapseAdapter
synapseChanged(NetworkEvent<Synapse>) - Method in interface org.simbrain.network.listeners.SynapseListener: Notify this listener that synapse's state changed.
synapseChanged(NetworkEvent<Synapse>) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Notify this listener that synapse's state changed.
synapseClampButton - Variable in class org.simbrain.network.gui.NetworkPanel: Toggle button for weight clamping.
synapseClampMenuItem - Variable in class org.simbrain.network.gui.NetworkPanel: Menu item for weight clamping.
SynapseDialog - Class in org.simbrain.network.gui.dialogs.synapse: The SynapseDialog is initialized with a list of synapses.
SynapseGroup - Class in org.simbrain.network.groups: A group of synapses.
SynapseGroup(NeuronGroup, NeuronGroup) - Constructor for class org.simbrain.network.groups.SynapseGroup: Creates a blank synapse group between a source and target neuron group using the default connection manager.
SynapseGroup(NeuronGroup, NeuronGroup, ConnectNeurons) - Constructor for class org.simbrain.network.groups.SynapseGroup: Creates a blank synapse group between a source and target neuron group.
synapseGroup - Variable in class org.simbrain.network.gui.nodes.SynapseGroupNode: Reference to represented group node.
SynapseGroupAdjustmentPanel - Class in org.simbrain.network.gui.dialogs.synapse: A panel for adjusting the polarity and weights of a synapse group as well as its weight randomizers, and displaying the results in a histogram.
SynapseGroupAdjustmentPanel.Stats - Class in org.simbrain.network.gui.dialogs.synapse: A panel for displaying basic statistics about the synapse group
SynapseGroupArrow - Interface in org.simbrain.network.gui.nodes: An interface that any synapse group node which uses a curved arrow (not an arc) should implement.
SynapseGroupDialog - Class in org.simbrain.network.gui.dialogs.group: Dialog for editing synapse groups.
SynapseGroupInteractionBox - Class in org.simbrain.network.gui.nodes: Interaction box for synapse groups.
SynapseGroupInteractionBox(NetworkPanel, SynapseGroup) - Constructor for class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Construct the custom interaction box.
SynapseGroupNode - Class in org.simbrain.network.gui.nodes: PNode representation of a group of synapses.
SynapseGroupNode(NetworkPanel, SynapseGroup) - Constructor for class org.simbrain.network.gui.nodes.SynapseGroupNode: Create a Synapse Group PNode.
SynapseGroupNodeBidirectional - Class in org.simbrain.network.gui.nodes: A bidirectional simple synapse group node.
SynapseGroupNodeRecurrent - Class in org.simbrain.network.gui.nodes: Creates a simple synapse group node that represents a recurrent synapse group.
SynapseGroupNodeSimple - Class in org.simbrain.network.gui.nodes: PNode representation of a group of synapses, where the synapses themselves are not visible.
SynapseGroupNodeSimple(NetworkPanel, SynapseGroup) - Constructor for class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple: Create a Synapse Group PNode.
SynapseGroupNodeSimple(NetworkPanel, SynapseGroup, float) - Constructor for class org.simbrain.network.gui.nodes.SynapseGroupNodeSimple
SynapseGroupNodeVisible - Class in org.simbrain.network.gui.nodes: PNode representation of a group of synapses, where the synapses themselves are visible.
SynapseGroupNodeVisible(NetworkPanel, SynapseGroup) - Constructor for class org.simbrain.network.gui.nodes.SynapseGroupNodeVisible: Create a Synapse Group PNode.
synapseIsAdjustable(Synapse) - Method in enum org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.SynapseView
SynapseListener - Interface in org.simbrain.network.listeners: Listener interface for receiving network events relating to synapses.
SynapseNode - Class in org.simbrain.network.gui.nodes: SynapseNode is a Piccolo PNode corresponding to a Neuron in the neural network model.
SynapseNode(NetworkPanel, NeuronNode, NeuronNode, Synapse) - Constructor for class org.simbrain.network.gui.nodes.SynapseNode: Create a new synapse node connecting a source and target neuron.
SynapsePolarityAndRandomizerPanel - Class in org.simbrain.network.gui.dialogs.connect: Display preferences for regarding the ratio of excitatory to inhibitory connections.
SynapsePolarityAndRandomizerPanel.EditableRandomizerPanel - Class in org.simbrain.network.gui.dialogs.connect
SynapsePolarityAndRandomizerPanel.RandBehavior - Enum in org.simbrain.network.gui.dialogs.connect
SynapsePropertiesExtended - Class in org.simbrain.network.gui.dialogs.synapse: Panel which displays the specific parameters of a particular synapse learning rule.
SynapsePropertiesExtended(Collection<Synapse>) - Constructor for class org.simbrain.network.gui.dialogs.synapse.SynapsePropertiesExtended
SynapsePropertiesPanel - Class in org.simbrain.network.gui.dialogs.synapse: This panel combines synapse editing sub-panels and handles changes to one being applied to the others.
SynapsePropertiesSimple - Class in org.simbrain.network.gui.dialogs.synapse: Panel showing basic properties of a set of synapses, e.g.
synapseRemoved(NetworkEvent<Synapse>) - Method in class org.simbrain.network.listeners.SynapseAdapter
synapseRemoved(NetworkEvent<Synapse>) - Method in interface org.simbrain.network.listeners.SynapseListener: Notify this listener of a synapse removed event.
synapseRemoved(NetworkEvent<Synapse>) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Notify this listener of a synapse removed event.
synapseTypeChanged(NetworkEvent<SynapseUpdateRule>) - Method in class org.simbrain.network.listeners.SynapseAdapter
synapseTypeChanged(NetworkEvent<SynapseUpdateRule>) - Method in interface org.simbrain.network.listeners.SynapseListener: Invoked when a synapse's update rule changes.
synapseTypeChanged(NetworkEvent<SynapseUpdateRule>) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Invoked when a synapse's update rule changes.
SynapseUpdateRule - Class in org.simbrain.network.core: A rule for updating a synapse.
SynapseUpdateRule() - Constructor for class org.simbrain.network.core.SynapseUpdateRule
SynchronizationPoint - Class in org.simbrain.network.update_actions.concurrency_tools
SynchronizationPoint(int) - Constructor for class org.simbrain.network.update_actions.concurrency_tools.SynchronizationPoint
SynchronizingInvocationEvent - Class in org.simbrain.workspace.updater: Class used to wrap InvocationEvents such that they are synchronized when executed.
SynchronizingInvocationEvent(InvocationEvent, Workspace, CompletionSignal) - Constructor for class org.simbrain.workspace.updater.SynchronizingInvocationEvent: Creates an invocation event for the provided event using the workspace for synchronization and calling signal.done() when finished.
syncOnAllComponents(Callable<E>) - Method in class org.simbrain.workspace.Workspace: Synchronizes on all components and executes task, returning the result of that callable.
syncParseStyleButtons() - Method in class org.simbrain.world.textworld.ReaderPanel: Syncs the parse style buttons to the underlying model state.
syncRest(Iterator<? extends Object>, Callable<E>) - Static method in class org.simbrain.workspace.Workspace: Recursively synchronizes on the components in the provided iterator and executes the provided task if there are no more components.
syncToModel() - Method in class org.simbrain.network.gui.NetworkPanel: Synchronize model and view.

