Index (Simbrain API)

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A

AbstractEntity - Class in org.simbrain.world.odorworld: AbstractEntity is an abstract class providing a basic structure for all items in the world.
AbstractEntity() - Constructor for class org.simbrain.world.odorworld.AbstractEntity
AbstractFilter - Class in org.simbrain.network.filters: Abstract filter, implements both PNodeFilter and Predicate interfaces.
AbstractFilter() - Constructor for class org.simbrain.network.filters.AbstractFilter
AbstractLayoutPanel - Class in org.simbrain.network.dialog.network.layout: AbstractLayoutPanel.
AbstractLayoutPanel() - Constructor for class org.simbrain.network.dialog.network.layout.AbstractLayoutPanel
AbstractNeuronPanel - Class in org.simbrain.network.dialog.neuron: AbstractNeuronPanel.
AbstractNeuronPanel() - Constructor for class org.simbrain.network.dialog.neuron.AbstractNeuronPanel: This method is the default constructor.
AbstractSpikeResponsePanel - Class in org.simbrain.network.dialog.synapse: AbstractSpikeResponsePanel.
AbstractSpikeResponsePanel() - Constructor for class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel: This method is the default constructor.
AbstractSynapsePanel - Class in org.simbrain.network.dialog.synapse: AbstractSynapsePanel.
AbstractSynapsePanel() - Constructor for class org.simbrain.network.dialog.synapse.AbstractSynapsePanel: This method is the default constructor.
accept(PNode) - Method in class org.simbrain.network.filters.AbstractFilter
accept(File) - Method in class org.simbrain.util.SFileChooser.FileFilter: Determines if the file has the correct extension type.
acceptChildrenOf(PNode) - Method in class org.simbrain.network.filters.AbstractFilter
actionListener - Variable in class org.simbrain.util.StandardDialog: Action listener.
actionPerformed(ActionEvent) - Method in class org.simbrain.gauge.GaugeFrame: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.gauge.graphics.DialogCoordinate: Respond to button pressing events.
actionPerformed(ActionEvent) - Method in class org.simbrain.gauge.graphics.DialogGeneral
actionPerformed(ActionEvent) - Method in class org.simbrain.gauge.graphics.DialogGraphics
actionPerformed(ActionEvent) - Method in class org.simbrain.gauge.graphics.DialogSammon
actionPerformed(ActionEvent) - Method in class org.simbrain.gauge.graphics.GaugePanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.AddGaugeAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.AlignHorizontalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.AlignVerticalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ClampNeuronsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ClampWeightsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ClearNeuronsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ClearSelectionAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.CloseNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ConnectNeuronsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.CopyAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.CutAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.DeleteAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.EditModeAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.InteractionModeAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.IterateNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewBackpropNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewCompetitiveNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewElmanNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewHopfieldNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewLMSNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewNeuronAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewStandardNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.NewWTANetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.OpenNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.PasteAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.RandomizeObjectsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.RunNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SaveAsNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SaveNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SelectAllAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SelectAllNeuronsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SelectAllWeightsAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SetAutoZoomAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SetNeuronPropertiesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SetSynapsePropertiesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ShowClampToolBarAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ShowDebugAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ShowEditToolBarAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ShowHelpAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ShowIOInfoAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ShowMainToolBarAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.ShowNetworkPreferencesAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SpaceHorizontalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.SpaceVerticalAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.actions.StopNetworkAction
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.network.BackpropTrainingDialog: Responds to action within the dialog.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.network.CompetitiveDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.network.CompetitivePropertiesDialog
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.network.layout.LayoutPanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.network.LMSTrainingDialog: Responds to action within the dialog.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.NetworkDialog: Respond to button pressing events with immediate changes to network panel, where relevant.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.neuron.DecayNeuronPanel: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.neuron.NakaRushtonNeuronPanel: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.neuron.NeuronDialog: Respond to neuron type changes.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.RandomPanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.synapse.SpikeResponsePanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.dialog.synapse.SynapseDialog: Respond to synapse type changes.
actionPerformed(ActionEvent) - Method in class org.simbrain.network.NetworkPanel
actionPerformed(ActionEvent) - Method in class org.simbrain.network.nodes.NeuronNode
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.Workspace: React to menu selections.
actionPerformed(ActionEvent) - Method in class org.simbrain.workspace.WorkspaceChangedDialog: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.dataworld.DataWorldFrame: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.DialogOdorWorld: Performs an appropriate action on the given event.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.DialogOdorWorldEntity: Respond to button pressing events.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.DialogOdorWorldWall: Respond to button pressing events.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.DialogScript: Responds to actionevents.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.OdorWorld: Tasks to perform when actions are performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.OdorWorldFrame: Responds to actions performed.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.odorworld.PanelStimulus: Acton Listener.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.textworld.DialogTextWorld
actionPerformed(ActionEvent) - Method in class org.simbrain.world.textworld.TextWorld: Responds to action events.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.textworld.TextWorldFrame: Responds to action events.
actionPerformed(ActionEvent) - Method in class org.simbrain.world.visionworld.VisionWorldFrame: Handles button and menu firing events.
activation - Variable in class org.simnet.interfaces.Neuron: Activation value of the neuron.
add(ArrayList) - Static method in class org.simbrain.network.Clipboard: Add objects to the clipboard.
add(Object) - Method in class org.simbrain.network.NetworkSelectionModel: Add the specified element to the selection.
addActivation(double) - Method in class org.simnet.interfaces.Neuron: Add specified amount of activation to this neuron.
addAgent(Point) - Method in class org.simbrain.world.odorworld.OdorWorld: Add an agent at point p.
addAll(Collection) - Method in class org.simbrain.network.NetworkSelectionModel: Add all of the specified elements to the selection.
addBottomText(String) - Method in class org.simbrain.network.dialog.neuron.AbstractNeuronPanel: Add notes or other text to bottom of panel.
addBottomText(String) - Method in class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel: Add notes or other text to bottom of panel.
addBottomText(String) - Method in class org.simbrain.network.dialog.synapse.AbstractSynapsePanel: Add notes or other text to bottom of panel.
addButton(JButton) - Method in class org.simbrain.util.StandardDialog: Adds a new button to the panel.
addChild(PNode) - Method in class org.simbrain.network.nodes.SubnetworkNode
addClipboardListener(ClipboardListener) - Static method in class org.simbrain.network.Clipboard: Add the specified clipboard listener.
addCommandTarget(NetworkPanel) - Method in class org.simbrain.world.textworld.TextWorld: Adds command to agent selected.
addCommandTarget(NetworkPanel) - Method in class org.simbrain.world.visionworld.VisionWorld
addConsole() - Method in class org.simbrain.workspace.Workspace: Add a beanshell console.
AddData - Class in org.simbrain.gauge.core: AddData is a set of functions for adding new datapoints to existing datasets, when a projection is being used in real-time.
AddData() - Constructor for class org.simbrain.gauge.core.AddData
addDatapoint(double[]) - Method in class org.simbrain.gauge.core.Gauge: Add a new point to the dataset, using the currently selected add method.
addDatapoint(double[]) - Method in class org.simbrain.gauge.core.Projector: Add a datapoint to the upstairs dataset, and a corresponding point to the downstairs dataset.
addDataWorld(boolean) - Method in class org.simbrain.workspace.Workspace: Add a new world to the workspace, to be initialized with default values.
addDataWorld(DataWorldFrame, boolean) - Method in class org.simbrain.workspace.Workspace: Add a world to the workspace.
addEntity(Point) - Method in class org.simbrain.world.odorworld.OdorWorld: Add a world object at point p.
addGauge() - Method in class org.simbrain.network.NetworkPanel: Add a gauge which by default gauges all neurons of current network.
addGauge(boolean) - Method in class org.simbrain.workspace.Workspace: Add a new gauge to the workspace, to be initialized with default values.
addGauge(GaugeFrame, boolean) - Method in class org.simbrain.workspace.Workspace: Add a gauge to the workspace.
AddGaugeAction - Class in org.simbrain.network.actions: Add Gauge to workspace which by default gauges all neuronnodes on this networkpanel.
AddGaugeAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.AddGaugeAction: Create a new add gauge action with the specified network panel.
addItem(String, JComponent) - Method in class org.simbrain.network.dialog.neuron.AbstractNeuronPanel: Adds a new item.
addItem(String, JComponent) - Method in class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel: Adds an item.
addItem(String, JComponent) - Method in class org.simbrain.network.dialog.synapse.AbstractSynapsePanel: Adds an item.
addItem(String, JComponent) - Method in class org.simbrain.util.LabelledItemPanel: This method adds a labelled item to the panel.
addItemLabel(JLabel, JComponent) - Method in class org.simbrain.network.dialog.neuron.AbstractNeuronPanel: Adds a new item label.
addItemLabel(JLabel, JComponent) - Method in class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel: Adds an item label.
addItemLabel(JLabel, JComponent) - Method in class org.simbrain.network.dialog.synapse.AbstractSynapsePanel: 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.
AdditiveNeuron - Class in org.simnet.neurons: AdditiveNeuron See haykin (2002), section 14.5.
AdditiveNeuron() - Constructor for class org.simnet.neurons.AdditiveNeuron: Default constructor needed for external calls which create neurons then set their parameters.
AdditiveNeuron(Neuron) - Constructor for class org.simnet.neurons.AdditiveNeuron: This constructor is used when creating a neuron of one type from another neuron of another type Only values common to different types of neuron are copied.
AdditiveNeuronPanel - Class in org.simbrain.network.dialog.neuron: AdditiveNeuronPanel.
AdditiveNeuronPanel(Network) - Constructor for class org.simbrain.network.dialog.neuron.AdditiveNeuronPanel: Creates an instance of this panel.
addMatrix(String[][]) - Method in class org.simbrain.world.dataworld.TableModel: Add a matrix of string data to the table, as doubles.
addMenuBar(DataWorld) - Method in class org.simbrain.world.dataworld.DataWorldFrame: Creates the Menu Bar and adds it to the frame.
addMethod - Variable in class org.simbrain.gauge.core.Projector: Current selected add methods.
addMethod - Variable in class org.simbrain.gauge.core.Settings: Method to add new datapoints.
addNetwork(boolean) - Method in class org.simbrain.workspace.Workspace: Add a network to the workspace, to be initialized with default values.
addNetwork(NetworkFrame, boolean) - Method in class org.simbrain.workspace.Workspace: Add a network to the workspace.
addNetwork(Network) - Method in class org.simnet.interfaces.Network: Adds a new network.
addNetworkList(ArrayList) - Method in class org.simnet.interfaces.Network: Add an array of networks and set their parents to this.
addNetworkListener(NetworkListener) - Method in class org.simnet.interfaces.Network: Add the specified network listener.
addNeuron() - Method in class org.simbrain.network.NetworkPanel: Add a new neural network.
addNeuron(Neuron, boolean) - Method in class org.simnet.interfaces.Network: Adds a new neuron.
addNeuron(Neuron) - Method in class org.simnet.interfaces.Network: Adds a new neuron.
addNeuronList(ArrayList) - Method in class org.simnet.interfaces.Network: Add an array of neurons and set their parents to this.
addNoise(double[], double) - Static method in class org.simbrain.util.SimbrainMath: Add noise to an vector.
addOdorWorld(boolean) - Method in class org.simbrain.workspace.Workspace: Add a new world to the workspace, to be initialized with default values.
addOdorWorld(OdorWorldFrame, boolean) - Method in class org.simbrain.workspace.Workspace: Add a world to the workspace.
addPoint(double[], double) - Method in class org.simbrain.gauge.core.Dataset: Add a new datapoint to the dataset.
addPoint(double[]) - Method in class org.simbrain.gauge.core.Dataset: Add datapoint without checking whether it is unique or not.
addSelectionHandleTo(PNode) - Static method in class org.simbrain.network.nodes.SelectionHandle: Add a selection handle to the specified node, if one does not exist already.
addSelectionListener(NetworkSelectionListener) - Method in class org.simbrain.network.NetworkPanel: Add the specified network selection listener.
addSelectionListener(NetworkSelectionListener) - Method in class org.simbrain.network.NetworkSelectionModel: Add the specified network selection listener.
addSource(Synapse) - Method in class org.simnet.interfaces.Neuron: Connect this neuron to source neuron via a weight.
addTarget(Synapse) - Method in class org.simnet.interfaces.Neuron: Connect this neuron to target neuron via a weight.
addTextWorld(boolean) - Method in class org.simbrain.workspace.Workspace: Adds a new text world to the workspace.
addTextWorld(TextWorldFrame, boolean) - Method in class org.simbrain.workspace.Workspace: Adds a new text world to the workspace.
addUpstairs(File) - Method in class org.simbrain.gauge.core.Projector: Add new high-d datapoints and reinitialize the datasets.
addVariable(GaugeSource) - Method in class org.simbrain.gauge.GaugedVariables: Add a new gauged variable.
addVector(double[], double[]) - Static method in class org.simbrain.util.SimbrainMath: Add these vectors.
addVisionWorld(boolean) - Method in class org.simbrain.workspace.Workspace: Add a new world to the workspace, to be initialized with default values.
addVisionWorld(VisionWorldFrame, boolean) - Method in class org.simbrain.workspace.Workspace: Add a world to the workspace.
addWall() - Method in class org.simbrain.world.odorworld.OdorWorld: Adds a wall to the world.
addWeight(Synapse, boolean) - Method in class org.simnet.interfaces.Network: Adds a weight to the neuron network, where that weight already has designated source and target neurons.
addWeight(Synapse) - Method in class org.simnet.interfaces.Network: Adds a weight to the neuron network, where that weight already has designated source and target neurons.
addWorldListener(WorldListener) - Method in class org.simbrain.world.World: Add the specified world listener.
Agent - Interface in org.simbrain.world: Agent.
alignHorizontal() - Method in class org.simbrain.network.NetworkPanel: Aligns neurons horizontally.
AlignHorizontalAction - Class in org.simbrain.network.actions: Aligns horizontal.
AlignHorizontalAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.AlignHorizontalAction: Create a new align horizontal action with the specified network panel.
alignVertical() - Method in class org.simbrain.network.NetworkPanel: Aligns neurons vertically.
AlignVerticalAction - Class in org.simbrain.network.actions: Aligns vertical.
AlignVerticalAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.AlignVerticalAction: Create a new align vertical action with the specified network panel.
