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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
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
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
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.