T

tabbedPane - Variable in class org.simbrain.network.gui.dialogs.network.HopfieldEditTrainDialog: Main tabbed pane.
tabbedPane - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: Tabbed pane.
table - Variable in class org.simbrain.network.gui.trainer.DataPanel: JTable contained in scroller.
TableActionManager - Class in org.simbrain.util.table: Contains actions for use in SimbrainJTables.
TableActionManager() - Constructor for class org.simbrain.util.table.TableActionManager
TableDataException - Exception in org.simbrain.util.table: The wrong type of data is being read in to this table.
TableDataException(String) - Constructor for exception org.simbrain.util.table.TableDataException: Construct the exception.
take() - Method in class org.simbrain.network.update_actions.ConcurrentBufferedUpdate.CyclicTaskQueue
tanh(double, double, double, double) - Static method in enum org.simbrain.util.math.SquashingFunction: The hyperbolic tangent given an upper and lower limit and slope for a particular value.
targsUseSynapticInputs(Collection<Synapse>) - Static method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog: Tests to make sure that at least one source neuron in the provided list of synapses is a spiking neuron.
Task - Interface in org.simbrain.network.update_actions.concurrency_tools: An interface used to perform a task and which is tagged with information for flagging the tasks with whether or not it is used to make consumers wait or poison (kill) consumer threads.
TaskSynchronizationManager - Interface in org.simbrain.workspace.updater: Interface for integrating user interface threads with an updater.
tau_minus - Variable in class org.simbrain.network.synapse_update_rules.STDPRule: Time constant for LTD.
TAU_MINUS_DEFAULT - Static variable in class org.simbrain.network.synapse_update_rules.STDPRule: Default tau minus.
tau_plus - Variable in class org.simbrain.network.synapse_update_rules.STDPRule: Time constant for LTP.
TAU_PLUS_DEFAULT - Static variable in class org.simbrain.network.synapse_update_rules.STDPRule: Default tau plus.
testAndSetIfSpiking() - Method in class org.simbrain.network.groups.NeuronGroup: Tests if this neuron group can be considered a spiking neuron group and sets that value to true/false acordingly.
TestInputAction - Class in org.simbrain.network.gui.actions: Action to construct a test input panel.
TestInputAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.TestInputAction: Construct action.
TestInputPanel - Class in org.simbrain.network.gui.dialogs: Panel for sending inputs from a table to a network.
testInputsAction - Variable in class org.simbrain.network.gui.nodes.NeuronGroupNode: Open a window for sending inputs to this neuron group.
TestObject - Class in org.simbrain.util.propertyeditor.gui: For testing ReflectivePropertyEditor.
TestObject() - Constructor for class org.simbrain.util.propertyeditor.gui.TestObject
TestObject.TestEnum - Enum in org.simbrain.util.propertyeditor.gui
testRecurrence(List<Neuron>, List<Neuron>) - Static method in class org.simbrain.network.connections.ConnectionUtilities: Tests whether or not these connections are recurrent, that is, whether or not the neurons in the source list are the same as those in the target list.
TEXT - Static variable in class org.simbrain.network.gui.EditMode: Text edit mode.
TextAdapter() - Constructor for class org.simbrain.world.textworld.TextListener.TextAdapter
textAdded(NetworkTextObject) - Method in interface org.simbrain.network.listeners.TextListener: Notify this listener of a text added event.
textChanged(NetworkTextObject) - Method in interface org.simbrain.network.listeners.TextListener: Notify this listener that text's state changed.
textChanged() - Method in class org.simbrain.world.textworld.TextListener.TextAdapter
textChanged() - Method in interface org.simbrain.world.textworld.TextListener: The text has changed.
TextDialog - Class in org.simbrain.network.gui.dialogs.text: Font dialog.
TextDialog(ArrayList<TextNode>) - Constructor for class org.simbrain.network.gui.dialogs.text.TextDialog: Construct text dialog.
TextEditModeAction - Class in org.simbrain.network.gui.actions.edit: Text edit mode action.
TextEditModeAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.TextEditModeAction: Create a new text edit mode action with the specified network panel.
TextEventHandler - Class in org.simbrain.network.gui: Event handler for text nodes, so that they can be edited directly on the screen.
TextEventHandler(NetworkPanel) - Constructor for class org.simbrain.network.gui.TextEventHandler: Construct text event handler.
TextItem(int, int, String) - Constructor for class org.simbrain.world.textworld.TextWorld.TextItem: Construct this text item.
TextListener - Interface in org.simbrain.network.listeners: Listener interface for receiving network events relating to network text objects.
TextListener - Interface in org.simbrain.world.textworld: Listen for changes in the text world.
TextListener.TextAdapter - Class in org.simbrain.world.textworld: Adapter class so users of the interface don't have to implement every method.
TextNode - Class in org.simbrain.network.gui.nodes: An editable text element, which wraps a PStyledText object.
TextNode(NetworkPanel, NetworkTextObject) - Constructor for class org.simbrain.network.gui.nodes.TextNode: Construct text object at specified location.
textRemoved(NetworkTextObject) - Method in interface org.simbrain.network.listeners.TextListener: Notify this listener of a text removed event.
TextTable - Class in org.simbrain.util.table: A mutable text table.
TextTable(int, int) - Constructor for class org.simbrain.util.table.TextTable: Construct a text table.
TextTable(Set<String>) - Constructor for class org.simbrain.util.table.TextTable: Construct table from a set of strings.
TextTable() - Constructor for class org.simbrain.util.table.TextTable: No arg constructor.
TextWorld - Class in org.simbrain.world.textworld: TextWorld is an environment for modeling speech and reading and other linguistic phenomena.
TextWorld() - Constructor for class org.simbrain.world.textworld.TextWorld: Constructs an instance of TextWorld.
TextWorld.TextItem - Class in org.simbrain.world.textworld: Represents the "current item" as String, and includes a representation of the beginning and ending of the item in the main text.
TextWorldActions - Class in org.simbrain.world.textworld: Contains actions relating to Text World.
TextWorldActions() - Constructor for class org.simbrain.world.textworld.TextWorldActions
tfBias - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: Bias field.
tfSlope - Variable in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AbstractSigmoidalRulePanel: Slope field.
theBool - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theBooleanObject - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theColor - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theDouble - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theDoubleObject - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theFloat - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theFloatObject - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theInt - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theIntObject - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theLong - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theLongObject - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theShort - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theShortObject - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
theString - Variable in class org.simbrain.util.propertyeditor.gui.TestObject