ARCTAN - Static variable in class org.simnet.neurons.SigmoidalNeuron: Arctan.
attachAgentsToCouplings(ArrayList) - Method in class org.simbrain.workspace.Workspace: Look for "null" couplings (couplings with no agent field), and try to find suitable agents to attach them to.
attachAgentsToCouplings() - Method in class org.simbrain.workspace.Workspace: When a new world is opened, see if any open networks have "null" couplings that that world's agents can attach to.
attachInputsAndOutputs() - Method in class org.simnet.networks.Backprop: Attach training files to SNARLI network.

B

backgroundColor - Variable in class org.simbrain.gauge.graphics.GaugePanel: Color of background.
Backprop - Class in org.simnet.networks: Backprop implements a standard three layer backpropagation network.
Backprop() - Constructor for class org.simnet.networks.Backprop: Default constructor.
Backprop(int, int, int, Layout) - Constructor for class org.simnet.networks.Backprop: Construct a backprop network with a specified number of input, hidden, and output layers.
BackpropDialog - Class in org.simbrain.network.dialog.network: BackpropDialog is a dialog box for creating backprop networks.
BackpropDialog(NetworkPanel) - Constructor for class org.simbrain.network.dialog.network.BackpropDialog: Default constructor.
BackpropNetworkNode - Class in org.simbrain.network.nodes.subnetworks: BackpropNetworkNode is the graphical representation of a Backprop network.
BackpropNetworkNode(NetworkPanel, Backprop, double, double) - Constructor for class org.simbrain.network.nodes.subnetworks.BackpropNetworkNode: Create a new CompetitiveNetworkNode.
BackpropPropertiesDialog - Class in org.simbrain.network.dialog.network: BackpropPropertiesDialog is a dialog box for setting the properties of a backprop network.
BackpropPropertiesDialog(Backprop) - Constructor for class org.simbrain.network.dialog.network.BackpropPropertiesDialog: Default constructor.
BackpropTrainingDialog - Class in org.simbrain.network.dialog.network: BackpropTrainingDialog is a dialog box for training backprop networks.
BackpropTrainingDialog(Backprop) - Constructor for class org.simbrain.network.dialog.network.BackpropTrainingDialog: This method is the default constructor.
BackpropTrainingDialog.BPTDialogThread - Class in org.simbrain.network.dialog.network: BPTDialogThreadcreates a system thread to be run when training backprop networks.
BackpropTrainingDialog.BPTDialogThread(BackpropTrainingDialog) - Constructor for class org.simbrain.network.dialog.network.BackpropTrainingDialog.BPTDialogThread: Backprop training dialog thread constructor.
BARE - Static variable in class org.simnet.neurons.SigmoidalNeuron: Tanh.
batchIterate() - Method in class org.simnet.networks.Backprop: Batch train for one iteration.
batchIterate() - Method in class org.simnet.networks.Elman: Batch train for one iteration.
batchTrain() - Method in class org.simnet.networks.Backprop: Forwards to Snarli batchTrain() method.
BinaryNeuron - Class in org.simnet.neurons: BinaryNeuron type to be used in creating different types of networks.
BinaryNeuron() - Constructor for class org.simnet.neurons.BinaryNeuron: Default constructor needed for external calls which create neurons then set their parameters.
BinaryNeuron(Neuron) - Constructor for class org.simnet.neurons.BinaryNeuron: This constructor is used when creating a neuron of one type from another neuron of another type Only values common to different types of neuron are copied.
BinaryNeuronPanel - Class in org.simbrain.network.dialog.neuron: BinaryNeuronPanel creates a dialog for setting preferences of binary neurons.
BinaryNeuronPanel() - Constructor for class org.simbrain.network.dialog.neuron.BinaryNeuronPanel: Creates binary neuron preferences panel.
BlankSpikerPanel - Class in org.simbrain.network.dialog.synapse: BlankSpikerPanel.
BlankSpikerPanel() - Constructor for class org.simbrain.network.dialog.synapse.BlankSpikerPanel: This method is the default constructor.
BOTH_WAYS - Static variable in class org.simnet.coupling.InteractionMode: Both ways interaction mode.
BothWaysInteractionModeAction - Class in org.simbrain.network.actions: Both ways interaction mode action.
BothWaysInteractionModeAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.BothWaysInteractionModeAction: Create a new both ways interaction mode action.
BrowserLauncher - Class in org.simbrain.util: BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
buildInitialNetwork() - Method in class org.simnet.networks.Backprop: Build the default network.
buildInitialNetwork() - Method in class org.simnet.networks.Elman: Build the default network.
buildPopupMenu() - Method in class org.simbrain.world.dataworld.DataWorld
buildPopupMenu(AbstractEntity) - Method in class org.simbrain.world.odorworld.OdorWorld: Create a popup menu based on location of mouse click.
buildSnarliNetwork() - Method in class org.simnet.networks.Backprop: Create the Snarli network.
buildSnarliNetwork() - Method in class org.simnet.networks.Elman: Create the Snarli network.
ButtonEditor - Class in org.simbrain.world.dataworld: The ButtonEditor class provides an editor for buttons that allows you to change their names.
ButtonEditor(DataWorld) - Constructor for class org.simbrain.world.dataworld.ButtonEditor: Create a new button editor for the specified data world.
ButtonRenderer - Class in org.simbrain.world.dataworld: ButtonRenderer is necessary to keep the print buttons of the table rendered correctly.
ButtonRenderer(TableCellRenderer) - Constructor for class org.simbrain.world.dataworld.ButtonRenderer: Create a new button renderer with the specified default renderer.

C

C_VALUES - Static variable in class org.simnet.coupling.InteractionMode: Collection of interaction mode values.
calcCenter(Point2D, Point2D) - Method in class org.simbrain.network.nodes.SynapseNode: Calculates the position of the synapse circle based on the positions of the source and target NeuronNodes.
calculateDistances() - Method in class org.simbrain.gauge.core.Dataset: Calculate inter-point distancese.
canBeCopied(PNode, NetworkPanel) - Static method in class org.simbrain.network.Clipboard: Determines whether or not a pnode can be copied.
centerCamera() - Method in class org.simbrain.gauge.graphics.GaugePanel: Scale the data so that it fits on the screen Assumes 2-d data.
centerCamera() - Method in class org.simbrain.network.NetworkPanel: Centers the neural network in the middle of the PCanvas.
changeNeuron(Neuron, Neuron) - Method in class org.simnet.interfaces.Network: Replace one neuron with another.
changeNeurons() - Method in class org.simbrain.network.dialog.neuron.NeuronDialog: Change all the neurons from their current type to the new selected type.
changesExist() - Method in class org.simbrain.workspace.Workspace: Check whether there have been changes in the workspace or its components.
changeSynapse(Synapse, Synapse) - Method in class org.simnet.interfaces.Network: Change synapse type / replace one synapse with another.
changeSynapses() - Method in class org.simbrain.network.dialog.synapse.SynapseDialog: Change all the synapses from their current type to the new selected type.
changeVariable(GaugeSource, GaugeSource) - Method in class org.simbrain.gauge.GaugedVariables: Update a gauged variable.
checkAllBounds() - Method in class org.simnet.interfaces.Network: Calls Neuron.checkBounds() for each neuron, which makes sure the neuron has not exceeded its upper bound or gone below its lower bound.
checkBounds() - Method in class org.simnet.interfaces.Neuron: If activation is above or below its bounds set it to those bounds.
checkBounds() - Method in class org.simnet.interfaces.Synapse: If weight value is above or below its bounds set it to those bounds.
checkConsistentDimensions() - Method in class org.simbrain.gauge.core.Dataset: Check that all the vectors in the dataset have the same dimension.
checkCoordinates() - Method in class org.simbrain.gauge.core.ProjectCoordinate: If the current coordinate axes are outside acceptable bounds, set them to acceptable values (currently 0 and 1).
checkDatasets() - Method in class org.simbrain.gauge.core.Projector: Check validity of datasets.
clampChanged() - Method in class org.simbrain.gauge.GaugeFrame
clampChanged() - Method in class org.simbrain.network.NetworkPanel: Update clamp toolbar buttons and menu items.
clampChanged() - Method in interface org.simnet.interfaces.NetworkListener: Notify listeners of a clamp changed event, when the statu of the "clamp fields" changes.
ClampedNeuron - Class in org.simnet.neurons: ClampedNeuron.
ClampedNeuron() - Constructor for class org.simnet.neurons.ClampedNeuron: Default constructor needed for external calls which create neurons then set their parameters.
ClampedNeuron(Neuron) - Constructor for class org.simnet.neurons.ClampedNeuron: This constructor is used when creating a neuron of one type from another neuron of another type Only values common to different types of neuron are copied.
ClampedNeuronPanel - Class in org.simbrain.network.dialog.neuron: ClampedNeuronPanel.
ClampedNeuronPanel() - Constructor for class org.simbrain.network.dialog.neuron.ClampedNeuronPanel: This method is the default constructor.
ClampedSynapse - Class in org.simnet.synapses: ClampedSynapse.
ClampedSynapse(Neuron, Neuron, double, String) - Constructor for class org.simnet.synapses.ClampedSynapse: Creates a weight of some value connecting two neurons.
ClampedSynapse(Neuron, Neuron) - Constructor for class org.simnet.synapses.ClampedSynapse: Creates a weight connecting source and target neurons.
ClampedSynapse() - Constructor for class org.simnet.synapses.ClampedSynapse: Default constructor needed for external calls which create neurons then set their parameters.
ClampedSynapse(Synapse) - Constructor for class org.simnet.synapses.ClampedSynapse: This constructor is used when creating a neuron of one type from another neuron of another type Only values common to different types of neuron are copied.
ClampedSynapsePanel - Class in org.simbrain.network.dialog.synapse: ClampedSynapsePanel.
ClampedSynapsePanel() - Constructor for class org.simbrain.network.dialog.synapse.ClampedSynapsePanel: This method is the default constructor.
ClampNeuronsAction - Class in org.simbrain.network.actions: Clamps neurons action.
ClampNeuronsAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.ClampNeuronsAction: Create a new clamp neurons action with the specified network panel.
ClampWeightsAction - Class in org.simbrain.network.actions: Clamps weights action.
ClampWeightsAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.ClampWeightsAction: Create a new clamp weights action with the specified network panel.
clear() - Method in class org.simbrain.gauge.core.Dataset: Clear all data, high and low dimensional.
clear() - Method in class org.simbrain.gauge.GaugedVariables: Clears all variables for new gauge.
clear() - Static method in class org.simbrain.network.Clipboard: Clear the clipboard.
clear() - Method in class org.simbrain.network.NetworkSelectionModel: Clear the selection.
clear() - Method in class org.simbrain.world.odorworld.OdorWorld: Remove all objects from world.
clear() - Method in class org.simnet.interfaces.Neuron: Set activation to 0; override for other "clearing" behavior.
clear() - Method in class org.simnet.neurons.NakaRushtonNeuron
clear() - Method in class org.simnet.neurons.TraceNeuron
clearActivations() - Method in class org.simnet.interfaces.Network: Set the activation level of all neurons to zero.
clearAllEntities() - Method in class org.simbrain.world.odorworld.OdorWorld: Clears all entities from the world.
clearClipboard() - Static method in class org.simbrain.world.odorworld.WorldClipboard: Clear all items from clipboard.
clearInputs() - Method in class org.simnet.interfaces.Network: Clears out input values of network nodes, which otherwise linger and cause problems.
ClearNeuronsAction - Class in org.simbrain.network.actions: Clear selected neurons action.
ClearNeuronsAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.ClearNeuronsAction: Create a new clear selected neurons action with the specified network panel.
clearSelection() - Method in class org.simbrain.network.NetworkPanel: Clear the selection.
ClearSelectionAction - Class in org.simbrain.network.actions: Clear selection action.
ClearSelectionAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.ClearSelectionAction: Create a new clear selection action with the specified network panel.
clearWorkspace() - Method in class org.simbrain.workspace.Workspace: Remove all items (networks, worlds, etc.) from this workspace.
clip(double) - Method in class org.simnet.interfaces.Neuron: If value is above or below its bounds set it to those bounds.
clip(double) - Method in class org.simnet.interfaces.Synapse: If value is above or below its bounds set it to those bounds.
Clipboard - Class in org.simbrain.network: Buffer which holds network objects.
Clipboard() - Constructor for class org.simbrain.network.Clipboard
clipboardChanged() - Method in interface org.simbrain.network.ClipboardListener: Notify of clipboard changed.
ClipboardEvent - Class in org.simbrain.network: An event object representing a change in clipboard content.
ClipboardEvent() - Constructor for class org.simbrain.network.ClipboardEvent: Create a new clipboard event with the specified source.
ClipboardListener - Interface in org.simbrain.network: Model listener.
close() - Method in class org.simnet.interfaces.Network: Notify any objects observing this network that it has closed.
closeDialogCancel() - Method in class org.simbrain.network.dialog.network.BackpropTrainingDialog
closeDialogCancel() - Method in class org.simbrain.network.dialog.network.LMSTrainingDialog
closeDialogCancel() - Method in class org.simbrain.network.dialog.NetworkDialog
closeDialogCancel() - Method in class org.simbrain.util.StandardDialog: Overriden to perform specific clean up when dialog closed.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.BackpropDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.BackpropPropertiesDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.BackpropTrainingDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.CompetitiveDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.CompetitivePropertiesDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.HopfieldDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.HopfieldPropertiesDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.LMSDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.LMSPropertiesDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.LMSTrainingDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.StandardNetworkDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.WTADialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.network.WTAPropertiesDialog: Called when dialog closes.
closeDialogOk() - Method in class org.simbrain.network.dialog.NetworkDialog
closeDialogOk() - Method in class org.simbrain.network.dialog.neuron.NeuronDialog
closeDialogOk() - Method in class org.simbrain.network.dialog.synapse.SynapseDialog
closeDialogOk() - Method in class org.simbrain.util.StandardDialog: Overrideen to perform specific clean up when dialog closed.
closeNetwork() - Method in class org.simbrain.network.NetworkPanel: Close model network.
CloseNetworkAction - Class in org.simbrain.network.actions: Close network action.
CloseNetworkAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.CloseNetworkAction: Create a new close network action with the specified network panel.
colorPoints() - Method in class org.simbrain.gauge.graphics.GaugePanel: Color every seventh point a different color; allows tracking of order.
colorToFloat(Color) - Static method in class org.simbrain.util.Utils: returns the Hue associated with a Color.