thread - Variable in class org.simbrain.workspace.updater.UpdateThread: The thread number.
ThreadViewerPanel - Class in org.simbrain.workspace.gui: Display updater and thread information.
ThreadViewerPanel(Workspace) - Constructor for class org.simbrain.workspace.gui.ThreadViewerPanel: Constructor for viewer panel.
ThreeValueRule - Class in org.simbrain.network.neuron_update_rules: ThreeValuedNeuron is a natural extension of a binary neuron, which takes one of three values depending on the inputs to the neuron in relation to two thresholds.
ThreeValueRule() - Constructor for class org.simbrain.network.neuron_update_rules.ThreeValueRule
ThreeValueRulePanel - Class in org.simbrain.network.gui.dialogs.neuron.rule_panels: ThreeValuedNeuronPanel creates a dialog for setting preferences of three valued neurons.
ThreeValueRulePanel() - Constructor for class org.simbrain.network.gui.dialogs.neuron.rule_panels.ThreeValueRulePanel: Creates binary neuron preferences panel.
tickGroupifyOption(boolean) - Method in class org.simbrain.network.gui.dialogs.neuron.AddNeuronsDialog
TicTacToeGui - Class in org.simbrain.world.game.tictactoe: Interface for a tic-tac-toe (naughts and crosses) game.
TicTacToeGui() - Constructor for class org.simbrain.world.game.tictactoe.TicTacToeGui
TicTacToeGui.Listener - Interface in org.simbrain.world.game.tictactoe: The listener interface for this gui.
TicTacToeModel - Class in org.simbrain.world.game.tictactoe: Holds the state of the game.
TicTacToeModel() - Constructor for class org.simbrain.world.game.tictactoe.TicTacToeModel: Creates a new tic-tac-toe game.
TicTacToeModel.Listener - Interface in org.simbrain.world.game.tictactoe
TicTacToeModel.State - Enum in org.simbrain.world.game.tictactoe: Type for the state of a square.
TileMap - Class in org.simbrain.world.odorworld: The TileMap class contains the data for a tile-based map, including Sprites.
TileMap(int, int) - Constructor for class org.simbrain.world.odorworld.TileMap: Creates a new TileMap with the specified width and height (in number of tiles) of the map.
TileSensor - Class in org.simbrain.world.odorworld.sensors: A sensor which detects whether the entity is in a given sector or "tile" of the world.
TileSensor(OdorWorldEntity, int, int, int, int) - Constructor for class org.simbrain.world.odorworld.sensors.TileSensor: Construct a tile sensor.
TileSensorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel to add a single tile sensor to an entity or to modify an existing one.
TileSensorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.TileSensorPanel: Constructor for the case where a sensor is being created.
TileSensorPanel(OdorWorldEntity, TileSensor) - Constructor for class org.simbrain.world.odorworld.dialogs.TileSensorPanel: Constructor for the case where an effector is being edited.
tileSensorType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
TileSetPanel - Class in org.simbrain.world.odorworld.dialogs: Panel to add a set of tile sensors to an entity.
TileSetPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.TileSetPanel: Default constructor.
TimedAccumulatorRule - Class in org.simbrain.network.neuron_update_rules
TimedAccumulatorRule() - Constructor for class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
TimeLabel - Class in org.simbrain.network.gui: The visible label showing the time step as defined by the model network class.
TimeLabel(NetworkPanel) - Constructor for class org.simbrain.network.gui.TimeLabel: Construct time label with reference to networkPanel.
TimeSeriesModel - Class in org.simbrain.plot.timeseries: Data model for a time series plot.
TimeSeriesModel() - Constructor for class org.simbrain.plot.timeseries.TimeSeriesModel: Time series model constructor.
TimeSeriesModel(int) - Constructor for class org.simbrain.plot.timeseries.TimeSeriesModel: Initialize model to specified number of data sources.
TimeSeriesPlotActions - Class in org.simbrain.plot.timeseries: Contains actions for use in Time Series Component.
TimeSeriesPlotActions() - Constructor for class org.simbrain.plot.timeseries.TimeSeriesPlotActions
TimeSeriesPlotComponent - Class in org.simbrain.plot.timeseries: Represents time series data.
TimeSeriesPlotComponent(String) - Constructor for class org.simbrain.plot.timeseries.TimeSeriesPlotComponent: Create new time series plot component.
TimeSeriesPlotComponent(String, TimeSeriesModel) - Constructor for class org.simbrain.plot.timeseries.TimeSeriesPlotComponent: Creates a new time series component from a specified model.
TimeSeriesPlotComponent(String, int) - Constructor for class org.simbrain.plot.timeseries.TimeSeriesPlotComponent: Initializes a JFreeChart with specific number of data sources.
TimeSeriesPlotGui - Class in org.simbrain.plot.timeseries: Display a TimeSeriesPlot.
TimeSeriesPlotGui(GenericFrame, TimeSeriesPlotComponent) - Constructor for class org.simbrain.plot.timeseries.TimeSeriesPlotGui: Construct a time series plot gui.
TimeSeriesPlotPanel - Class in org.simbrain.plot.timeseries: Display a TimeSeriesPlot.
TimeSeriesPlotPanel(TimeSeriesModel) - Constructor for class org.simbrain.plot.timeseries.TimeSeriesPlotPanel: Construct a time series panel.
TITLE - Static variable in class org.simbrain.network.gui.dialogs.network.ESNCreationDialog
title() - Method in enum org.simbrain.util.SimbrainConstants.Polarity: The appropriate name for the enum member, for use in the GUI.
ToggleButton - Class in org.simbrain.util.widgets: Toggle button.
ToggleButton(List) - Constructor for class org.simbrain.util.widgets.ToggleButton: Create a new toggle button with the specified list of actions.
toggleDock() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Provisional Code for toggling tab dock's visibility.
toggleSelection(Object) - Method in class org.simbrain.network.gui.NetworkPanel: Toggle the selected state of the specified element; if it is selected, remove it from the selection, if it is not selected, add it to the selection.
toggleSelection(Sensor) - Method in class org.simbrain.world.visionworld.SensorSelectionModel: Toggle the selection state for the specified sensor.
tokenDictionary - Variable in class org.simbrain.world.textworld.TextWorld: Set of a strings that can be coupled to via scalar couplings.
TokenDictionaryPanel - Class in org.simbrain.world.textworld.dictionary: Panel for editing dictionaries which only consist of a list of string tokens, used in scalar couplings.
TokenDictionaryPanel(TextWorld) - Constructor for class org.simbrain.world.textworld.dictionary.TokenDictionaryPanel: Construct the editor.
TokenToVectorPanel - Class in org.simbrain.world.textworld.dictionary: Dialog for editing token to vector dictionary (which associates string tokens with numerical vectors.).
TokenToVectorPanel(ReaderWorld) - Constructor for class org.simbrain.world.textworld.dictionary.TokenToVectorPanel: Construct the panel.
tolerance - Variable in class org.simbrain.util.projection.Projector: Distance within which added points are considered old and are thus not added.
toolbars - Variable in class org.simbrain.network.gui.trainer.DataPanel: The toolbar panel.
ToolTipTextUpdater - Class in org.simbrain.network.gui.nodes: Input event handler for a network node that updates tool tip text for its NetworkPanel as the mouse enters and exits that node.
ToolTipTextUpdater(NetworkPanel) - Constructor for class org.simbrain.network.gui.nodes.ToolTipTextUpdater: Construct a new tool tip text updater with a reference to a network panel.
toString() - Method in class org.simbrain.network.connections.AllToAll
toString() - Method in class org.simbrain.network.connections.OneToOne
toString() - Method in class org.simbrain.network.connections.Radial
toString() - Method in class org.simbrain.network.connections.RadialSimple
toString() - Method in class org.simbrain.network.connections.Sparse
toString() - Method in class org.simbrain.network.core.Network
toString() - Method in class org.simbrain.network.core.NetworkTextObject
toString() - Method in class org.simbrain.network.core.Neuron
toString() - Method in class org.simbrain.network.core.Synapse
toString() - Method in class org.simbrain.network.groups.Group
toString() - Method in class org.simbrain.network.groups.NeuronGroup
toString() - Method in class org.simbrain.network.groups.Subnetwork
toString() - Method in class org.simbrain.network.groups.SynapseGroup
toString() - Method in class org.simbrain.network.gui.NetworkPanel
toString() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Returns String representation of this NeuronNode.
toString() - Method in class org.simbrain.network.gui.nodes.SynapseNode: Returns String representation of this NeuronNode.
toString() - Method in class org.simbrain.network.layouts.GridLayout
toString() - Method in class org.simbrain.network.layouts.HexagonalGridLayout
toString() - Method in class org.simbrain.network.layouts.LineLayout
toString() - Method in enum org.simbrain.network.neuron_update_rules.PointNeuronRule.OutputFunction
toString() - Method in enum org.simbrain.util.environment.SmellSource.DecayFunction
toString() - Method in enum org.simbrain.util.math.ProbDistribution
toString() - Method in class org.simbrain.util.projection.DataPoint
toString() - Method in class org.simbrain.util.projection.Dataset
toString() - Method in class org.simbrain.util.projection.Projector
toString() - Method in enum org.simbrain.util.propertyeditor.gui.TestObject.TestEnum
toString() - Method in class org.simbrain.util.propertyeditor.gui.TestObject
toString() - Method in class org.simbrain.workspace.AttributeType
toString() - Method in class org.simbrain.workspace.Coupling: Returns the string representation of this coupling.
toString() - Method in class org.simbrain.workspace.Workspace
toString() - Method in class org.simbrain.workspace.WorkspaceComponent
toString() - Method in class org.simbrain.world.textworld.TextWorld.TextItem
toString() - Method in class org.simbrain.world.visionworld.filter.editor.PixelAccumulatorEditor
toString() - Method in class org.simbrain.world.visionworld.filter.editor.RandomFilterEditor
toString() - Method in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor
toString() - Method in class org.simbrain.world.visionworld.filter.editor.UniformFilterEditor
toString() - Method in class org.simbrain.world.visionworld.pixelmatrix.editor.BufferedImagePixelMatrixEditor
toString() - Method in class org.simbrain.world.visionworld.pixelmatrix.editor.ScreenCapturePixelMatrixEditor
toString() - Method in class org.simbrain.world.visionworld.sensormatrix.editor.DenseSensorMatrixEditor
toString() - Method in class org.simbrain.world.visionworld.sensormatrix.editor.SparseSensorMatrixEditor
toXml(OutputStream) - Method in class org.simbrain.workspace.ArchiveContents: Writes this instance to XML.
trace(Object) - Method in class org.simbrain.util.Logger
Trainable - Interface in org.simbrain.network.trainers: Interface that must be implemented by any object that can be trained by a Trainer.
Trainer - Class in org.simbrain.network.trainers: Superclass for all trainer classes, which trains a trainable object, typically a network.
Trainer(Trainable) - Constructor for class org.simbrain.network.trainers.Trainer: Construct the trainer and pass in a reference to the trainable element.
Trainer.DataNotInitializedException - Exception in org.simbrain.network.trainers: Exception thrown when a training algorithm is applied but no data have been initialized.
TrainerGuiActions - Class in org.simbrain.network.gui.trainer: Contains actions for use in Trainer GUI.
TrainerGuiActions() - Constructor for class org.simbrain.network.gui.trainer.TrainerGuiActions
TrainerListener - Interface in org.simbrain.network.trainers: Classes with implement this interface fire events indicating changes in the status of a trainer.
TrainingSet - Class in org.simbrain.network.trainers: Represents input data, target data, a way of iterating through it, a validation subset, etc.
TrainingSet() - Constructor for class org.simbrain.network.trainers.TrainingSet: Construct training set object.
TrainingSet(double[][], double[][]) - Constructor for class org.simbrain.network.trainers.TrainingSet: Construct training set from given data.
TrainingSetPanel - Class in org.simbrain.network.gui.trainer: Display input data and target data.
TrainingSetPanel(Trainable, int) - Constructor for class org.simbrain.network.gui.trainer.TrainingSetPanel: Construct a new pane for displaying training sets.
TrainingSetPanel(List<Neuron>, NumericMatrix, List<Neuron>, NumericMatrix, int) - Constructor for class org.simbrain.network.gui.trainer.TrainingSetPanel: For data that is not embedded in traineable, so that all the data must be specified.
TrainingSetPanel() - Constructor for class org.simbrain.network.gui.trainer.TrainingSetPanel: Create a panel for use in testing.
trainIterativelyAction - Variable in class org.simbrain.network.gui.nodes.subnetworkNodes.LMSNetworkNode: Action to train LMS Iteratively.
trainOfflineAction - Variable in class org.simbrain.network.gui.nodes.subnetworkNodes.ESNNetworkNode: Action to train ESN Offline
trainOfflineAction - Variable in class org.simbrain.network.gui.nodes.subnetworkNodes.LMSNetworkNode: Action to train LMS Offline.
trainOnCurrentPattern() - Method in class org.simbrain.network.subnetworks.Hopfield: Apply the basic Hopfield rule to the current pattern.
transferNeuronsToGroup(List<Neuron>, NeuronGroup) - Method in class org.simbrain.network.core.Network: Remove the given neurons from the neuron list (without firing an event) and add them to the provided group.
translate(double, double) - Method in class org.simbrain.network.core.Network: Translate all neurons (the only objects with position information).
translate(ArrayList, double, double) - Static method in class org.simbrain.network.gui.Clipboard: Translate a set of objects.
TristateDropDown - Class in org.simbrain.util.widgets: TristateDropDown ceates a combo box that has three states; True, false and null.
TristateDropDown() - Constructor for class org.simbrain.util.widgets.TristateDropDown: Default constructor.
TristateDropDown(String, String) - Constructor for class org.simbrain.util.widgets.TristateDropDown: Create custom three-state combo box using text other than "Yes" and "No".
turn(double) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Turn by the specified amount, positive or negative.
Turning - Class in org.simbrain.world.odorworld.effectors: Effector for turning.
Turning(RotatingEntity, String, double) - Constructor for class org.simbrain.world.odorworld.effectors.Turning: Construct a turning effector.
TurningEffectorPanel - Class in org.simbrain.world.odorworld.dialogs: Panel to add a turning effector to an entity or to modify an existing one.
TurningEffectorPanel(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.dialogs.TurningEffectorPanel: Constructor for the case where an effector is being created.
TurningEffectorPanel(OdorWorldEntity, Turning) - Constructor for class org.simbrain.world.odorworld.dialogs.TurningEffectorPanel: Constructor for the case where an effector is being edited.
turningType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent
turnLeft(double) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Rotate left by the specified amount.
turnRight(double) - Method in class org.simbrain.world.odorworld.entities.RotatingEntity: Rotate right by the specified amount.