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.
commit() - Method in class org.simbrain.gauge.graphics.DialogCoordinate: Set projector values based on fields.
commit() - Method in class org.simbrain.gauge.graphics.DialogGeneral: Set projector values based on fields.
commit() - Method in class org.simbrain.gauge.graphics.DialogGraphics: Set projector values based on fields.
commit() - Method in class org.simbrain.gauge.graphics.DialogSammon: Set projector values based on fields.
commit() - Method in class org.simbrain.util.StandardDialog: Commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.AbstractNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.AdditiveNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.BinaryNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.ClampedNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.DecayNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.ExponentialDecayNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.IACNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.IntegrateAndFireNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.IzhikevichNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.LinearNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.LMSNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.LogisticNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.NakaRushtonNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.NeuronDialog: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.RandomNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.RunningAverageNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.SigmoidalNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.SinusoidalNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.StochasticNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.TemporalDifferenceNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.ThreeValuedNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.neuron.TraceNeuronPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.AbstractSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.BlankSpikerPanel: Called externally to commit changes.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.ClampedSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.HebbianSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.HebbianThresholdSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.JumpAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.OjaSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.RandomSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.RiseAndDecayPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.ShortTermPlasticitySynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.SignalSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.SpikeResponsePanel: Called exterally to commit changes when dialog is closed.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.StepSpikerPanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.SubtractiveNormalizationSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.SynapseDialog: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.network.dialog.synapse.TraceSynapsePanel: Called externally when the dialog is closed, to commit any changes made.
commitChanges() - Method in class org.simbrain.world.odorworld.DialogOdorWorldEntity: Commits changes to the entity that are shown in the dialog.
commitChanges() - Method in class org.simbrain.world.odorworld.DialogOdorWorldWall: Commits the changes edited here.
commitChanges() - Method in class org.simbrain.world.odorworld.PanelAgent: Set values based on fields.
commitChanges() - Method in class org.simbrain.world.odorworld.PanelStimulus: Set values based on fields.
commitChanges() - Method in class org.simbrain.world.textworld.DialogTextWorld: Commits any changes made in dialog.
commitRandom(RandomSource) - Method in class org.simbrain.network.dialog.RandomPanel: Called externally when dialog is being closed.
Comparator - Class in org.simbrain.util: Comparator is used to compare positions of PNodes.
Comparator(int) - Constructor for class org.simbrain.util.Comparator: Constructor for Comparator.
compare(Object, Object) - Method in class org.simbrain.util.Comparator
COMPARE_X - Static variable in class org.simbrain.util.Comparator: Compare PNodes by their x dimension.
COMPARE_Y - Static variable in class org.simbrain.util.Comparator: Compare PNodes by their y dimension.
compareDatasets() - Method in class org.simbrain.gauge.core.Projector: Chcek 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.
Competitive - Class in org.simnet.networks: Competitive implements a Competitive network.
Competitive() - Constructor for class org.simnet.networks.Competitive: Default constructor used by Castor.
Competitive(int, Layout) - Constructor for class org.simnet.networks.Competitive: Constructs a competitive network with specified number of neurons.
CompetitiveDialog - Class in org.simbrain.network.dialog.network: CompetitiveDialog is used as an assistant to create competitive networks.
CompetitiveDialog(NetworkPanel) - Constructor for class org.simbrain.network.dialog.network.CompetitiveDialog: This method is the default constructor.
CompetitiveNetworkNode - Class in org.simbrain.network.nodes.subnetworks: CompetitiveNetworkNode is the graphical representation of Competitive Networks.
CompetitiveNetworkNode(NetworkPanel, Competitive, double, double) - Constructor for class org.simbrain.network.nodes.subnetworks.CompetitiveNetworkNode: Create a new CompetitiveNetworkNode.
CompetitivePropertiesDialog - Class in org.simbrain.network.dialog.network: CompetitivePropertiesDialog is a dialog box for setting the properties of a competitive network.
CompetitivePropertiesDialog(Competitive) - Constructor for class org.simbrain.network.dialog.network.CompetitivePropertiesDialog: Default constructor.
completedInputRound() - Method in interface org.simbrain.world.Agent: Use when a full set of stimuli has been gathered, to initiate post-stimulus gathering activties.
completedInputRound() - Method in class org.simbrain.world.dataworld.DataWorld
completedInputRound() - Method in class org.simbrain.world.odorworld.OdorWorldAgent: Complicated input round.
completedInputRound() - Method in class org.simbrain.world.visionworld.VisionWorld: Completed input round.
componentHidden(ComponentEvent) - Method in class org.simbrain.workspace.Workspace: Responds to component hidden events.
componentHidden(ComponentEvent) - Method in class org.simbrain.world.visionworld.VisionWorldFrame
componentMoved(ComponentEvent) - Method in class org.simbrain.workspace.Workspace: Responds to component moved events.
componentMoved(ComponentEvent) - Method in class org.simbrain.world.visionworld.VisionWorldFrame
componentResized(ComponentEvent) - Method in class org.simbrain.workspace.Workspace: Responds to component resized events.
componentResized(ComponentEvent) - Method in class org.simbrain.world.visionworld.VisionWorldFrame: Ensures that the world keeps up with the frame resizing.
componentShown(ComponentEvent) - Method in class org.simbrain.workspace.Workspace: Responds to component shown events.
componentShown(ComponentEvent) - Method in class org.simbrain.world.visionworld.VisionWorldFrame
connectedToWeight(Synapse) - Method in class org.simnet.interfaces.Neuron: Check if this neuron is connected to a given weight.
ConnectNets - Class in org.simnet.util: ConnectNets provides utilities for connecting the nodes of networks together.
ConnectNeuronsAction - Class in org.simbrain.network.actions: Connect neurons action.
ConnectNeuronsAction(NetworkPanel, Collection, Collection) - Constructor for class org.simbrain.network.actions.ConnectNeuronsAction: Create a new connect neurons action.
containsName(ArrayList, String) - Static method in class org.simbrain.util.Utils: Checks whether an array list cantains a name, and warns you if it does.
containsString(ArrayList, String) - Method in class org.simnet.interfaces.Neuron: Utility method to see if an array of names (from the world) contains a target string.
ContextMenuEventHandler - Class in org.simbrain.network: Context menu event handler.
ContextMenuEventHandler() - Constructor for class org.simbrain.network.ContextMenuEventHandler
CONTINUOUS - Static variable in class org.simnet.interfaces.Network: If this is a continuous-time network.
coordinate(int, int, double[]) - Static method in class org.simbrain.gauge.core.AddData: Coordinate project new points.
copy() - Method in class org.simbrain.network.NetworkPanel: Copy to the clipboard.
CopyAction - Class in org.simbrain.network.actions: Copy action.
CopyAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.CopyAction: Create a new copy action with the specified network panel.
copyAgent(OdorWorldAgent) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Copy an agent from a world.
copyEntity(OdorWorldEntity) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Copy an entity from a world.
copyItem(AbstractEntity) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Copy an abstract entity from a world.
copyWall(Wall) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Copy a wall from a world.
Coupling - Class in org.simnet.coupling: Coupling represents a relation between an agent and an input or output node.
Coupling() - Constructor for class org.simnet.coupling.Coupling: Create a new coupling.
Coupling(Agent, Neuron) - Constructor for class org.simnet.coupling.Coupling: Create a new coupling with the specified agent and neuron.
Coupling(Neuron) - Constructor for class org.simnet.coupling.Coupling: Create a new coupling with the specified neuron.
Coupling(Agent) - Constructor for class org.simnet.coupling.Coupling: Create a new coupling with the specified agent.
couplingChanged(NetworkEvent) - Method in class org.simbrain.gauge.GaugeFrame
couplingChanged(NetworkEvent) - Method in class org.simbrain.network.NetworkPanel
couplingChanged(NetworkEvent) - Method in interface org.simnet.interfaces.NetworkListener: Notify this listener of a CouplingChanged event.
CouplingMenuItem - Class in org.simnet.coupling: CouplingMenuItem allows a menu-item to carry a reference to an associated coupling object.
CouplingMenuItem(String, Coupling) - Constructor for class org.simnet.coupling.CouplingMenuItem: Create a new coupling menu item with the specified menu text and coupling.
createAlignMenu() - Method in class org.simbrain.network.NetworkPanel: Return the align sub menu.
createClampToolBar() - Method in class org.simbrain.network.NetworkPanel: Create the clamp tool bar.
createConnections() - Method in class org.simnet.networks.Hopfield: Create full symmetric connections without self-connections.
createContextMenu() - Method in class org.simbrain.network.nodes.NeuronNode
createEditMenu() - Method in class org.simbrain.network.NetworkPanel: Create and return a new Edit menu for this network panel.
createEditToolBar() - Method in class org.simbrain.network.NetworkPanel: Create the edit tool bar.
createFileMenu() - Method in class org.simbrain.network.NetworkPanel: Create and return a new File menu for this network panel.
createGaugeMenu() - Method in class org.simbrain.network.NetworkPanel: Create and return a new Gauge menu for this network panel.
createHelpMenu() - Method in class org.simbrain.network.NetworkPanel: Create and return a new Help menu for this network panel.
createInsertMenu() - Method in class org.simbrain.network.NetworkPanel: Create and return a new Insert menu for this network panel.
createMainToolBar() - Method in class org.simbrain.network.NetworkPanel: Create the main tool bar.
createMenuBar() - Method in class org.simbrain.workspace.Workspace: Build the menu bar.
createRow(String, String, JComponent) - Static method in class org.simbrain.network.NetworkUtils: Helper method for creating formatted rows in dialog boxes, which consist of a label, a component, and some tool-tip for the label.
createSelectionMenu() - Method in class org.simbrain.network.NetworkPanel: Create a selection JMenu.
createSpacingMenu() - Method in class org.simbrain.network.NetworkPanel: Return the space sub menu.
createViewMenu() - Method in class org.simbrain.network.NetworkPanel: Create and return a new View menu for this network panel.
cut() - Method in class org.simbrain.network.NetworkPanel: Cut to the clipboard.
CutAction - Class in org.simbrain.network.actions: Cut action.
CutAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.CutAction: Create a new cut action with the specified network panel.
cutItem(AbstractEntity, OdorWorld) - Static method in class org.simbrain.world.odorworld.WorldClipboard: Cuts an object from a world.

D

Dataset - Class in org.simbrain.gauge.core: Dataset represents a set of n-dimensional points.
Dataset() - Constructor for class org.simbrain.gauge.core.Dataset: Default constructor for adding datasets.
Dataset(ArrayList) - Constructor for class org.simbrain.gauge.core.Dataset: Creates an instance of dataset.
Dataset(int) - Constructor for class org.simbrain.gauge.core.Dataset: Creates and instance of Dataset.
DataWorld - Class in org.simbrain.world.dataworld: DataWorld creates a table and then adds it to the viewport.
DataWorld(DataWorldFrame) - Constructor for class org.simbrain.world.dataworld.DataWorld: Creates a new instance of the data world.
DataWorldFrame - Class in org.simbrain.world.dataworld: DataWorldFrame is a "spreadsheet world" used to send rows of raw data to input nodes.
DataWorldFrame() - Constructor for class org.simbrain.world.dataworld.DataWorldFrame: This method is the default constructor.
DataWorldFrame(Workspace) - Constructor for class org.simbrain.world.dataworld.DataWorldFrame: Construct a new world panel.
DataWorldPreferences - Class in org.simbrain.world.dataworld: Preferences for the data world package.
debug() - Method in class org.simnet.interfaces.Neuron: Sends relevant information about the network to standard output.
DECAYFUNCTIONS - Static variable in class org.simbrain.world.odorworld.Stimulus: String array of decay functions.
DecayNeuron - Class in org.simnet.neurons: DecayNeuron.
DecayNeuron() - Constructor for class org.simnet.neurons.DecayNeuron: Default constructor needed for external calls which create neurons then set their parameters.
DecayNeuron(Neuron) - Constructor for class org.simnet.neurons.DecayNeuron: This constructor is used when creating a neuron of one type from another neuron of another type Only values common to different types of neuron are copied.
DecayNeuronPanel - Class in org.simbrain.network.dialog.neuron: DecayNeuronPanel.
DecayNeuronPanel() - Constructor for class org.simbrain.network.dialog.neuron.DecayNeuronPanel: This method is the default constructor.
decrementActivation() - Method in class org.simnet.interfaces.Neuron: Decrement this neuron by increment.
decrementSelectedObjects() - Method in class org.simbrain.network.NetworkPanel: Decreases neuron and synapse activation levels.
decrementWeight() - Method in class org.simnet.interfaces.Synapse: Decrement this weight by increment.
defaultColor - Variable in class org.simbrain.gauge.graphics.GaugePanel: Color of all other points.
defaultInit() - Method in class org.simnet.networks.Backprop: Build network and initialize nodes and weights to appropriate values.
defaultInit() - Method in class org.simnet.networks.Elman: Build network and initialize nodes and weights to appropriate values.
DeleteAction - Class in org.simbrain.network.actions: Delete action.
DeleteAction(NetworkPanel) - Constructor for class org.simbrain.network.actions.DeleteAction: Create a new delete action with the specified network panel.
deleteConnectedSynapses() - Method in class org.simnet.interfaces.Neuron: Delete connected synapses.
deleteFanIn() - Method in class org.simnet.interfaces.Neuron: Delete fan in.
deleteFanOut() - Method in class org.simnet.interfaces.Neuron: Delete fan out.
deleteNetwork(Network) - Method in class org.simnet.interfaces.Network: Delete network.
deleteNeuron(Neuron, boolean) - Method in class org.simnet.interfaces.Network: Deletes a neuron from the network.
deleteNeuron(Neuron) - Method in class org.simnet.interfaces.Network: Deletes a neuron from the network.
deleteSelectedObjects() - Method in class org.simbrain.network.NetworkPanel: Delete selected itemes.
deleteWeight(Synapse, boolean) - Method in class org.simnet.interfaces.Network: Delete a specified weight.
deleteWeight(Synapse) - Method in class org.simnet.interfaces.Network: Delete a specified weight.
DialogCoordinate - Class in org.simbrain.gauge.graphics: DialogCoordinate is a dialog box for setting the properties of the coordinate projection algorithm.
DialogCoordinate(Gauge) - Constructor for class org.simbrain.gauge.graphics.DialogCoordinate: This method is the default constructor.
DialogGeneral - Class in org.simbrain.gauge.graphics: DialogGeneral is a dialog box for setting general Gauge properties.
DialogGeneral(GaugePanel) - Constructor for class org.simbrain.gauge.graphics.DialogGeneral: This method is the default constructor.
DialogGraphics - Class in org.simbrain.gauge.graphics: DialogGraphics is a dialog box for setting the properties of the GUI.
DialogGraphics(GaugePanel) - Constructor for class org.simbrain.gauge.graphics.DialogGraphics: This method is the default constructor.
DialogOdorWorld - Class in org.simbrain.world.odorworld: DialogOdorWorld is used to set the enivronment's parameters, in particular, the way stimuli are constructed to be sent the network, and the way outputs from the network are expressed in the world.
DialogOdorWorld(OdorWorld) - Constructor for class org.simbrain.world.odorworld.DialogOdorWorld: Constructor initalizes a settings dialog for the odorworld from which it was called.
DialogOdorWorldEntity - Class in org.simbrain.world.odorworld: DialogWorldEntity displays the dialog box for settable values of creatures and entities within a world environment.
DialogOdorWorldEntity(OdorWorldEntity) - Constructor for class org.simbrain.world.odorworld.DialogOdorWorldEntity: Create and show the world entity dialog box.
DialogOdorWorldWall - Class in org.simbrain.world.odorworld: DialogOdorWorldWall is a dialog box for setting the properties of a wall.
DialogOdorWorldWall(OdorWorld, Wall) - Constructor for class org.simbrain.world.odorworld.DialogOdorWorldWall: This method is the default constructor.
DialogSammon - Class in org.simbrain.gauge.graphics: DialogSammon is a dialog box for setting the properties of the Sammon mapping algorithm.
DialogSammon(Gauge) - Constructor for class org.simbrain.gauge.graphics.DialogSammon: This method is the default constructor.
DialogScript - Class in org.simbrain.world.odorworld: DialogScript is used to manage world scripts, which control creature behavior in a pre-programmed way.
DialogScript(OdorWorld) - Constructor for class org.simbrain.world.odorworld.DialogScript: Constructor built for the odorworld.
DialogTextWorld - Class in org.simbrain.world.textworld: DialogTextWorld displays a dialog for setting textworld preferences such as how to parse text fields.
DialogTextWorld(TextWorld) - Constructor for class org.simbrain.world.textworld.DialogTextWorld: Dialog Constructor.
Dictionary - Class in org.simbrain.world.textworld: Dictionary associates words with neural inputs and outputs.
Dictionary(TextWorldFrame) - Constructor for class org.simbrain.world.textworld.Dictionary: Creates a new dictionary for the TextWorldFrame.
DISCRETE - Static variable in class org.simnet.interfaces.Network: If this is a discrete-time network.
displayRandomizeDialog() - Method in class org.simbrain.world.dataworld.DataWorld: Displays the randomize dialog.
disposeAllFrames() - Method in class org.simbrain.workspace.Workspace: Disposes all frames.
disposeSplash() - Static method in class org.simbrain.workspace.SplashWindow: Closes the splash window.
distance(Point, Point) - Static method in class org.simbrain.util.SimbrainMath: Calculates the Euclidean distance between two points.
doubleArrayToString(double[]) - Static method in class org.simbrain.util.Utils: Utility to class to convert arrays of doubles to strings.
downstairs - Variable in class org.simbrain.gauge.core.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.SelectionEventHandler
drag(PInputEvent) - Method in class org.simbrain.network.ZoomEventHandler
duplicate(Neuron) - Method in class org.simnet.interfaces.Neuron: Creates a duplicate of this neuron; used in copy/paste.
duplicate() - Method in class org.simnet.interfaces.Neuron
duplicate() - Method in class org.simnet.interfaces.SpikeResponder
duplicate(SpikeResponder) - Method in class org.simnet.interfaces.SpikeResponder: Duplicates synapses of type Spiker.
duplicate(Synapse) - Method in class org.simnet.interfaces.Synapse: Create duplicate weights.
duplicate() - Method in class org.simnet.interfaces.Synapse
duplicate() - Method in class org.simnet.neurons.AdditiveNeuron
duplicate() - Method in class org.simnet.neurons.BinaryNeuron
duplicate() - Method in class org.simnet.neurons.ClampedNeuron: Returns a duplicate ClampedNeuron (used, e.g., in copy/paste).
duplicate() - Method in class org.simnet.neurons.DecayNeuron
duplicate() - Method in class org.simnet.neurons.ExponentialDecayNeuron: Returns a duplicate ClampedNeuron (used, e.g., in copy/paste).
duplicate() - Method in class org.simnet.neurons.IACNeuron
duplicate() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
duplicate() - Method in class org.simnet.neurons.IzhikevichNeuron
duplicate() - Method in class org.simnet.neurons.LinearNeuron
duplicate() - Method in class org.simnet.neurons.LMSNeuron: Returns a duplicate ClampedNeuron (used, e.g., in copy/paste).
duplicate() - Method in class org.simnet.neurons.LogisticNeuron
duplicate() - Method in class org.simnet.neurons.NakaRushtonNeuron
duplicate() - Method in class org.simnet.neurons.RandomNeuron
duplicate() - Method in class org.simnet.neurons.RunningAverageNeuron: Returns a duplicate ClampedNeuron (used, e.g., in copy/paste).
duplicate() - Method in class org.simnet.neurons.SigmoidalNeuron
duplicate() - Method in class org.simnet.neurons.SinusoidalNeuron
duplicate() - Method in class org.simnet.neurons.StochasticNeuron
duplicate() - Method in class org.simnet.neurons.TemporalDifferenceNeuron: Returns a duplicate TemporalDifference (used, e.g., in copy/paste).
duplicate() - Method in class org.simnet.neurons.ThreeValuedNeuron
duplicate() - Method in class org.simnet.neurons.TraceNeuron: Returns a duplicate TraceNeuron (used, e.g., in copy/paste).
duplicate() - Method in class org.simnet.synapses.ClampedSynapse
duplicate() - Method in class org.simnet.synapses.Hebbian
duplicate() - Method in class org.simnet.synapses.HebbianThresholdSynapse
duplicate() - Method in class org.simnet.synapses.OjaSynapse
duplicate() - Method in class org.simnet.synapses.RandomSynapse
duplicate() - Method in class org.simnet.synapses.ShortTermPlasticitySynapse
duplicate() - Method in class org.simnet.synapses.SignalSynapse
duplicate() - Method in class org.simnet.synapses.spikeresponders.JumpAndDecay
duplicate() - Method in class org.simnet.synapses.spikeresponders.RiseAndDecay: Duplicates a spike responder synapse.
duplicate() - Method in class org.simnet.synapses.spikeresponders.Step
duplicate() - Method in class org.simnet.synapses.SubtractiveNormalizationSynapse
duplicate() - Method in class org.simnet.synapses.TraceSynapse
duplicate(RandomSource) - Method in class org.simnet.util.RandomSource: Returns a duplicate random source.

E

editButtons - Static variable in class org.simbrain.world.dataworld.DataWorld: Edit buttons boolean.
EditMode - Class in org.simbrain.network: Typesafe enumeration of edit modes.
EditModeAction - Class in org.simbrain.network.actions: Build mode action.
EditModeAction(String, NetworkPanel, EditMode) - Constructor for class org.simbrain.network.actions.EditModeAction: Create a new edit mode action with the specified name, network panel, and edit mode.
Elman - Class in org.simnet.networks: Elman networks are simple recurrent networks based on the work of Jeff Elman.
Elman() - Constructor for class org.simnet.networks.Elman: Default constructor.
ElmanDialog - Class in org.simbrain.network.dialog.network: ElmanDialog is a dialog box for creating Elman networks.
ElmanDialog(NetworkPanel) - Constructor for class org.simbrain.network.dialog.network.ElmanDialog: This method is the default constructor.
ElmanNetworkNode - Class in org.simbrain.network.nodes.subnetworks: BackpropNetworkNode is the graphical representation of a Backprop network.
ElmanNetworkNode(NetworkPanel, Elman, double, double) - Constructor for class org.simbrain.network.nodes.subnetworks.ElmanNetworkNode: Create a new CompetitiveNetworkNode.
endDrag(PInputEvent) - Method in class org.simbrain.network.SelectionEventHandler
endDrag(PInputEvent) - Method in class org.simbrain.network.ZoomEventHandler
Entry - Class in org.simbrain.world.textworld: Entry.
Entry(String, String) - Constructor for class org.simbrain.world.textworld.Entry: Entry.
evaluate(Object) - Method in class org.simbrain.network.filters.AbstractFilter
ExponentialDecayNeuron - Class in org.simnet.neurons: Expoential decay.
ExponentialDecayNeuron() - Constructor for class org.simnet.neurons.ExponentialDecayNeuron: Default constructor needed for external calls which create neurons then set their parameters.
ExponentialDecayNeuron(Neuron) - Constructor for class org.simnet.neurons.ExponentialDecayNeuron: This constructor is used when creating a neuron of one type from another neuron of another type Only values common to different types of neuron are copied.
ExponentialDecayNeuronPanel - Class in org.simbrain.network.dialog.neuron: ClampedNeuronPanel.
ExponentialDecayNeuronPanel(Network) - Constructor for class org.simbrain.network.dialog.neuron.ExponentialDecayNeuronPanel: This method is the default constructor.
exportHigh() - Method in class org.simbrain.gauge.GaugeFrame: Export high dimensional data to csv (comma-separated-values).
exportLow() - Method in class org.simbrain.gauge.GaugeFrame: Export low-dimensional data to csv (comma-separated-values).
exportWorkspace() - Method in class org.simbrain.workspace.Workspace: Export a workspace file: that is, save all workspace components and then a simple workspace file correpsonding to them.

F

fanIn - Variable in class org.simnet.interfaces.Neuron: List of synpases this neuron attaches to.
fanOut - Variable in class org.simnet.interfaces.Neuron: List of synapses attaching to this neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.AbstractNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.AdditiveNeuronPanel: Fill field values to default values for additive neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.BinaryNeuronPanel: Fill field values to default values for binary neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.ClampedNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.DecayNeuronPanel: Fill field values to default values for additive neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.ExponentialDecayNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.IACNeuronPanel: Fill field values to default values for binary neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.IntegrateAndFireNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.IzhikevichNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.LinearNeuronPanel: Fill field values to default values for linear neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.LMSNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.LogisticNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.NakaRushtonNeuronPanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.RandomNeuronPanel: Fill field values to default values for random neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.RunningAverageNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.SigmoidalNeuronPanel: Fill field values to default values for sigmoidal neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.SinusoidalNeuronPanel: Populates the fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.StochasticNeuronPanel: Populates the fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.TemporalDifferenceNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.ThreeValuedNeuronPanel: Fill field values to default values for binary neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.neuron.TraceNeuronPanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.RandomPanel: Fills fields with default values.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.AbstractSynapsePanel: Populate fields with default data.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.BlankSpikerPanel: Fills fields with the default values.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.ClampedSynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.HebbianSynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.HebbianThresholdSynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.JumpAndDecayPanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.OjaSynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.RandomSynapsePanel: Fill field values to default values for random neuron.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.RiseAndDecayPanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.ShortTermPlasticitySynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.SignalSynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.StepSpikerPanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.SubtractiveNormalizationSynapsePanel: Fill field values to default values for this synapse type.
fillDefaultValues() - Method in class org.simbrain.network.dialog.synapse.TraceSynapsePanel: Fill field values to default values for this synapse type.
fillFieldValues() - Method in class org.simbrain.gauge.graphics.DialogCoordinate: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.gauge.graphics.DialogGeneral: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.gauge.graphics.DialogGraphics: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.gauge.graphics.DialogSammon: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.BackpropPropertiesDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.BackpropTrainingDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.CompetitivePropertiesDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.ElmanDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.HopfieldDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.HopfieldPropertiesDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.LMSPropertiesDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.LMSTrainingDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.network.WTAPropertiesDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.NetworkDialog: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.AbstractNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.AdditiveNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.BinaryNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.ClampedNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.DecayNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.ExponentialDecayNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.IACNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.IntegrateAndFireNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.IzhikevichNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.LinearNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.LMSNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.LogisticNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.NakaRushtonNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.RandomNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.RunningAverageNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.SigmoidalNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.SinusoidalNeuronPanel: Populates the field with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.StochasticNeuronPanel: Populates the fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.TemporalDifferenceNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.ThreeValuedNeuronPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.neuron.TraceNeuronPanel: Populate fields with current data.
fillFieldValues(ArrayList) - Method in class org.simbrain.network.dialog.RandomPanel: Populates the fields with current values.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.AbstractSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.BlankSpikerPanel: Fills fields with the values.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.ClampedSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.HebbianSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.HebbianThresholdSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.JumpAndDecayPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.OjaSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.RandomSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.RiseAndDecayPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.ShortTermPlasticitySynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.SignalSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.SpikeResponsePanel: Populates the fields with current values.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.StepSpikerPanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.SubtractiveNormalizationSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.network.dialog.synapse.TraceSynapsePanel: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.world.odorworld.DialogOdorWorld: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.world.odorworld.DialogOdorWorldWall: Populate fields with current data.
fillFieldValues() - Method in class org.simbrain.world.odorworld.PanelAgent: Populate fields with current data.
Filters - Class in org.simbrain.network.filters: Filters.
findMatchingAgent(Coupling) - Method in class org.simbrain.workspace.Workspace: Associates a coupling with a matching agent in the current workspace.
findNeuronNode(Neuron) - Method in class org.simbrain.network.NetworkPanel: Find the NeuronNode corresponding to a given model Neuron.
findSubnetworkNode(Network) - Method in class org.simbrain.network.NetworkPanel: Find the SubnetworkNode corresponding to a given model subnetwork.
findSynapseNode(Synapse) - Method in class org.simbrain.network.NetworkPanel: Find the SynapseNode corresponding to a given model Synapse.
fireClampChanged() - Method in class org.simnet.interfaces.Network: Fire a clamp changed event to all registered model listeners.
fireClipboardChanged() - Static method in class org.simbrain.network.Clipboard: Fire a clipboard changed event to all registered model listeners.
fireCouplingChanged(Neuron) - Method in class org.simnet.interfaces.Network: Fire a coupling changed event to all registered model listeners.
fireNetworkChanged() - Method in class org.simnet.interfaces.Network: Fire a network changed event to all registered model listeners.
fireNeuronAdded(Neuron) - Method in class org.simnet.interfaces.Network: Fire a neuron added event to all registered model listeners.
fireNeuronChanged(Neuron, Neuron) - Method in class org.simnet.interfaces.Network: Fire a neuron changed event to all registered model listeners.
fireNeuronDeleted(Neuron) - Method in class org.simnet.interfaces.Network: Fire a neuron deleted event to all registered model listeners.
fireSelectionChanged(Set, Set) - Method in class org.simbrain.network.NetworkSelectionModel: Fire a wholesale selection model changed event to all registered selection listeners.
fireSubnetAdded(Network) - Method in class org.simnet.interfaces.Network: Fire a subnetwork added event to all registered model listeners.
fireSubnetDeleted(Network) - Method in class org.simnet.interfaces.Network: Fire a subnetwork deleted event to all registered model listeners.
fireSynapseAdded(Synapse) - Method in class org.simnet.interfaces.Network: Fire a neuron added event to all registered model listeners.
fireSynapseChanged(Synapse, Synapse) - Method in class org.simnet.interfaces.Network: Fire a neuron deleted event to all registered model listeners.
fireSynapseDeleted(Synapse) - Method in class org.simnet.interfaces.Network: Fire a neuron deleted event to all registered model listeners.
fireWorldChanged() - Method in class org.simbrain.world.World: Notify all world listeners that this world has changed.