U

UDF - Class in org.simbrain.network.synapse_update_rules.spikeresponders: An experimental no-GUI only implementation of the UDF synapse.
UDF() - Constructor for class org.simbrain.network.synapse_update_rules.spikeresponders.UDF: Default constructor.
UmatchedAttributesException - Exception in org.simbrain.workspace: Exception thrown when a coupling is created with mismatched attributes.
UmatchedAttributesException(String) - Constructor for exception org.simbrain.workspace.UmatchedAttributesException
unclampNeuronsAction - Variable in class org.simbrain.network.gui.nodes.NeuronGroupNode: Action for unclamping neurons
undo() - Method in class org.simbrain.network.gui.UndoManager: Undo the last undoable action.
undo() - Method in interface org.simbrain.network.gui.UndoManager.UndoableAction: Undo this action.
undoManager - Variable in class org.simbrain.network.gui.NetworkPanel: Undo manager.
UndoManager - Class in org.simbrain.network.gui: Manage undo / redo operations in the network panel.
UndoManager() - Constructor for class org.simbrain.network.gui.UndoManager
UndoManager.UndoableAction - Interface in org.simbrain.network.gui: Interface for actions that can be undone and redone.
unfreezeSynapsesAction - Variable in class org.simbrain.network.gui.nodes.SynapseGroupInteractionBox: Action for unfreezing synapses
unGroup(ViewGroupNode, boolean) - Method in class org.simbrain.network.gui.NetworkPanel: Ungroup specified object.
UngroupAction - Class in org.simbrain.network.gui.actions: Ungroup group.
UngroupAction(NetworkPanel, ViewGroupNode) - Constructor for class org.simbrain.network.gui.actions.UngroupAction: Ungroup selected objects.
UNIFORM - Static variable in class org.simbrain.world.visionworld.filter.editor.FilterEditors: Uniform filter editor.
UniformFilter - Class in org.simbrain.world.visionworld.filter: Uniform filter.
UniformFilter(double) - Constructor for class org.simbrain.world.visionworld.filter.UniformFilter: Create a new uniform filter with the specified value.
UniformFilterEditor - Class in org.simbrain.world.visionworld.filter.editor: Uniform filter editor.
UniformFilterEditor() - Constructor for class org.simbrain.world.visionworld.filter.editor.UniformFilterEditor: Create a new uniform filter editor.
uninstallUI(JComponent) - Method in class org.simbrain.util.MultiLineToolTipUI
union(Collection, Collection) - Static method in class org.simbrain.util.Utils: Re-implementation of same method from org.apache.commons.collections.CollectionUtils.
untangle(LinkedHashMap<Point2D, Point2D>, HashMap<Point2D, SynapseGroupArrow>) - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
update() - Method in class org.simbrain.console.ConsoleComponent
update() - Method in class org.simbrain.console.ConsoleDesktopComponent
update() - Method in class org.simbrain.docviewer.DocViewerComponent
update() - Method in class org.simbrain.docviewer.DocViewerDesktopComponent
update() - Method in class org.simbrain.network.core.Network: The core update function of the neural network.
update() - Method in class org.simbrain.network.core.Neuron: Updates neuron.
update(Neuron) - Method in class org.simbrain.network.core.NeuronUpdateRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.core.SpikingNeuronUpdateRule: Apply the update rule.
update() - Method in class org.simbrain.network.core.Synapse: Update this synapse using its current learning rule.
update(Synapse) - Method in class org.simbrain.network.core.SynapseUpdateRule: Apply the update rule.
update() - Method in class org.simbrain.network.groups.Group: Update this group.
update() - Method in class org.simbrain.network.groups.NeuronGroup: Updates all the neurons in the neuron group according to their NeuronUpdateRule(s).
update() - Method in class org.simbrain.network.groups.Subnetwork
update() - Method in class org.simbrain.network.groups.SynapseGroup: Update group.
update() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseGroupAdjustmentPanel.Stats
update() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Update the neuron view based on the model neuron.
update() - Method in class org.simbrain.network.gui.nodes.TextNode: Update the styled text object based on the model object.
update() - Method in class org.simbrain.network.gui.TimeLabel: Update the text based on the network time.
update() - Method in class org.simbrain.network.NetworkComponent
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.LogisticRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.RandomNeuronRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.SinusoidalRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.activity_generators.StochasticRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.AdditiveRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.AdExIFRule
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.BinaryRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.ContinuousSigmoidalRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.DecayRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.FitzhughNagumo: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.IACRule
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.IntegrateAndFireRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.IzhikevichRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.LinearRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.MorrisLecarRule
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.NakaRushtonRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.PointNeuronRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.RunningAverageRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.SigmoidalRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.SpikingThresholdRule
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.ThreeValueRule: Apply the update rule.
update(Neuron) - Method in class org.simbrain.network.neuron_update_rules.TimedAccumulatorRule
update() - Method in class org.simbrain.network.subnetworks.BPTTNetwork
update() - Method in class org.simbrain.network.subnetworks.CompetitiveGroup
update() - Method in class org.simbrain.network.subnetworks.EchoStateNetwork: Update this group.
update(Hopfield) - Method in enum org.simbrain.network.subnetworks.Hopfield.HopfieldUpdate
update() - Method in class org.simbrain.network.subnetworks.Hopfield
update() - Method in class org.simbrain.network.subnetworks.KWTA
update() - Method in class org.simbrain.network.subnetworks.SimpleRecurrentNetwork
update() - Method in class org.simbrain.network.subnetworks.SOMGroup: Update the network.
update() - Method in class org.simbrain.network.subnetworks.WinnerTakeAll
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.HebbianCPCARule
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.HebbianRule
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.HebbianThresholdRule
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.LogSTDPRule: Updates the synapse's strength using Log-STDP.
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.OjaRule
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.ShortTermPlasticityRule
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay: Update the synapse.
update(Synapse, double) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ConvolvedJumpAndDecay
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.JumpAndDecay: Update the synapse.
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.ProbabilisticResponder: Update the synapse.
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.RiseAndDecay: Update the synapse.
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder: Update the synapse.
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.Step: Update the synapse.
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.spikeresponders.UDF
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.StaticSynapseRule
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.STDPRule
update(Synapse) - Method in class org.simbrain.network.synapse_update_rules.SubtractiveNormalizationRule
update() - Method in class org.simbrain.plot.barchart.BarChartGui
update() - Method in class org.simbrain.plot.histogram.HistogramGui
update() - Method in class org.simbrain.plot.piechart.PieChartComponent
update() - Method in class org.simbrain.plot.piechart.PieChartGui
update() - Method in class org.simbrain.plot.projection.ProjectionComponent: Get the current state of the dimension objects, send this to the projection algorithm, and update the graphics.
update() - Method in class org.simbrain.plot.projection.ProjectionGui: Update labels at bottom of component.
update() - Method in class org.simbrain.plot.rasterchart.RasterModel: Update the model; currently used to remove unused data when in "fixed width" mode.
update() - Method in class org.simbrain.plot.rasterchart.RasterPlotComponent
update() - Method in class org.simbrain.plot.rasterchart.RasterPlotGui
update() - Method in class org.simbrain.plot.scatterplot.ScatterPlotComponent
update() - Method in class org.simbrain.plot.scatterplot.ScatterPlotGui
update() - Method in class org.simbrain.plot.timeseries.TimeSeriesModel: Update the model; currently used to remove unused data when in "fixed width" mode.
update() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotComponent
update() - Method in class org.simbrain.plot.timeseries.TimeSeriesPlotGui
update() - Method in class org.simbrain.util.environment.SmellSource: Update the source.
update() - Method in class org.simbrain.workspace.Coupling: Update this coupling.
update() - Method in class org.simbrain.workspace.gui.GuiComponent: Optional gui update method, which can be overridden for custom GUI update needs.
update(Graphics) - Method in class org.simbrain.workspace.gui.SplashWindow: Updates the display area of the window.
update() - Method in class org.simbrain.workspace.WorkspaceComponent: Called by Workspace to update the state of the component.
update() - Method in class org.simbrain.world.dataworld.DataWorldComponent
update() - Method in class org.simbrain.world.dataworld.DataWorldDesktopComponent
update(TicTacToeModel) - Method in class org.simbrain.world.game.tictactoe.TicTacToeGui: Updates the gui with the current model state.
update() - Method in class org.simbrain.world.odorworld.effectors.Effector: Move the agent in a manner appropriate to the effector type.
update() - Method in class org.simbrain.world.odorworld.effectors.Speech
update() - Method in class org.simbrain.world.odorworld.effectors.StraightMovement
update() - Method in class org.simbrain.world.odorworld.effectors.Turning
update() - Method in class org.simbrain.world.odorworld.entities.Animation: Updates this animation's current image (frame), if necessary.
update() - Method in class org.simbrain.world.odorworld.entities.BasicEntity
update() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Updates this OdorWorldEntity's Animation and its position based on the velocity.
update() - Method in class org.simbrain.world.odorworld.entities.RotatingEntity
update() - Method in class org.simbrain.world.odorworld.LifeCycle: Life and death.
update(int) - Method in class org.simbrain.world.odorworld.OdorWorld: Update world.
update() - Method in class org.simbrain.world.odorworld.OdorWorldComponent
update() - Method in class org.simbrain.world.odorworld.sensors.BumpSensor: Update the sensor.
update() - Method in class org.simbrain.world.odorworld.sensors.Hearing
update() - Method in class org.simbrain.world.odorworld.sensors.Sensor: Update the sensor.
update() - Method in class org.simbrain.world.odorworld.sensors.SmellSensor: Update the sensor.
update() - Method in class org.simbrain.world.odorworld.sensors.TileSensor: Update the sensor.
update() - Method in class org.simbrain.world.oscworld.OscWorldComponent: Called by Workspace to update the state of the component.
update() - Method in class org.simbrain.world.textworld.DisplayComponent
update() - Method in class org.simbrain.world.textworld.DisplayWorld