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.
FS - Static variable in class org.simbrain.gauge.GaugeFrame: File system seperator.
FS - Static variable in class org.simbrain.gauge.GaugePreferences: File system seperator.
FS - Static variable in class org.simbrain.network.NetworkSerializer: File Separator constant.
FS - Static variable in class org.simbrain.world.dataworld.DataWorldPreferences: System file separator property.
FS - Static variable in class org.simbrain.world.odorworld.OdorWorldPreferences: System specific file system seperator.
FS - Static variable in class org.simbrain.world.textworld.TextWorldFrame: File system seperator based on current operating system.

G

Gauge - Class in org.simbrain.gauge.core: Gauge is the main class of the high dimensional visualizer, which provides methods for changing and initializing various projection algorithms.
Gauge() - Constructor for class org.simbrain.gauge.core.Gauge: Default constructor for gauge.
GaugedVariables - Class in org.simbrain.gauge: GaugedVariables contains information about what data this gauge represents.
GaugedVariables() - Constructor for class org.simbrain.gauge.GaugedVariables: Default constructor for creating gauged variables.
GaugedVariables(Gauge) - Constructor for class org.simbrain.gauge.GaugedVariables: Creates gauged Variables.
GaugeFrame - Class in org.simbrain.gauge: GaugeFrame wraps a Gauge object in a Simbrain workspace frame, which also stores information about the variables the Gauge is representing.
GaugeFrame() - Constructor for class org.simbrain.gauge.GaugeFrame: Default constructor.
GaugeFrame(Workspace) - Constructor for class org.simbrain.gauge.GaugeFrame: Instance of gauge frame.
GaugePanel - Class in org.simbrain.gauge.graphics: GaugePanel is the main panel in which data are displayed.
GaugePanel() - Constructor for class org.simbrain.gauge.graphics.GaugePanel: Instance of gauge panel.
GaugePreferences - Class in org.simbrain.gauge: GaugePreferences handles storage and retrieval of user preferences, e.g.
GaugePreferences() - Constructor for class org.simbrain.gauge.GaugePreferences
GaugeSource - Interface in org.simbrain.gauge: GaugeSource is implemented by objects whose state can be gauged.
GaugeThread - Class in org.simbrain.gauge.graphics: GaugeThread updates the Gauge Panel; Used for repeatedly iterating iterative projection algorithms.
GaugeThread(GaugePanel) - Constructor for class org.simbrain.gauge.graphics.GaugeThread
GAUSSIAN - Static variable in class org.simbrain.world.odorworld.Stimulus: String value.
GAUSSIAN - Static variable in class org.simnet.util.RandomSource: A gaussian distribution.
get() - Static method in class org.simnet.util.UniqueID: Returns a unique identifier.
getA() - Method in class org.simnet.neurons.IzhikevichNeuron
getAbstractEntityList() - Method in class org.simbrain.world.odorworld.OdorWorld
getActivation() - Method in class org.simnet.interfaces.Neuron
getActivation() - Static method in class org.simnet.NetworkPreferences: Return the activation preference setting.
getActivationFunction() - Static method in class org.simnet.NetworkPreferences: Return the activation function preference setting.
getActivationThreshold() - Static method in class org.simnet.NetworkPreferences: Return the activation threshold preference setting.
getAdaptationParameter() - Method in class org.simnet.neurons.NakaRushtonNeuron: Return the adaptation parameter.
getAdaptationTimeConstant() - Method in class org.simnet.neurons.NakaRushtonNeuron
getAddAgentItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getAddGaugeAction() - Method in class org.simbrain.network.NetworkActionManager: Return the add gauge action.
getAddItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getAddMethod() - Method in class org.simbrain.gauge.core.Projector
getAddMethod() - Method in class org.simbrain.gauge.core.Settings
getAddMethod() - Static method in class org.simbrain.gauge.GaugePreferences
getAddMethodIndex() - Method in class org.simbrain.gauge.core.Projector: Indices sed in populating combo box in general dialog.
getAddMethods() - Static method in class org.simbrain.gauge.core.Settings
getAddNoise() - Method in class org.simbrain.world.odorworld.Stimulus: Return the add noise.
getAddNoise() - Method in class org.simnet.neurons.AdditiveNeuron
getAddNoise() - Method in class org.simnet.neurons.DecayNeuron
getAddNoise() - Method in class org.simnet.neurons.IACNeuron
getAddNoise() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getAddNoise() - Method in class org.simnet.neurons.IzhikevichNeuron
getAddNoise() - Method in class org.simnet.neurons.LinearNeuron
getAddNoise() - Method in class org.simnet.neurons.NakaRushtonNeuron
getAddNoise() - Method in class org.simnet.neurons.SigmoidalNeuron
getAddNoise() - Method in class org.simnet.neurons.SinusoidalNeuron
getAgent() - Method in class org.simnet.coupling.Coupling: Return the agent for this coupling.
getAgentList() - Method in class org.simbrain.workspace.Workspace: Get a list of all agents in the workspace.
getAgentList() - Method in class org.simbrain.world.dataworld.DataWorld: Dataworlds contain one agent, themselves.
getAgentList() - Method in class org.simbrain.world.odorworld.OdorWorld
getAgentList() - Method in class org.simbrain.world.odorworld.OdorWorldFrame: Return the arraylist of agents.
getAgentList() - Method in class org.simbrain.world.textworld.TextWorld
getAgentList() - Method in class org.simbrain.world.visionworld.VisionWorld
getAgentList() - Method in class org.simbrain.world.World: Return the list of agents for this world.
getAgentName() - Method in class org.simnet.coupling.Coupling: Return the agent name for this coupling.
getAgentPanel() - Method in class org.simbrain.world.odorworld.DialogOdorWorldEntity
getAlignHorizontalAction() - Method in class org.simbrain.network.NetworkActionManager: Return the align horizontal action.
getAlignVerticalAction() - Method in class org.simbrain.network.NetworkActionManager: Return the align vertical action.
getAlpha() - Method in class org.simnet.neurons.TemporalDifferenceNeuron
getAutoFind() - Static method in class org.simbrain.gauge.GaugePreferences
getAutoZoomMode() - Method in class org.simbrain.network.NetworkPanel
getAverage(double[]) - Static method in class org.simbrain.util.SimbrainMath: Helper function for computing mean values of an array of doubles.
getAverageInput() - Method in class org.simnet.interfaces.Neuron
getB() - Method in class org.simnet.neurons.IzhikevichNeuron
getBackgroundColor() - Static method in class org.simbrain.gauge.GaugePreferences
getBackgroundColor() - Method in class org.simbrain.gauge.graphics.GaugePanel
getBackgroundColor() - Method in class org.simbrain.network.NetworkPanel: Get the background color.
getBackgroundColor() - Static method in class org.simbrain.network.NetworkPreferences: Network background color.
getBackgroundColor() - Method in class org.simbrain.world.odorworld.OdorWorld
getBackpropSubnetwork() - Method in class org.simbrain.network.nodes.subnetworks.BackpropNetworkNode
getBackpropSubnetwork() - Method in class org.simbrain.network.nodes.subnetworks.ElmanNetworkNode
getBaseLine() - Method in class org.simnet.neurons.DecayNeuron
getBaseLine() - Method in class org.simnet.synapses.spikeresponders.JumpAndDecay
getBaseLineStrength() - Method in class org.simnet.synapses.ShortTermPlasticitySynapse
getBeta() - Method in class org.simnet.neurons.TemporalDifferenceNeuron
getBias() - Static method in class org.simnet.NetworkPreferences: Return the bias preference setting.
getBias() - Method in class org.simnet.neurons.BinaryNeuron
getBias() - Method in class org.simnet.neurons.LinearNeuron
getBias() - Method in class org.simnet.neurons.SigmoidalNeuron
getBias() - Method in class org.simnet.neurons.ThreeValuedNeuron
getBiases(StandardNetwork) - Method in class org.simnet.networks.Backprop: Returns bias values.
getBites() - Method in class org.simbrain.world.odorworld.AbstractEntity
getBites() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getBites() - Method in class org.simbrain.world.odorworld.Wall: Return the bites.
getBitesToDie() - Method in class org.simbrain.world.odorworld.AbstractEntity
getBitesToDie() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getBitesToDie() - Method in class org.simbrain.world.odorworld.Wall: Return the bites to die.
getBothWaysInteractionModeAction() - Method in class org.simbrain.network.NetworkActionManager: Return the both ways interaction mode action.
getBottomPanel() - Method in class org.simbrain.gauge.graphics.GaugePanel
getBuffer() - Method in class org.simnet.interfaces.Neuron
getBumpRate() - Method in class org.simnet.synapses.ShortTermPlasticitySynapse
getC() - Method in class org.simnet.neurons.IzhikevichNeuron
getC1() - Method in class org.simnet.neurons.TraceNeuron
getC2() - Method in class org.simnet.neurons.TraceNeuron
getCbDistribution() - Method in class org.simbrain.network.dialog.RandomPanel
getCellEditorValue() - Method in class org.simbrain.world.dataworld.ButtonEditor
getCenter() - Method in class org.simbrain.network.nodes.NeuronNode: Return the center of this node (the circle) in global coordinates.
getClampNeurons() - Method in class org.simnet.interfaces.Network
getClampNeuronsMenuItem() - Method in class org.simbrain.network.NetworkActionManager: Return the clamp neurons check box menu item.
getClampToolBar() - Method in class org.simbrain.network.NetworkPanel
getClampWeights() - Method in class org.simnet.interfaces.Network
getClampWeightsMenuItem() - Method in class org.simbrain.network.NetworkActionManager: Return the clamp weight check box menu item.
getClearAction() - Method in class org.simbrain.network.NetworkActionManager: Return the clear action.
getClearAllItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getClearNeuronsAction() - Method in class org.simbrain.network.NetworkActionManager: Return the clear neurons action.
getClearSelectionAction() - Method in class org.simbrain.network.NetworkActionManager: Return the clear selection action.
getClipboardActions() - Method in class org.simbrain.network.NetworkActionManager: Return clipboard actions.
getClipboardEntity() - Static method in class org.simbrain.world.odorworld.WorldClipboard
getClipping() - Method in class org.simnet.neurons.AdditiveNeuron
getClipping() - Method in class org.simnet.neurons.DecayNeuron
getClipping() - Method in class org.simnet.neurons.IACNeuron
getClipping() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getClipping() - Method in class org.simnet.neurons.LinearNeuron
getClipping() - Method in class org.simnet.neurons.SigmoidalNeuron
getClipping() - Method in class org.simnet.util.RandomSource
getClose() - Method in class org.simbrain.gauge.GaugeFrame
getClose() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getCloseNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the close network action.
getClosestDistance(double[]) - Method in class org.simbrain.gauge.core.Dataset: Returns the point closest to a given point.
getClosestIndex(double[]) - Method in class org.simbrain.gauge.core.Dataset: Returns the index of the closest point.
getColor() - Method in class org.simbrain.network.dialog.NetworkDialog: Show the color pallette and get a color.
getColor() - Method in class org.simbrain.world.odorworld.DialogOdorWorld: Show the color pallette and get a color.
getColor() - Method in class org.simbrain.world.odorworld.DialogOdorWorldWall: Show the color pallette and get a color.
getColor() - Method in class org.simbrain.world.textworld.DialogTextWorld: Show the color pallette and get a color.
getColorDataPoints() - Static method in class org.simbrain.gauge.GaugePreferences
getColumnIdentifiers() - Method in class org.simbrain.world.dataworld.TableModel: Return a vector of column identifiers.
getColumnIteration() - Method in class org.simbrain.world.dataworld.DataWorld
getCommandArray() - Method in class org.simnet.coupling.MotorCoupling: Return the array of command names for this motor coupling.
getCommandTargets() - Method in class org.simbrain.world.textworld.TextWorld: Gets commands currently attached to agent.
getCommandTargets() - Method in class org.simbrain.world.visionworld.VisionWorld
getCompetitiveSubnetwork() - Method in class org.simbrain.network.nodes.subnetworks.CompetitiveNetworkNode
getComponent(int, int) - Method in class org.simbrain.gauge.core.Dataset: Get a specific coordinate of a specific datapoint.
getConnectedSynapses() - Method in class org.simbrain.network.nodes.NeuronNode
getContentPane() - Method in class org.simbrain.util.StandardDialog: This method gets the content pane for adding components.
getContextMenu() - Method in class org.simbrain.network.NetworkPanel: Return the context menu for this network panel.
getContextMenu() - Method in class org.simbrain.network.nodes.NeuronNode
getContextMenu() - Method in class org.simbrain.network.nodes.ScreenElement: Return a context menu specific to this screen element.
getContextMenu() - Method in class org.simbrain.network.nodes.SubnetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.BackpropNetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.CompetitiveNetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.ElmanNetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.HopfieldNetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.LMSNetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.StandardNetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.WTANetworkNode
getContextMenu() - Method in class org.simbrain.network.nodes.SynapseNode
getCoolColor() - Method in class org.simbrain.network.NetworkPanel
getCoolColor() - Static method in class org.simbrain.network.NetworkPreferences: Network cool node color.
getCopyAction() - Method in class org.simbrain.network.NetworkActionManager: Return the copy action.
getCopyItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getCopyItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getCoupledNodes() - Method in class org.simbrain.network.NetworkPanel: Returns model network elements corresponding to selected screen elements.
getCoupling() - Method in class org.simnet.coupling.CouplingMenuItem: Return the coupling for this menu item.
getCouplingList() - Method in class org.simbrain.workspace.Workspace
getCouplingList() - Method in class org.simnet.interfaces.Network: Returns a list of all couplings associated with neurons in this network.
getCovariance(int, int) - Method in class org.simbrain.gauge.core.Dataset: Returns the covariance of the ith component of the dataset with respect to the jth component.
getCovarianceMatrix() - Method in class org.simbrain.gauge.core.Dataset: Returns a covariance matrix for the dataset.
getCurrentBackpropDirectory() - Static method in class org.simbrain.network.NetworkPreferences: Current backprop files directory.
getCurrentCloseness() - Method in class org.simbrain.gauge.core.ProjectSammon
getCurrentDirectory() - Static method in class org.simbrain.gauge.GaugePreferences
getCurrentDirectory() - Method in class org.simbrain.network.NetworkPanel: Returns a string representation of the current directory.
getCurrentDirectory() - Static method in class org.simbrain.network.NetworkPreferences: Current network files directory.
getCurrentDirectory() - Method in class org.simbrain.network.NetworkSerializer
getCurrentDirectory() - Static method in class org.simbrain.workspace.WorkspacePreferences: Return the current workspace directory.
getCurrentDirectory() - Static method in class org.simbrain.world.dataworld.DataWorldPreferences: Return the current directory preference setting.
getCurrentDirectory() - Static method in class org.simbrain.world.odorworld.OdorWorldPreferences: Return the current directory.
getCurrentDirectory() - Method in class org.simbrain.world.textworld.TextWorldFrame
getCurrentFile() - Method in class org.simbrain.gauge.graphics.GaugePanel
getCurrentFile() - Method in class org.simbrain.network.NetworkSerializer: Get a reference to the current network file.
getCurrentFile() - Method in class org.simbrain.workspace.Workspace
getCurrentFile() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getCurrentFile() - Method in class org.simbrain.world.odorworld.OdorWorldFrame: Return the current file.
getCurrentLine() - Method in class org.simbrain.world.textworld.TextWorld: Returns the current line of text.
getCurrentLocation() - Method in class org.simbrain.util.SFileChooser: Returns the directory this chooser is in.
getCurrentProjector() - Method in class org.simbrain.gauge.core.Gauge
getCurrentProjectorC() - Method in class org.simbrain.gauge.core.Gauge
getCurrentRow() - Method in class org.simbrain.world.dataworld.DataWorld
getCursor() - Method in class org.simbrain.network.EditMode: Return the cursor for this edit mode.
getCutAction() - Method in class org.simbrain.network.NetworkActionManager: Return the cut action.
getCutItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getCutItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getD() - Method in class org.simbrain.gauge.core.ProjectSammon
getD() - Method in class org.simnet.neurons.IzhikevichNeuron
getDataset() - Method in class org.simbrain.gauge.core.Dataset
getDataWorldChangeList() - Method in class org.simbrain.workspace.Workspace
getDataWorldList() - Method in class org.simbrain.workspace.Workspace
getDataWorldList() - Method in class org.simbrain.workspace.WorkspaceSerializer
getDeadEntityList() - Method in class org.simbrain.world.odorworld.OdorWorld
getDecay() - Static method in class org.simnet.NetworkPreferences: Return the decay preference setting.
getDecay() - Method in class org.simnet.neurons.IACNeuron
getDecayAmount() - Method in class org.simnet.neurons.DecayNeuron
getDecayFraction() - Method in class org.simnet.neurons.DecayNeuron
getDecayFunction() - Method in class org.simbrain.world.odorworld.Stimulus: Return the decay function.
getDecayFunctionIndex(String) - Method in class org.simbrain.world.odorworld.Stimulus: Helper function for combo boxes.
getDecayFunctions() - Static method in class org.simbrain.world.odorworld.Stimulus: Return the decay functions.
getDecayRate() - Method in class org.simnet.synapses.ShortTermPlasticitySynapse
getDecayRate() - Method in class org.simnet.synapses.spikeresponders.JumpAndDecay
getDecayRate() - Method in class org.simnet.synapses.spikeresponders.RiseAndDecay
getDefaultAddMethod() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultAutoFind() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultBackgroundColor() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultBackgroundColor() - Static method in class org.simbrain.network.NetworkPreferences: Network background color.
getDefaultBackpropDirectory() - Static method in class org.simbrain.network.NetworkPreferences: Current backprop files directory.
getDefaultColor() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultColor() - Method in class org.simbrain.gauge.graphics.GaugePanel
getDefaultColorDataPoints() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultCoolColor() - Static method in class org.simbrain.network.NetworkPreferences: Network cool node color.
getDefaultCurrentDirectory() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultCurrentDirectory() - Static method in class org.simbrain.network.NetworkPreferences: Current network files directory.
getDefaultCurrentDirectory() - Static method in class org.simbrain.workspace.WorkspacePreferences: Return the default current workspace directory.
getDefaultCurrentDirectory() - Static method in class org.simbrain.world.dataworld.DataWorldPreferences: Return the default current directory.
getDefaultCurrentDirectory() - Static method in class org.simbrain.world.odorworld.OdorWorldPreferences: Return the default current directory.
getDefaultDefaultColor() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultDefaultFile() - Static method in class org.simbrain.workspace.WorkspacePreferences: Return the default defalut file.
getDefaultDefaultProjector() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultEpsilon() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultExcitatoryColor() - Static method in class org.simbrain.network.NetworkPreferences: Network excitatory color.
getDefaultFile() - Static method in class org.simbrain.workspace.WorkspacePreferences: Return the default file.
getDefaultHiDim1() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultHiDim2() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultHotColor() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultHotColor() - Static method in class org.simbrain.network.NetworkPreferences: Network hot node color.
getDefaultInhibitoryColor() - Static method in class org.simbrain.network.NetworkPreferences: Network inhibitory color.
getDefaultInputs() - Method in class org.simnet.networks.LMSNetwork
getDefaultIterationsBetweenUpdates() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultLassoColor() - Static method in class org.simbrain.network.NetworkPreferences: Network lasso color.
getDefaultLineColor() - Static method in class org.simbrain.network.NetworkPreferences: Network line color.
getDefaultMaxDiameter() - Static method in class org.simbrain.network.NetworkPreferences: Network max node radius.
getDefaultMinDiameter() - Static method in class org.simbrain.network.NetworkPreferences: Network min node radius.
getDefaultNeuron() - Method in class org.simnet.networks.Backprop: Return the default neuron, with settings, for backprop nets.
getDefaultNeuron() - Method in class org.simnet.networks.LMSNetwork: Return the default neuron, with settings, for LMS nets.
getDefaultNudgeAmount() - Static method in class org.simbrain.network.NetworkPreferences: Network nudging.
getDefaultOutputs() - Method in class org.simnet.networks.LMSNetwork
getDefaultPerturbationAmount() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultPointSize() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultPrecision() - Static method in class org.simbrain.network.NetworkPreferences: Network precision.
getDefaultProjector() - Method in class org.simbrain.gauge.core.Gauge
getDefaultProjector() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultSelectionColor() - Static method in class org.simbrain.network.NetworkPreferences: Network selection color.
getDefaultShowError() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultShowStatusBar() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultSignalColor() - Static method in class org.simbrain.network.NetworkPreferences: Network signal synapse color.
getDefaultSpikingColor() - Static method in class org.simbrain.network.NetworkPreferences: Returns the default spiking synapse color.
getDefaultTimeStep() - Static method in class org.simbrain.network.NetworkPreferences: Netowork time step.
getDefaultTimeUnits() - Static method in class org.simbrain.network.NetworkPreferences: Network time units.
getDefaultTolerance() - Static method in class org.simbrain.gauge.GaugePreferences
getDefaultUsingIndent() - Static method in class org.simbrain.network.NetworkPreferences: Network files indenting.
getDefaultWeightValues() - Static method in class org.simbrain.network.NetworkPreferences: Network weight values.
getDefaultZeroWeightColor() - Static method in class org.simbrain.network.NetworkPreferences: Network zero weight color.
getDelay() - Method in class org.simnet.interfaces.Synapse
getDeleteItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getDepth() - Method in class org.simnet.interfaces.Network
getDescription() - Method in class org.simbrain.util.SFileChooser.FileFilter
getDIAMETER() - Static method in class org.simbrain.network.nodes.NeuronNode
getDifference() - Method in class org.simnet.neurons.TraceNeuron: Returns the difference betwen the predicted and actual output of this neuron.
getDifferenceHistory() - Method in class org.simnet.neurons.TraceNeuron: Returns the difference betwen the predicted and actual output of this neuron.
getDimensions() - Method in class org.simbrain.gauge.core.Dataset
getDir(File) - Static method in class org.simbrain.util.Utils: Get the directory component of a file.
getDispersion() - Method in class org.simbrain.world.odorworld.Stimulus: Return the dispersion.
getDistance(int, int) - Method in class org.simbrain.gauge.core.Dataset: Get the distance between two points.
getDistance(double[], double[]) - Method in class org.simbrain.gauge.core.Dataset: Returns tyhe euclidean distance between two points.
getDistances() - Method in class org.simbrain.gauge.core.Dataset: Returns a matrix of interpoint distances, between the points in the dataset.
getDistributionIndex() - Method in class org.simnet.util.RandomSource
getDoubleMatrix(File) - Static method in class org.simbrain.util.Utils: Read a csv (comma-separated-values) files.
getDoubles() - Method in class org.simbrain.gauge.core.Dataset: Returns a matrix of double, one row for each datapoint, representing the dataset.
getDoubleStrings() - Method in class org.simbrain.gauge.core.Dataset: Returns a matrix of strings, one row for each datapoint, representing the dataset.
getDownstairs() - Method in class org.simbrain.gauge.core.Gauge: Convenience method to get downstairs dataset.
getDownstairs() - Method in class org.simbrain.gauge.core.Projector
getDownstairsText() - Method in class org.simbrain.gauge.graphics.ToolTipTextUpdater: Get the low dimensional coordinates of a point.
getDstar() - Method in class org.simbrain.gauge.core.ProjectSammon
getDstarSum() - Method in class org.simbrain.gauge.core.ProjectSammon
getE() - Method in class org.simbrain.gauge.core.ProjectSammon
getEdible() - Method in class org.simbrain.world.odorworld.AbstractEntity
getEdible() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getEdible() - Method in class org.simbrain.world.odorworld.Wall: Return the edible.
getEditMenu() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getEditMode() - Method in class org.simbrain.network.NetworkPanel: Return the current edit mode for this network panel.
getEditToolBar() - Method in class org.simbrain.network.NetworkPanel
getEntityList() - Method in class org.simbrain.world.odorworld.OdorWorld
getEntityNames() - Method in class org.simbrain.world.odorworld.OdorWorld
getEpochs() - Method in class org.simnet.networks.Backprop
getEpochs() - Method in class org.simnet.networks.LMSNetwork
getEpsilon() - Method in class org.simbrain.gauge.core.ProjectSammon
getEpsilon() - Method in class org.simbrain.gauge.core.Settings
getEpsilon() - Static method in class org.simbrain.gauge.GaugePreferences
getEpsilon() - Method in class org.simnet.networks.Competitive: Return the epsilon.
getError() - Method in class org.simbrain.gauge.core.Gauge: Returns error, which is only set by some projection functions.
getError() - Method in class org.simnet.networks.Backprop
getErrorInterval() - Method in class org.simnet.networks.Backprop
getEta() - Method in class org.simnet.networks.Backprop
getEta() - Method in class org.simnet.networks.LMSNetwork
getExcitatoryColor() - Method in class org.simbrain.network.NetworkPanel
getExcitatoryColor() - Static method in class org.simbrain.network.NetworkPreferences: Network excitatory color.
getExportHigh() - Method in class org.simbrain.gauge.GaugeFrame
getExportLow() - Method in class org.simbrain.gauge.GaugeFrame
getFALSE() - Static method in class org.simbrain.util.TristateDropDown
getFanIn() - Method in class org.simnet.interfaces.Neuron
getFanOut() - Method in class org.simnet.interfaces.Neuron
getFileMenu() - Method in class org.simbrain.gauge.GaugeFrame
getFileMenu() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getFileOpsMenu() - Method in class org.simbrain.gauge.GaugeFrame
getFiringProbability() - Method in class org.simnet.neurons.StochasticNeuron
getFiringThreshold() - Method in class org.simnet.synapses.ShortTermPlasticitySynapse
getFlatNetworkList() - Method in class org.simnet.interfaces.Network: Create "flat" list of all subnetworks.
getFlatNeuronList() - Method in class org.simnet.interfaces.Network: Create "flat" list of neurons, which includes the top-level neurons plus all subnet neurons.
getFlatSynapseList() - Method in class org.simnet.interfaces.Network: Create "flat" list of synapses, which includes the top-level synapses plus all subnet synapses.
getFrequency() - Method in class org.simnet.neurons.SinusoidalNeuron
getFunctionList() - Static method in class org.simnet.neurons.SigmoidalNeuron
getFunctionList() - Static method in class org.simnet.util.RandomSource
getGauge() - Method in class org.simbrain.gauge.graphics.GaugePanel
getGauge(String) - Method in class org.simbrain.workspace.Workspace: Return a named gauge, null otherwise.
getGaugeAssociatedWithNetwork(String) - Method in class org.simbrain.workspace.Workspace: Return the gauge associated with a network (by name), null otherwise.
getGaugeChangeList() - Method in class org.simbrain.workspace.Workspace
getGaugedVars() - Method in class org.simbrain.gauge.core.Gauge
getGaugedVars() - Method in class org.simbrain.gauge.GaugeFrame
getGaugeList() - Method in class org.simbrain.workspace.Workspace
getGaugeList() - Method in class org.simbrain.workspace.WorkspaceSerializer
getGaugeMenu(ActionListener) - Method in class org.simbrain.workspace.Workspace: Returns a menu which shows what gauges are currently in the workspace Returns null if ther are no gauges.
getGaugePanel() - Method in class org.simbrain.gauge.GaugeFrame
getGauges(NetworkFrame) - Method in class org.simbrain.workspace.Workspace: Get those gauges gauged by the given network.
getGaugeValue() - Method in interface org.simbrain.gauge.GaugeSource
getGaugeValue() - Method in class org.simnet.interfaces.Neuron
getGaugeValue() - Method in class org.simnet.interfaces.Synapse
getGeneralPrefs() - Method in class org.simbrain.gauge.GaugeFrame
getGenericPath() - Method in class org.simbrain.gauge.GaugeFrame
getGenericPath() - Method in class org.simbrain.network.NetworkFrame: Return the platform-specific path for this network frame.