update() - Method in class org.simbrain.world.textworld.ReaderComponent
update() - Method in class org.simbrain.world.textworld.ReaderWorld: Advance the position in the text, and update the current item.
update() - Method in class org.simbrain.world.textworld.TextWorld: Advance the position in the text, and update the current item.
update() - Method in class org.simbrain.world.threedee.sensors.Sight
update() - Method in class org.simbrain.world.visionworld.VisionWorldComponent: Called by Workspace to update the state of the component.
UpdateAction - Interface in org.simbrain.workspace.updater: Classes that implement this interface describe individual actions that together comprise a workspace update.
UpdateActionCustom - Class in org.simbrain.workspace.updater: Update using a custom action saved as a beanshell script.
UpdateActionCustom(WorkspaceUpdater, String) - Constructor for class org.simbrain.workspace.updater.UpdateActionCustom: Create a new custom update action from a file containing the custom script.
UpdateActionCustom(Workspace, File) - Constructor for class org.simbrain.workspace.updater.UpdateActionCustom: Create a new custom update action from a file containing the custom script.
UpdateActionManager - Class in org.simbrain.workspace.updater: Maintain a list of workspace update actions.
UpdateActionManager(WorkspaceUpdater) - Constructor for class org.simbrain.workspace.updater.UpdateActionManager: Construct a new update manager.
UpdateActionManager.UpdateManagerListener - Interface in org.simbrain.workspace.updater: Listen from changes to update manager.
UpdateAllBuffered - Class in org.simbrain.workspace.updater: Update all components and couplings as follows.
UpdateAllBuffered(WorkspaceUpdater) - Constructor for class org.simbrain.workspace.updater.UpdateAllBuffered
updateAllCouplings() - Method in class org.simbrain.workspace.CouplingManager: Updates all couplings in the workspace.
updateAllGroups() - Method in class org.simbrain.network.core.Network: Update all neuron groups and other groups.
updateAllSynapses() - Method in class org.simbrain.network.core.Network: Calls Synapse.update() for each weight.
updateColor() - Method in class org.simbrain.network.gui.nodes.SynapseNode: Calculates the color for a weight, based on its current strength.
UpdateComponent - Class in org.simbrain.workspace.updater: Update a specific workspace component.
UpdateComponent(WorkspaceUpdater, WorkspaceComponent) - Constructor for class org.simbrain.workspace.updater.UpdateComponent
updateComponent(WorkspaceComponent, CompletionSignal) - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Update the provided workspace component.
updateConstituentNodes() - Method in interface org.simbrain.network.gui.nodes.GroupNode: Update all pnode constituents of this group node to update their visible state (in the case of synapse group nodes, only do this if there are visible synapses).
updateConstituentNodes() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode
updateConstituentNodes() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode
updateConstituentNodes() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNode
updateConstituentNodes() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional
updateConstituentNodes() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeVisible
UpdateCoupling - Class in org.simbrain.workspace.updater: Updates a coupling
UpdateCoupling(Coupling<?>) - Constructor for class org.simbrain.workspace.updater.UpdateCoupling: Construct the action.
updateCouplings(List<Coupling<?>>) - Method in class org.simbrain.workspace.CouplingManager: Convenience method for updating a set of couplings.
updateCouplings() - Method in class org.simbrain.workspace.updater.WorkspaceUpdater: Update couplings.
updateCurrentRow() - Method in interface org.simbrain.util.table.IterableRowsTable: Increment the current row.
updateCurrentRow() - Method in class org.simbrain.util.table.NumericTable
updateCursor() - Method in class org.simbrain.network.gui.NetworkPanel: Update the cursor.
updated(int, int) - Method in interface org.simbrain.world.game.tictactoe.TicTacToeGui.Listener: Called when the given coordinate is selected.
updated() - Method in interface org.simbrain.world.game.tictactoe.TicTacToeModel.Listener
updated() - Method in interface org.simbrain.world.odorworld.WorldListener: World updated.
updated() - Method in class org.simbrain.world.odorworld.WorldListenerAdapter
updateDataPointColors(Dataset) - Method in class org.simbrain.util.projection.DataColoringManager: Update the colors of all the datapoints in a dataset.
updatedCouplings(int) - Method in class org.simbrain.workspace.gui.ComponentPanel
updatedCouplings(int) - Method in interface org.simbrain.workspace.updater.WorkspaceUpdaterListener: Called when the couplings are updated.
updateDiameter() - Method in class org.simbrain.network.gui.nodes.SynapseNode: Update the diameter of the drawn weight based on the logical weight's strength.
updateFanIn() - Method in class org.simbrain.network.core.Neuron: A helper method which iterates over each afferent synapse to this neuron and calls their update functions.
updateFieldVisibility(NeuronUpdateRule) - Method in class org.simbrain.network.gui.dialogs.neuron.NeuronPropertiesExtended: Update field visibility based on whether rule is bounded and/or clipped.
UpdateGroup - Class in org.simbrain.network.update_actions: Loose neurons (neurons not in groups) are updated in accordance with an ordered priority list.
UpdateGroup(Group) - Constructor for class org.simbrain.network.update_actions.UpdateGroup
updateHelp() - Method in class org.simbrain.network.gui.dialogs.synapse.SynapseDialog: Set the help page based on the currently selected synapse type.
updateMacheps() - Static method in class org.simbrain.util.math.Matrices: Updates MACHEPS for the executing machine.
updateMatcher() - Method in class org.simbrain.world.textworld.ReaderWorld: Reset the parser and specify the region focused on by it, to go from the current cursor position to the end of the text.
updateNetwork() - Method in class org.simbrain.network.trainers.BackpropTrainer: Update internally constructed network.
updateNetwork() - Method in class org.simbrain.network.trainers.SRNTrainer
updateNeurons(List<Neuron>) - Static method in class org.simbrain.network.core.Network: Convenience method for asynchronously updating a set of neurons, by calling each neuron's update function (which sets a buffer), and then setting each neuron's activation to the buffer state.
updateNeurons() - Method in class org.simbrain.network.listeners.NetworkAdapter
updateNeurons(Collection<Neuron>) - Method in class org.simbrain.network.listeners.NetworkAdapter
updateNeurons() - Method in interface org.simbrain.network.listeners.NetworkListener: Neuron states have been updated.
updateNeurons(Collection<Neuron>) - Method in interface org.simbrain.network.listeners.NetworkListener: Neuron states in specified neurons have been updated.
updateNeuronsByPriority() - Method in class org.simbrain.network.core.Network: This function is used to update the neuron and sub-network activation values if the user chooses to set different priority values for a subset of neurons and sub-networks.
updatePosition() - Method in class org.simbrain.network.gui.nodes.SynapseNode: Update position of synapse.
updatePriorityList() - Method in class org.simbrain.network.core.Network: Update the priority list used for priority based update.
updateRowSelection() - Method in class org.simbrain.util.table.SimbrainJTable: Select current row.
updateSensors() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Update all sensors.
updateSmellSource() - Method in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Update this object's smell source, if any.
updateStopped() - Method in class org.simbrain.workspace.Workspace: Should be called when updating is stopped.
updateSubSamplingStuff() - Method in class org.simbrain.network.gui.dialogs.NetworkPropertiesPanel: Update the num subsamples text field (enabled only if subsampling is selected).
updateSynapseNodePositions() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Call update synapse node positions on all constituent neuron nodes.
updateSynapseNodePositions() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Update connected synapse node positions.
updateSynapseNodePositions() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Call update synapse node positions on all constituent neuron group nodes, which does the same on all constituent neuron nodes.
updateSynapses() - Method in class org.simbrain.network.listeners.NetworkAdapter
updateSynapses(Collection<Synapse>) - Method in class org.simbrain.network.listeners.NetworkAdapter
updateSynapses() - Method in interface org.simbrain.network.listeners.NetworkListener: Synapse states have been updated.
updateSynapses(Collection<Synapse>) - Method in interface org.simbrain.network.listeners.NetworkListener: Synapse states in specified synapses have been updated.
updateText() - Method in class org.simbrain.network.gui.nodes.InteractionBox: Update the text label bounds.
updateText() - Method in class org.simbrain.network.gui.nodes.NeuronGroupNode: Update the text in the interaction box.
updateText() - Method in class org.simbrain.network.gui.nodes.neuronGroupNodes.SOMGroupNode
updateText() - Method in class org.simbrain.network.gui.nodes.SubnetworkNode: Update the text in the interaction box.
updateText() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNode: Update the text in the interaction box.
updateText() - Method in class org.simbrain.network.gui.nodes.SynapseGroupNodeBidirectional: Updates the text in the interaction boxes of the group.
updateTextLabel() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Update the text label.
updateTextVisibility() - Method in class org.simbrain.network.gui.nodes.NeuronNode: Update the visibility of all text nodes depending on view scale.
UpdateThread - Class in org.simbrain.workspace.updater: This thread class adds some special methods specific to this class.
UpdateThread(WorkspaceUpdater, Runnable, int) - Constructor for class org.simbrain.workspace.updater.UpdateThread: Creates a new instance with the given runnable and thread.
updateTime() - Method in class org.simbrain.network.core.Network: Increment the time counter, using a different method depending on whether this is a continuous or discrete.
updateTime() - Method in class org.simbrain.network.gui.NetworkPanel
updateTimeLabel() - Method in class org.simbrain.workspace.gui.SimbrainDesktop: Update time label.
updateTimeType() - Method in class org.simbrain.network.core.Network: If there is a single continuous neuron in the network, consider this a continuous network.
updateTotalValue() - Method in class org.simbrain.plot.piechart.PieChartModel: Updates the total value across all data items.
updateUI() - Method in class org.simbrain.util.JMultiLineToolTip
updatingFinished() - Method in class org.simbrain.workspace.gui.ComponentPanel
updatingFinished() - Method in interface org.simbrain.workspace.updater.WorkspaceUpdaterListener: Called when workspace "run" ends.
updatingStarted() - Method in class org.simbrain.workspace.gui.ComponentPanel
updatingStarted() - Method in interface org.simbrain.workspace.updater.WorkspaceUpdaterListener: Called when workspace "run" begins.
upper - Variable in class org.simbrain.world.visionworld.filter.editor.RgbFilterEditor: The output upper bound.
upperBound - Variable in class org.simbrain.network.neuron_update_rules.AbstractSigmoidalRule: The upper bound of the activity if clipping is used.
upperBound - Variable in class org.simbrain.util.randomizer.Randomizer: Upper bound of the random distribution.
upstairs - Variable in class org.simbrain.util.projection.Projector: A set of hi-d datapoints, each of which is an array of doubles The data to be projected.
Utils - Class in org.simbrain.util: Utils.
Utils() - Constructor for class org.simbrain.util.Utils

V

validateFullBounds() - Method in class org.simbrain.network.gui.nodes.OutlinedObjects: This is a crucial step.
value - Variable in class org.simbrain.network.synapse_update_rules.spikeresponders.SpikeResponder: Value.
value(double) - Method in enum org.simbrain.util.SimbrainConstants.Polarity: Get the appropriate value, e.g.
valueChanged(ListSelectionEvent) - Method in class org.simbrain.network.gui.dialogs.text.TextDialog
valueOf(String) - Static method in enum org.simbrain.network.core.Network.TimeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.core.NeuronUpdateRule.InputType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.groups.NeuronLayer.LayerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.gui.actions.ConditionallyEnabledAction.EnablingCondition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.RandBehavior: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel.CompetitivePropsPanelType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel.SOMPropsPanelType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.SynapseView: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.gui.NeuronComparator.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.gui.nodes.NeuronGroupNode.Port: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.layouts.LineLayout.LineOrientation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.neuron_update_rules.PointNeuronRule.OutputFunction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.subnetworks.CompetitiveGroup.UpdateMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.subnetworks.Hopfield.HopfieldUpdate: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.trainers.IterableTrainer.StoppingCondition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.trainers.LMSOffline.SolutionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.util.io_utilities.GroupSerializer.Precision: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.util.NetworkLayoutManager.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.network.util.OrientationComparator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.util.environment.SmellSource.DecayFunction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.util.math.ProbDistribution: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.util.math.SquashingFunction: Returns the enum constant of this type with the specified name.
valueOf(double, double, double, double) - Method in enum org.simbrain.util.math.SquashingFunction: Gives the value of the given squashing function for some input value, a ceiling, floor, and slope.
valueOf(String) - Static method in enum org.simbrain.util.propertyeditor.gui.TestObject.TestEnum: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.util.SimbrainConstants.Polarity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.util.widgets.DirectedCubicArrow.BezierTemplate: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.util.widgets.DropDownTriangle.UpDirection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel.ProducerOrConsumer: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.world.game.tictactoe.TicTacToeModel.State: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simbrain.world.textworld.ReaderWorld.ParseStyle: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.simbrain.network.core.Network.TimeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.core.NeuronUpdateRule.InputType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.groups.NeuronLayer.LayerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.gui.actions.ConditionallyEnabledAction.EnablingCondition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.gui.dialogs.connect.SynapsePolarityAndRandomizerPanel.RandBehavior: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.gui.dialogs.network.CompetitivePropertiesPanel.CompetitivePropsPanelType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.gui.dialogs.network.SOMPropertiesPanel.SOMPropsPanelType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.gui.dialogs.synapse.SynapseAdjustmentPanel.SynapseView: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.gui.NeuronComparator.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.gui.nodes.NeuronGroupNode.Port: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.layouts.LineLayout.LineOrientation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.neuron_update_rules.PointNeuronRule.OutputFunction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.subnetworks.CompetitiveGroup.UpdateMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.subnetworks.Hopfield.HopfieldUpdate: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.trainers.IterableTrainer.StoppingCondition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.trainers.LMSOffline.SolutionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.util.io_utilities.GroupSerializer.Precision: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.util.NetworkLayoutManager.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.network.util.OrientationComparator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.util.environment.SmellSource.DecayFunction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.util.math.ProbDistribution: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.util.math.SquashingFunction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.util.propertyeditor.gui.TestObject.TestEnum: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.util.SimbrainConstants.Polarity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.util.widgets.DirectedCubicArrow.BezierTemplate: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.util.widgets.DropDownTriangle.UpDirection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.workspace.gui.couplingmanager.PotentialAttributePanel.ProducerOrConsumer: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.world.game.tictactoe.TicTacToeModel.State: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.simbrain.world.textworld.ReaderWorld.ParseStyle: Returns an array containing the constants of this enum type, in the order they are declared.
VALUES - Static variable in class org.simbrain.world.visionworld.filter.editor.FilterEditors: Public list of filter editors.
VALUES - Static variable in class org.simbrain.world.visionworld.pixelmatrix.editor.PixelMatrixEditors: Public list of pixel matrix editors.
VALUES - Static variable in class org.simbrain.world.visionworld.sensormatrix.editor.SensorMatrixEditors: Public list of sensor matrix editors.
vClampValue - Variable in class org.simbrain.network.neuron_update_rules.HodgkinHuxleyRule
VectorDictionaryPanel - Class in org.simbrain.world.textworld.dictionary: Superclass for VectorToTokenPanel and TokenToVectorPanel.
VectorDictionaryPanel(String) - Constructor for class org.simbrain.world.textworld.dictionary.VectorDictionaryPanel: Construct the panel.
VectorToTokenPanel - Class in org.simbrain.world.textworld.dictionary: Dialog for editing vector to token dictionary (which associates vectors with matching tokens).
VectorToTokenPanel(DisplayWorld) - Constructor for class org.simbrain.world.textworld.dictionary.VectorToTokenPanel: Construct the panel.
view(ReceptiveField) - Method in class org.simbrain.world.visionworld.pixelmatrix.BufferedImagePixelMatrix: View this pixel matrix, returning an image for the specified receptive field.
view(ReceptiveField) - Method in class org.simbrain.world.visionworld.pixelmatrix.ScreenCapturePixelMatrix: View this pixel matrix, returning an image for the specified receptive field.
view(ReceptiveField) - Method in interface org.simbrain.world.visionworld.PixelMatrix: View this pixel matrix, returning an image for the specified receptive field.
ViewGroupNode - Class in org.simbrain.network.gui.nodes: A group of screen elements.
ViewGroupNode(NetworkPanel, ArrayList<ScreenElement>) - Constructor for class org.simbrain.network.gui.nodes.ViewGroupNode: Construct text object at specified location.
VisionWorld - Class in org.simbrain.world.visionworld: Vision world main canvas.
VisionWorld(VisionWorldModel) - Constructor for class org.simbrain.world.visionworld.VisionWorld: Create a new vision world with the specified model.
VisionWorldComponent - Class in org.simbrain.world.visionworld: Vision world frame.
VisionWorldComponent(String) - Constructor for class org.simbrain.world.visionworld.VisionWorldComponent: Create a new vision world frame with the specified name.
VisionWorldComponent(String, VisionWorldModel) - Constructor for class org.simbrain.world.visionworld.VisionWorldComponent: Create a new vision world frame with the specified name and model.
VisionWorldDesktopComponent - Class in org.simbrain.world.visionworld: Vision world frame.
VisionWorldDesktopComponent(GenericFrame, VisionWorldComponent) - Constructor for class org.simbrain.world.visionworld.VisionWorldDesktopComponent: Create a new vision world frame with the specified workspace.
VisionWorldModel - Interface in org.simbrain.world.visionworld: A vision world model has exactly one pixel matrix and exactly one sensor matrix.
VisionWorldModelAdapter - Class in org.simbrain.world.visionworld: Empty implementation of VisionWorldModelListener.
VisionWorldModelAdapter() - Constructor for class org.simbrain.world.visionworld.VisionWorldModelAdapter
VisionWorldModelEvent - Class in org.simbrain.world.visionworld: Event object representing a change in a VisionWorldModel.
VisionWorldModelEvent(VisionWorldModel, PixelMatrix, PixelMatrix) - Constructor for class org.simbrain.world.visionworld.VisionWorldModelEvent: Create a new vision world model event with the specified event source.
VisionWorldModelEvent(VisionWorldModel, SensorMatrix, SensorMatrix) - Constructor for class org.simbrain.world.visionworld.VisionWorldModelEvent: Create a new vision world model event with the specified event source.
VisionWorldModelListener - Interface in org.simbrain.world.visionworld: Event listener that receives notification of changes to a VisionWorldModel.
VisionWorldModelListenerSupport - Class in org.simbrain.world.visionworld: Support class that can be used via subclassing or delegation to provide VisionWorldModelListener management.
VisionWorldModelListenerSupport() - Constructor for class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Create a new vision world model listener support class meant to be subclassed.
VisionWorldModelListenerSupport(VisionWorldModel) - Constructor for class org.simbrain.world.visionworld.VisionWorldModelListenerSupport: Create a new vision world model listener support class with the specified VisionWorldModel as the source of events.