getGenericPath() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getGenericPath() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getGp() - Method in class org.simbrain.gauge.graphics.KeyEventHandler
getGp() - Method in class org.simbrain.gauge.graphics.MouseEventHandler
getGraphicsPrefs() - Method in class org.simbrain.gauge.GaugeFrame
getGrowthRate() - Method in class org.simnet.neurons.LogisticNeuron
getHeight() - Method in class org.simbrain.world.odorworld.AbstractEntity
getHeight() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getHeight() - Method in class org.simbrain.world.odorworld.Wall: Return the height.
getHelp() - Method in class org.simnet.interfaces.Neuron: Returns help information related to this neuron type.
getHelpItem() - Method in class org.simbrain.gauge.GaugeFrame
getHelpItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getHelpMenu() - Method in class org.simbrain.gauge.GaugeFrame
getHelpMenu() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getHid() - Method in class org.simnet.networks.Backprop
getHiD1() - Method in class org.simbrain.gauge.core.ProjectCoordinate
getHiD1() - Method in class org.simbrain.gauge.core.Settings
getHiD2() - Method in class org.simbrain.gauge.core.ProjectCoordinate
getHiD2() - Method in class org.simbrain.gauge.core.Settings
getHiDim1() - Static method in class org.simbrain.gauge.GaugePreferences
getHiDim2() - Static method in class org.simbrain.gauge.GaugePreferences
getHighDimension() - Method in class org.simbrain.gauge.core.ProjectSammon
getHighestDimensionalStimulus() - Method in class org.simbrain.world.odorworld.OdorWorld: Go through entities in this world and find the one with the greatest number of dimensions.
getHilightColor() - Method in class org.simbrain.world.textworld.TextWorld
getHopfieldSubnetwork() - Method in class org.simbrain.network.nodes.subnetworks.HopfieldNetworkNode
getHotColor() - Static method in class org.simbrain.gauge.GaugePreferences
getHotColor() - Method in class org.simbrain.gauge.graphics.GaugePanel
getHotColor() - Method in class org.simbrain.network.NetworkPanel
getHotColor() - Static method in class org.simbrain.network.NetworkPreferences: Network hot node color.
getHotPoint() - Method in class org.simbrain.gauge.graphics.GaugePanel
getId() - Method in interface org.simbrain.gauge.GaugeSource
getId() - Method in class org.simbrain.network.nodes.NeuronNode
getId() - Method in class org.simnet.interfaces.Network: Return the id of this neuron.
getId() - Method in class org.simnet.interfaces.Neuron
getId() - Method in class org.simnet.interfaces.Synapse
getImage(String) - Static method in class org.simbrain.resource.ResourceManager: Retrieve an Image based on its file name.
getImageIcon(String) - Static method in class org.simbrain.resource.ResourceManager: Retrieve an ImageIcon based on its file name.
getImageName() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getImageNameIndex(String) - Method in class org.simbrain.world.odorworld.OdorWorldEntity: Helper function for combo boxes.
getImageNames() - Static method in class org.simbrain.world.odorworld.OdorWorldEntity: Names of images.
getImplementationIndex() - Method in class org.simnet.neurons.SigmoidalNeuron
getImportCSV() - Method in class org.simbrain.gauge.GaugeFrame
getIncrement() - Method in class org.simnet.interfaces.Neuron
getIncrement() - Method in class org.simnet.interfaces.Synapse
getIndents() - Method in class org.simnet.interfaces.Network
getIndex() - Method in class org.simbrain.gauge.graphics.PNodeDatapoint
getInhibitoryColor() - Method in class org.simbrain.network.NetworkPanel
getInhibitoryColor() - Static method in class org.simbrain.network.NetworkPreferences: Network inhibitory color.
getInOutMode() - Method in class org.simbrain.network.NetworkPanel
getInp() - Method in class org.simnet.networks.Backprop
getInputNeurons() - Method in class org.simnet.interfaces.Network: Returns all Input Neurons.
getInputThreshold() - Method in class org.simnet.synapses.ShortTermPlasticitySynapse
getInputValue() - Method in class org.simnet.interfaces.Neuron
getInteractionMode() - Method in class org.simnet.interfaces.Network: Return the current interaction mode for this network panel.
getInteractionModeActions() - Method in class org.simbrain.network.NetworkActionManager: Return a list of interaction mode actions.
getIterateNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the iterate network action.
getIterationsBetweenUpdates() - Static method in class org.simbrain.gauge.GaugePreferences
getJumpHeight() - Method in class org.simnet.synapses.spikeresponders.JumpAndDecay
getKthNearestNeighbor(int, double[]) - Method in class org.simbrain.gauge.core.Dataset: Returns the k'th nearest neighbor.
getKthVariantDimension(int) - Method in class org.simbrain.gauge.core.Dataset: Returns the k'th most variant dimesion.
getLabel() - Method in class org.simbrain.network.nodes.SubnetworkNode: Return the label for this subnetwork node.
getLabel() - Method in class org.simnet.synapses.SignalSynapse
getLambda() - Method in class org.simnet.neurons.AdditiveNeuron
getLassoColor() - Static method in class org.simbrain.network.NetworkPreferences: Network lasso color.
getLastClickedPosition() - Method in class org.simbrain.network.NetworkPanel
getLastDataWorld() - Method in class org.simbrain.workspace.Workspace
getLastGauge() - Method in class org.simbrain.workspace.Workspace
getLastNetwork() - Method in class org.simbrain.workspace.Workspace
getLastOdorWorld() - Method in class org.simbrain.workspace.Workspace
getLastSelectedNeuron() - Method in class org.simbrain.network.NetworkPanel
getLayoutName() - Method in class org.simnet.layouts.GridLayout
getLayoutName() - Method in class org.simnet.layouts.LayersLayout
getLayoutName() - Method in interface org.simnet.layouts.Layout
getLayoutName() - Method in class org.simnet.layouts.LineLayout
getLeakyEpsilon() - Method in class org.simnet.networks.Competitive: Return leaky epsilon value.
getLearningRate() - Method in class org.simnet.neurons.LMSNeuron
getLearningRate() - Method in class org.simnet.synapses.Hebbian
getLearningRate() - Method in class org.simnet.synapses.HebbianThresholdSynapse
getLearningRate() - Method in class org.simnet.synapses.OjaSynapse
getLearningRate() - Method in class org.simnet.synapses.SubtractiveNormalizationSynapse
getLearningRate() - Method in class org.simnet.synapses.TraceSynapse
getLearningRule() - Static method in class org.simnet.NetworkPreferences: Return the learning rule preference setting.
getLeftWhisker() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getLineColor() - Method in class org.simbrain.network.NetworkPanel
getLineColor() - Static method in class org.simbrain.network.NetworkPreferences: Network line color.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.simbrain.util.ComboBoxRenderer: Puts images next to images in a combo box.
getListenerList() - Method in class org.simnet.interfaces.Network: Return the top level listener list.
getLMSSubnetwork() - Method in class org.simbrain.network.nodes.subnetworks.LMSNetworkNode
getLocation() - Method in class org.simbrain.world.odorworld.AbstractEntity
getLocation() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getLocation() - Method in class org.simbrain.world.odorworld.Wall: Return the location.
getLoseValue() - Method in class org.simnet.networks.Competitive: Return the loser value.
getLoseValue() - Method in class org.simnet.networks.WinnerTakeAll
getLowDimension() - Method in class org.simbrain.gauge.core.ProjectSammon
getLowerBound() - Method in class org.simbrain.world.dataworld.DataWorld
getLowerBound() - Method in class org.simnet.interfaces.Neuron
getLowerBound() - Method in class org.simnet.interfaces.Synapse
getLowerBound() - Method in class org.simnet.util.RandomSource
getLowerThreshold() - Method in class org.simnet.neurons.ThreeValuedNeuron
getLowerValue() - Method in class org.simnet.neurons.ThreeValuedNeuron
getMainToolBar() - Method in class org.simbrain.network.NetworkPanel
getMarqueeColor() - Static method in class org.simbrain.network.nodes.SelectionMarquee
getMaxDiameter() - Method in class org.simbrain.network.NetworkPanel
getMaxDiameter() - Static method in class org.simbrain.network.NetworkPreferences: Network max node radius.
getMaximum(double[]) - Static method in class org.simbrain.util.SimbrainMath: Finds the largest value in a vector array.
getMaximumDistance() - Method in class org.simbrain.gauge.core.Dataset: Get the maximimum interpoint distance between points in the dataset.
getMaximumResponse() - Method in class org.simnet.synapses.spikeresponders.RiseAndDecay
getMb() - Method in class org.simbrain.gauge.GaugeFrame
getMean(int) - Method in class org.simbrain.gauge.core.Dataset: Returns the mean of the dataset on a given dimension.
getMean() - Method in class org.simnet.util.RandomSource
getMenu() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getMiddleValue() - Method in class org.simnet.neurons.ThreeValuedNeuron
getMinDiameter() - Method in class org.simbrain.network.NetworkPanel
getMinDiameter() - Static method in class org.simbrain.network.NetworkPreferences: Network min node radius.
getMinimumDistance() - Method in class org.simbrain.gauge.core.Dataset: Get the minimum interpoint distance between points in the dataset.
getModel() - Method in class org.simbrain.world.dataworld.DataWorld
getMomentum() - Static method in class org.simnet.NetworkPreferences: Return the momentum preference setting.
getMotorCommandMenu(ActionListener, NeuronNode) - Method in class org.simbrain.workspace.Workspace: Returns a menu which shows what possible sources there are for motor couplings in this workspace.
getMotorCommandMenu(ActionListener) - Method in class org.simbrain.world.dataworld.DataWorld: Unused stub; data worlds don't receive commands.
getMotorCommandMenu(ActionListener) - Method in class org.simbrain.world.odorworld.OdorWorld: Returns a menu with the motor commands available to this agent.
getMotorCommandMenu(ActionListener) - Method in class org.simbrain.world.textworld.TextWorld
getMotorCommandMenu(ActionListener) - Method in class org.simbrain.world.visionworld.VisionWorld: Not yet implemented.
getMotorCommandMenu(ActionListener) - Method in class org.simbrain.world.World: Return a menu of motor commands for this world and register the specified action listener as an action listener for the menu items in the returned menu.
getMotorCoupling() - Method in class org.simnet.interfaces.Neuron
getMovementIncrement() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getMu() - Method in class org.simnet.networks.Backprop
getName() - Method in class org.simbrain.gauge.GaugeFrame
getName() - Method in interface org.simbrain.world.Agent: Return the name of this agent.
getName() - Method in class org.simbrain.world.dataworld.DataWorld
getName() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getName() - Static method in class org.simnet.neurons.AdditiveNeuron
getName() - Static method in class org.simnet.neurons.BinaryNeuron
getName() - Static method in class org.simnet.neurons.ClampedNeuron
getName() - Static method in class org.simnet.neurons.DecayNeuron
getName() - Static method in class org.simnet.neurons.ExponentialDecayNeuron
getName() - Static method in class org.simnet.neurons.IACNeuron
getName() - Static method in class org.simnet.neurons.IntegrateAndFireNeuron
getName() - Static method in class org.simnet.neurons.IzhikevichNeuron
getName() - Static method in class org.simnet.neurons.LinearNeuron
getName() - Static method in class org.simnet.neurons.LMSNeuron
getName() - Static method in class org.simnet.neurons.LogisticNeuron
getName() - Static method in class org.simnet.neurons.NakaRushtonNeuron
getName() - Static method in class org.simnet.neurons.RandomNeuron
getName() - Static method in class org.simnet.neurons.RunningAverageNeuron
getName() - Static method in class org.simnet.neurons.SigmoidalNeuron
getName() - Static method in class org.simnet.neurons.SinusoidalNeuron
getName() - Static method in class org.simnet.neurons.StochasticNeuron
getName() - Static method in class org.simnet.neurons.TemporalDifferenceNeuron
getName() - Static method in class org.simnet.neurons.ThreeValuedNeuron
getName() - Static method in class org.simnet.neurons.TraceNeuron
getName() - Static method in class org.simnet.synapses.ClampedSynapse
getName() - Static method in class org.simnet.synapses.Hebbian
getName() - Static method in class org.simnet.synapses.HebbianThresholdSynapse
getName() - Static method in class org.simnet.synapses.OjaSynapse
getName() - Static method in class org.simnet.synapses.RandomSynapse
getName() - Static method in class org.simnet.synapses.ShortTermPlasticitySynapse
getName() - Static method in class org.simnet.synapses.SignalSynapse
getName() - Static method in class org.simnet.synapses.spikeresponders.JumpAndDecay
getName() - Static method in class org.simnet.synapses.spikeresponders.RiseAndDecay
getName() - Static method in class org.simnet.synapses.spikeresponders.Step
getName() - Static method in class org.simnet.synapses.SubtractiveNormalizationSynapse
getName() - Static method in class org.simnet.synapses.TraceSynapse
getNameFromPath(String) - Static method in class org.simbrain.util.Utils: Extract file name from a path description.
getNeitherWayInteractionModeAction() - Method in class org.simbrain.network.NetworkActionManager: Return the neither way interaction mode action.
getNetwork() - Method in class org.simbrain.network.NetworkPanel
getNetwork(String) - Method in class org.simbrain.workspace.Workspace: Return a named network, null otherwise.
getNetwork(int) - Method in class org.simnet.interfaces.Network
getNetworkChangeList() - Method in class org.simbrain.workspace.Workspace
getNetworkControlActions() - Method in class org.simbrain.network.NetworkActionManager: Return a list of network control actions.
getNetworkEditingActions() - Method in class org.simbrain.network.NetworkActionManager: Return a list of network editing actions.
getNetworkFrame() - Method in class org.simbrain.network.NetworkPanel
getNetworkList() - Method in class org.simbrain.workspace.Workspace
getNetworkList() - Method in class org.simbrain.workspace.WorkspaceSerializer
getNetworkList() - Method in class org.simnet.interfaces.Network
getNetworkModeActions() - Method in class org.simbrain.network.NetworkActionManager: Return a list of network mode actions.
getNetworkName() - Method in class org.simbrain.gauge.GaugedVariables
getNetworkName() - Method in class org.simnet.coupling.Coupling: Return the network name for this coupling.
getNetworkPanel() - Method in class org.simbrain.network.NetworkFrame: Return the network panel for this network frame.
getNetworkPanel() - Method in class org.simbrain.network.NetworkSelectionEvent: Return the source of this event as a NetworkPanel.
getNetworkPanel() - Method in class org.simbrain.network.nodes.ScreenElement: Return the network panel for this screen element.
getNetworkParent() - Method in class org.simnet.interfaces.Network
getNetworkThread() - Method in class org.simnet.interfaces.Network
getNetworkToWorldInteractionModeAction() - Method in class org.simbrain.network.NetworkActionManager: Return the network to world interaction mode action.