W

W_minus - Variable in class org.simbrain.network.synapse_update_rules.STDPRule: Learning rate for LTP case.
W_MINUS_DEFAULT - Static variable in class org.simbrain.network.synapse_update_rules.STDPRule: Default W - .
W_plus - Variable in class org.simbrain.network.synapse_update_rules.STDPRule: Learning rate for LTP case.
W_PLUS_DEFAULT - Static variable in class org.simbrain.network.synapse_update_rules.STDPRule: Default W plus.
WAND - Static variable in class org.simbrain.network.gui.EditMode: Wand mode mode.
WandEditModeAction - Class in org.simbrain.network.gui.actions.edit: Wand edit mode action.
WandEditModeAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.WandEditModeAction: Create a new pan edit mode action with the specified network panel.
WandEventHandler - Class in org.simbrain.network.gui: Wand event handler.
WandEventHandler(NetworkPanel) - Constructor for class org.simbrain.network.gui.WandEventHandler: Create a new selection event handler.
wasBumped() - Method in class org.simbrain.world.odorworld.sensors.BumpSensor
weaken() - Method in class org.simbrain.network.core.Synapse: Decrease the absolute value of this weight by increment amount.
WeightMatrixViewer - Class in org.simbrain.network.gui: Widget to display the synaptic connections between two layers of neurons as a matrix, in a jtable.
WeightMatrixViewer(List<Neuron>, List<Neuron>, NetworkPanel) - Constructor for class org.simbrain.network.gui.WeightMatrixViewer: Construct a weight matrix viewer using a specified list of source and target neurons.
WeightMatrixViewer(NetworkPanel) - Constructor for class org.simbrain.network.gui.WeightMatrixViewer: Create a panel for viewing the matrices connecting a set of source and target neuron lists.
weinerHopfSolution(Trainable) - Method in class org.simbrain.network.trainers.LMSOffline: Implements the Wiener-Hopf solution to LMS linear regression.
width - Variable in class org.simbrain.world.threedee.sensors.Sight
WinnerTakeAll - Class in org.simbrain.network.subnetworks: WinnerTakeAll.The neuron with the highest weighted input in a winner-take-all network takes on an upper value, all other neurons take on the lower value.
WinnerTakeAll(Network, WinnerTakeAll) - Constructor for class org.simbrain.network.subnetworks.WinnerTakeAll: Copy constructor.
WinnerTakeAll(Network, int) - Constructor for class org.simbrain.network.subnetworks.WinnerTakeAll: Creates a new winner take all network.
workspace - Variable in class org.simbrain.workspace.actions.WorkspaceAction
workspace - Variable in class org.simbrain.workspace.gui.CouplingMenuConsumer: Reference to workspace.
workspace - Variable in class org.simbrain.workspace.gui.CouplingMenuProducer: Reference to workspace.
Workspace - Class in org.simbrain.workspace: A collection of components which interact via couplings.
Workspace() - Constructor for class org.simbrain.workspace.Workspace: Construct a workspace.
WorkspaceAction - Class in org.simbrain.workspace.actions
WorkspaceAction(String, Workspace) - Constructor for class org.simbrain.workspace.actions.WorkspaceAction
WorkspaceActionManager - Class in org.simbrain.workspace.gui: Workspace action manager.
WorkspaceActionManager(SimbrainDesktop) - Constructor for class org.simbrain.workspace.gui.WorkspaceActionManager: Create a new workspace action manager for the specified workspace.
WorkspaceActionManager.ScriptAction - Class in org.simbrain.workspace.gui: Create an action based on the name of a script.
WorkspaceChangedDialog - Class in org.simbrain.workspace.gui: WorkspaceChangedDialog tells the user what components have changed since the last time they saved.
WorkspaceChangedDialog(SimbrainDesktop) - Constructor for class org.simbrain.workspace.gui.WorkspaceChangedDialog: Constructor for workspace changed dialog.
workspaceCleared() - Method in class org.simbrain.workspace.gui.ComponentPanel: Called after the workspace has been cleared.
workspaceCleared() - Method in class org.simbrain.workspace.gui.CouplingMenuComponent: Called after the workspace has been cleared.
workspaceCleared() - Method in interface org.simbrain.workspace.WorkspaceListener: Called after the workspace has been cleared.
WorkspaceComponent - Class in org.simbrain.workspace: Represents a component in a Simbrain Workspace .
WorkspaceComponent(String) - Constructor for class org.simbrain.workspace.WorkspaceComponent: Construct a workspace component.
WorkspaceComponentDeserializer - Class in org.simbrain.workspace: Class used to assist with deserializing workspace components.
WorkspaceComponentDeserializer() - Constructor for class org.simbrain.workspace.WorkspaceComponentDeserializer
WorkspaceComponentListener - Interface in org.simbrain.workspace: Interface for workspace component listeners.
WorkspaceComponentSerializer - Class in org.simbrain.workspace: Class used to assist with serializing components.
WorkspaceComponentSerializer(OutputStream) - Constructor for class org.simbrain.workspace.WorkspaceComponentSerializer: Construct serializer.
WorkspaceDialog - Class in org.simbrain.workspace.gui: WorkspaceDialog is a dialog box for setting the properties of the Workspace.
WorkspaceDialog(Workspace) - Constructor for class org.simbrain.workspace.gui.WorkspaceDialog: This method is the default constructor.
WorkspaceKeyAdapter - Class in org.simbrain.workspace.gui: Workspace key adapter.
WorkspaceKeyAdapter(Workspace) - Constructor for class org.simbrain.workspace.gui.WorkspaceKeyAdapter: Construct the key adapter.
WorkspaceListener - Interface in org.simbrain.workspace: Interface for listeners on a workspace.
WorkspaceSerializer - Class in org.simbrain.workspace: Serializes and deserializes workspaces.
WorkspaceSerializer(Workspace) - Constructor for class org.simbrain.workspace.WorkspaceSerializer: Creates a new serializer.
workspaceUpdated() - Method in class org.simbrain.workspace.gui.ComponentPanel
workspaceUpdated() - Method in interface org.simbrain.workspace.updater.WorkspaceUpdaterListener: Called every time the workspace is updated.
WorkspaceUpdateManagerPanel - Class in org.simbrain.workspace.gui: Panel for display and ordering of workspace update actions.
WorkspaceUpdateManagerPanel(Workspace, StandardDialog) - Constructor for class org.simbrain.workspace.gui.WorkspaceUpdateManagerPanel: Construct workspace update manager panel.
WorkspaceUpdater - Class in org.simbrain.workspace.updater: This class manages workspace updates.
WorkspaceUpdater(Workspace, int) - Constructor for class org.simbrain.workspace.updater.WorkspaceUpdater: Constructor for the updater that uses the provided controller and threads.
WorkspaceUpdater(Workspace) - Constructor for class org.simbrain.workspace.updater.WorkspaceUpdater: Constructor for the updater that uses the default controller and default number of threads.
WorkspaceUpdaterListener - Interface in org.simbrain.workspace.updater: The listener interface for observers interested in events related to the workspace updater.
WorldClipboard - Class in org.simbrain.world.odorworld: WorldClipboard is a static clipboard utility class.
WorldListener - Interface in org.simbrain.world.odorworld: Listener for receiving odor world events.
WorldListenerAdapter - Class in org.simbrain.world.odorworld: Adapter for world listener class.
WorldListenerAdapter() - Constructor for class org.simbrain.world.odorworld.WorldListenerAdapter
writeActsToFile() - Method in class org.simbrain.network.groups.NeuronGroup: Writes the activations of the network to a file.
writeMatrix(double[][], File) - Static method in class org.simbrain.util.Utils: Write a matrix of doubles to a file.
writeMatrix(String[][], File) - Static method in class org.simbrain.util.Utils: Save data as CSV (comma-separated-value) file.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.AbstractNeuronRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.AdExIFRulePanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.LogisticGeneratorPanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.RandomGeneratorPanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.SinusoidalGeneratorPanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.generator_panels.StochasticGeneratorPanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.AdditiveRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.BinaryRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ContinuousSigmoidalRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.DecayRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.HodgkinHuxleyRulePanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IACRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IntegrateAndFireRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.IzhikevichRulePanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.LinearRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.NakaRushtonRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.PointNeuronRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.RunningAverageRulePanel
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SigmoidalRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.SpikingThresholdRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(List<Neuron>) - Method in class org.simbrain.network.gui.dialogs.neuron.rule_panels.ThreeValueRulePanel: Edits neuron update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSpikeResponsePanel: Used internally to actually write all changes to the spike responders of a given list of synapses.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.AbstractSynapseRulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianCPCARulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianRulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.HebbianThresholdRulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.OjaRulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.ShortTermPlasticityRulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.StaticSynapsePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.STDPRulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.plasticity_panels.SubtractiveNormalizationRulePanel: Edits synapse update rules that already exist.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ConvolvedJumpAndDecayPanel: Used internally to actually write all changes to the spike responders of a given list of synapses.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.JumpAndDecayPanel: Used internally to actually write all changes to the spike responders of a given list of synapses.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.ProbabilisticSpikeResponderPanel: Used internally to actually write all changes to the spike responders of a given list of synapses.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.RiseAndDecayPanel: Used internally to actually write all changes to the spike responders of a given list of synapses.
writeValuesToRules(Collection<Synapse>) - Method in class org.simbrain.network.gui.dialogs.synapse.spike_responders.StepSpikerPanel
WTACreationDialog - Class in org.simbrain.network.gui.dialogs.network: WTADialog is a dialog box for setting the properties of the Network GUI.
WTACreationDialog(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.WTACreationDialog: This method is the default constructor.
WTAPropertiesPanel - Class in org.simbrain.network.gui.dialogs.network: WTAPropertiesDialog is a dialog box for setting the properties of a winner take all network.
WTAPropertiesPanel(NetworkPanel) - Constructor for class org.simbrain.network.gui.dialogs.network.WTAPropertiesPanel: Default constructor.
WTAPropertiesPanel(NetworkPanel, WinnerTakeAll) - Constructor for class org.simbrain.network.gui.dialogs.network.WTAPropertiesPanel: Default constructor.

X

x - Variable in class org.simbrain.world.odorworld.entities.OdorWorldEntity: X Position.
xLocationType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent: Attribute types.
xstream() - Static method in class org.simbrain.workspace.ArchiveContents: Returns the XStream instance used to serialize and deserialize instances of this class.

Y

y - Variable in class org.simbrain.world.odorworld.entities.OdorWorldEntity: Y Position.
yLocationType - Variable in class org.simbrain.world.odorworld.OdorWorldComponent

Z

ZeroSelectedObjectsAction - Class in org.simbrain.network.gui.actions.edit: Clear selected neurons action.
ZeroSelectedObjectsAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.ZeroSelectedObjectsAction: Create a new clear selected neurons action with the specified network panel.
zoomToFitPage(boolean) - Method in class org.simbrain.network.gui.NetworkPanel: Rescales the camera so that all objects in the canvas can be seen.
ZoomToFitPageAction - Class in org.simbrain.network.gui.actions.edit: Action to re-scale the screen to fit all objects.
ZoomToFitPageAction(NetworkPanel) - Constructor for class org.simbrain.network.gui.actions.edit.ZoomToFitPageAction: Create a new zoom to fit page action.

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