getNeuron() - Method in class org.simbrain.network.nodes.NeuronNode: Return the neuron for this neuron node.
getNeuron() - Method in class org.simnet.coupling.Coupling: Return the neuron for this coupling.
getNeuron(int) - Method in class org.simnet.interfaces.Network
getNeuron(String) - Method in class org.simnet.interfaces.Network: Find a neuron with a given string id.
getNeuron() - Method in class org.simnet.interfaces.NetworkEvent
getNeuronCount() - Method in class org.simnet.interfaces.Network
getNeuronLayout() - Method in class org.simbrain.network.dialog.network.layout.AbstractLayoutPanel
getNeuronLayout() - Method in class org.simbrain.network.dialog.network.layout.GridLayoutPanel
getNeuronLayout() - Method in class org.simbrain.network.dialog.network.layout.LayoutPanel: Returns the layout that was built using this panel.
getNeuronLayout() - Method in class org.simbrain.network.dialog.network.layout.LineLayoutPanel
getNeuronList() - Method in class org.simbrain.network.dialog.neuron.AbstractNeuronPanel
getNeuronList() - Method in class org.simnet.interfaces.Network
getNeuronName() - Method in class org.simnet.coupling.Coupling: Return the neuron name for this coupling.
getNeuronNodeFilter() - Static method in class org.simbrain.network.filters.Filters: Return the neuron node filter.
getNeuronNodes() - Method in class org.simbrain.network.NetworkPanel: Return a collection of all neuron nodes.
getNeuronOrSynapseNodeFilter() - Static method in class org.simbrain.network.filters.Filters: Return the neuron or synapse node filter.
getNeuronTypeIndex(String) - Static method in class org.simnet.interfaces.Neuron: Helper function for combo boxes.
getNewBackpropNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the new backprop network action.
getNewCompetitiveNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the new competitive network action.
getNewElmanNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the new elman network action.
getNewHopfieldNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the new discrete hopfield network action.
getNewLMSNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the new LMSNetwork network action.
getNewNeuronAction() - Method in class org.simbrain.network.NetworkActionManager: Return the new neuron action.
getNewStandardNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the standard network action.
getNewWTANetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the new winner take all network action.
getNHidden() - Method in class org.simnet.networks.Backprop
getNHidden() - Method in class org.simnet.networks.Elman
getNInput() - Method in class org.simnet.networks.Elman
getNInputs() - Method in class org.simnet.networks.Backprop
getNodeList() - Method in class org.simbrain.network.NetworkPanel: Used by Castor.
getNoiseGenerator() - Method in class org.simnet.neurons.AdditiveNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.DecayNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.IACNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.IzhikevichNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.LinearNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.NakaRushtonNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.SigmoidalNeuron
getNoiseGenerator() - Method in class org.simnet.neurons.SinusoidalNeuron
getNoiseLevel() - Method in class org.simbrain.world.odorworld.Stimulus: Return the noise level.
getNormalizationFactor() - Method in class org.simnet.synapses.OjaSynapse
getNormalizeInputs() - Method in class org.simnet.networks.Competitive: Return the normalize inputs value.
getNOutputs() - Method in class org.simnet.networks.Backprop
getNrnIncrement() - Static method in class org.simnet.NetworkPreferences: Return the neuron increment preference setting.
getNrnLowerBound() - Static method in class org.simnet.NetworkPreferences: Return the neuron lower bound preference setting.
getNrnUpperBound() - Static method in class org.simnet.NetworkPreferences: Return the neuron upper bound preference setting.
getNudgeAmount() - Method in class org.simbrain.network.NetworkPanel
getNudgeAmount() - Static method in class org.simbrain.network.NetworkPreferences: Network nudging.
getNULL() - Static method in class org.simbrain.util.TristateDropDown
getNumberOfActiveInputs(int) - Method in class org.simnet.interfaces.Neuron: Returns the number of neurons attaching to this one which have activity above a specified threshold.
getNumberOfPastes() - Method in class org.simbrain.network.NetworkPanel
getNumIterationsBetweenUpdate() - Method in class org.simbrain.gauge.graphics.GaugePanel
getNumNeurons() - Method in class org.simnet.networks.Competitive
getNumNeurons() - Method in class org.simnet.networks.StandardNetwork: Returns the initial number of neurons.
getNumPixelsColumn() - Method in class org.simbrain.world.visionworld.VisionWorld
getNumPixelsRow() - Method in class org.simbrain.world.visionworld.VisionWorld
getNumPoints() - Method in class org.simbrain.gauge.core.Dataset
getNumPoints() - Method in class org.simbrain.gauge.core.ProjectSammon
getNumUnits() - Method in class org.simnet.networks.Hopfield
getNumUnits() - Method in class org.simnet.networks.WinnerTakeAll
getNumVariables() - Method in class org.simbrain.gauge.GaugedVariables: Returns the number of gauged variables.
getObjectDraggingInitiatesMovement() - Method in class org.simbrain.world.odorworld.OdorWorld
getObjectInhibitsMovement() - Method in class org.simbrain.world.odorworld.OdorWorld
getObjectPropsItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getObjectSize() - Method in class org.simbrain.world.odorworld.OdorWorld
getOdorWorldChangeList() - Method in class org.simbrain.workspace.Workspace
getOdorWorldList() - Method in class org.simbrain.workspace.Workspace
getOdorWorldList() - Method in class org.simbrain.workspace.WorkspaceSerializer
getOldNeuron() - Method in class org.simnet.interfaces.NetworkEvent
getOldSelection() - Method in class org.simbrain.network.NetworkSelectionEvent: Return the old selection.
getOldSynapse() - Method in class org.simnet.interfaces.NetworkEvent
getOnOffBox() - Method in class org.simbrain.gauge.graphics.GaugePanel
getOpen() - Method in class org.simbrain.gauge.GaugeFrame
getOpenCloseActions() - Method in class org.simbrain.network.NetworkActionManager: Return open and save actions.
getOpenItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getOpenNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the open network action.
getOrientation() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getOrientationRad() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getOut() - Method in class org.simnet.networks.Backprop
getOutlineStroke() - Method in class org.simbrain.network.nodes.SubnetworkNode: Return the outline stroke for this subnetwork node.
getOutlineStrokePaint() - Method in class org.simbrain.network.nodes.SubnetworkNode: Return the outline stroke paint for this subnetwork node.
getOutputFunction() - Static method in class org.simnet.NetworkPreferences: Return the output function preference setting.
getOutputNeurons() - Method in class org.simnet.interfaces.Network: Returns all Output Neurons.
getOutputSignal() - Static method in class org.simnet.NetworkPreferences: Return the output signal preference setting.
getOutputThreshold() - Static method in class org.simnet.NetworkPreferences: Return the output threshold preference setting.
getOutputThreshold() - Method in class org.simnet.synapses.HebbianThresholdSynapse
getOutputThresholdMomentum() - Method in class org.simnet.synapses.HebbianThresholdSynapse
getPanEditModeAction() - Method in class org.simbrain.network.NetworkActionManager: Return the pan edit mode action.
getParent() - Method in class org.simbrain.gauge.GaugedVariables
getParent() - Method in class org.simbrain.world.odorworld.AbstractEntity
getParent() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getParent() - Method in class org.simbrain.world.odorworld.Wall: Return the parent world.
getParent() - Method in class org.simnet.interfaces.SpikeResponder
getParent() - Method in class org.simnet.interfaces.Synapse
getParentFrame() - Method in class org.simbrain.world.dataworld.DataWorld
getParentFrame() - Method in class org.simbrain.world.odorworld.OdorWorld
getParentFrame() - Method in class org.simbrain.world.textworld.TextWorld
getParentFrame() - Method in class org.simbrain.world.visionworld.VisionWorld
getParentNetwork() - Method in class org.simnet.interfaces.Neuron
getParentWorkspace() - Method in class org.simbrain.world.odorworld.OdorWorld: Return the parent workspace.
getParentWorld() - Method in interface org.simbrain.world.Agent: Return the parent world for this agent.
getParentWorld() - Method in class org.simbrain.world.dataworld.DataWorld: Dataworlds are agents, hence this returns itself.
getParentWorld() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getParentWorld() - Method in class org.simbrain.world.visionworld.VisionWorld
getParseChar() - Method in class org.simbrain.world.textworld.TextWorld
getPartialSum() - Method in class org.simbrain.gauge.core.ProjectSammon
getPasteAction() - Method in class org.simbrain.network.NetworkActionManager: Return the paste action.
getPasteItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getPasteItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getPath() - Method in class org.simbrain.gauge.GaugeFrame
getPath() - Method in class org.simbrain.network.NetworkFrame: Return the path for this network frame.
getPath() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getPath() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getPeak() - Method in class org.simbrain.world.odorworld.Stimulus
getPersistentData() - Method in class org.simbrain.gauge.core.Dataset
getPersistentNodes() - Method in class org.simbrain.network.NetworkPanel: Return a collection of all persistent nodes, that is all neuron nodes and all synapse nodes.
getPersistentVariables() - Method in class org.simbrain.gauge.GaugedVariables
getPerturbationAmount() - Method in class org.simbrain.gauge.core.Projector
getPerturbationAmount() - Method in class org.simbrain.gauge.core.Settings
getPerturbationAmount() - Static method in class org.simbrain.gauge.GaugePreferences
getPhase() - Method in class org.simnet.neurons.SinusoidalNeuron
getPixel(int, int) - Method in class org.simbrain.world.visionworld.VisionWorld
getPlasticityType() - Method in class org.simnet.synapses.ShortTermPlasticitySynapse
getPoint(int) - Method in class org.simbrain.gauge.core.Dataset: Get a specificed point in the dataset.
getPointSize() - Static method in class org.simbrain.gauge.GaugePreferences
getPointSize() - Method in class org.simbrain.gauge.graphics.GaugePanel
getPrecision() - Static method in class org.simbrain.network.NetworkPreferences: Network precision.
getPrecision() - Method in class org.simnet.interfaces.Network
getPrefsItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getPrefsMenu() - Method in class org.simbrain.gauge.GaugeFrame
getProjectionPrefs() - Method in class org.simbrain.gauge.GaugeFrame
getProjectorByName(String) - Method in class org.simbrain.gauge.core.Gauge
getProjectorList() - Static method in class org.simbrain.gauge.core.Gauge
getPropertyDialog() - Method in class org.simbrain.network.nodes.NeuronNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.ScreenElement: Return a property dialog for this screen element.
getPropertyDialog() - Method in class org.simbrain.network.nodes.subnetworks.BackpropNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.subnetworks.CompetitiveNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.subnetworks.ElmanNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.subnetworks.HopfieldNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.subnetworks.LMSNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.subnetworks.StandardNetworkNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.subnetworks.WTANetworkNode
getPropertyDialog() - Method in class org.simbrain.network.nodes.SynapseNode
getPropsItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getPsRestingPotential() - Method in class org.simnet.interfaces.SpikeResponder
getRandom() - Method in class org.simnet.util.RandomSource: Returns a random number.
getRandomizeObjectsAction() - Method in class org.simbrain.network.NetworkActionManager: Return the randomize objects action.
getRandomizer() - Method in class org.simnet.neurons.RandomNeuron
getRandomizer() - Method in class org.simnet.synapses.RandomSynapse
getRateConstant() - Method in class org.simnet.neurons.RunningAverageNeuron
getRectangle() - Method in class org.simbrain.world.odorworld.AbstractEntity: Returns a Rectangle describing the location of the Entity (For Calculating Collisions).
getRectangle(Point) - Method in class org.simbrain.world.odorworld.AbstractEntity
getRectangle() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getRectangle(Point) - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getRectangle() - Method in class org.simbrain.world.odorworld.Wall: Return the rectangle.
getRectangle(Point) - Method in class org.simbrain.world.odorworld.Wall: Return the rectangle at the point.
getRefreshAction() - Method in class org.simbrain.util.SceneGraphBrowser: Return the refresh action for this scene graph browser.
getRelAbs() - Method in class org.simnet.neurons.DecayNeuron
getRelativePath(String, String) - Static method in class org.simbrain.util.Utils: Helper method to create a relative path for use in saving simulation files which refer to files within directories.
getResetPotential() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getResistance() - Method in class org.simnet.neurons.AdditiveNeuron
getResistance() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getResponseHeight() - Method in class org.simnet.synapses.spikeresponders.Step
getResponseTime() - Method in class org.simnet.synapses.spikeresponders.Step
getRest() - Method in class org.simnet.neurons.IACNeuron
getRestingPotential() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getResurrectionProb() - Method in class org.simbrain.world.odorworld.AbstractEntity
getResurrectionProb() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getResurrectionProb() - Method in class org.simbrain.world.odorworld.Wall: Return the resurrectin probability.
getRightWhisker() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getRMSError() - Method in class org.simnet.networks.LMSNetwork
getRoot() - Method in class org.simnet.interfaces.Network: Returns the top-level network in the hierarchy.
getRoundingOff() - Method in class org.simnet.interfaces.Network
getRunNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the run network action.
getSave() - Method in class org.simbrain.gauge.GaugeFrame
getSaveAs() - Method in class org.simbrain.gauge.GaugeFrame
getSaveAsItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getSaveAsNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the save as network action.
getSaveItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getSaveNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the save network action.
getScaleByPSPDifference() - Method in class org.simnet.interfaces.SpikeResponder
getScriptItem() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getScriptMenu() - Method in class org.simbrain.world.odorworld.OdorWorldFrameMenu
getSelectAllAction() - Method in class org.simbrain.network.NetworkActionManager: Return the select all action.
getSelectAllNeuronsAction() - Method in class org.simbrain.network.NetworkActionManager: Return the select all neurons action.
getSelectAllWeightsAction() - Method in class org.simbrain.network.NetworkActionManager: Return the select all weights action.
getSelectedEntity() - Method in class org.simbrain.world.odorworld.OdorWorld
getSelectedModelElements() - Method in class org.simbrain.network.NetworkPanel: Returns model network elements corresponding to selected screen elements.
getSelectedModelNeurons() - Method in class org.simbrain.network.NetworkPanel: Returns selected Neurons.
getSelectedNeurons() - Method in class org.simbrain.network.NetworkPanel: Returns selected Neurons.
getSelectedPixel(MouseEvent) - Method in class org.simbrain.world.visionworld.VisionWorld
getSelectedPixelToolTip(MouseEvent) - Method in class org.simbrain.world.visionworld.VisionWorld
getSelectedPoint() - Method in class org.simbrain.world.dataworld.DataWorld
getSelectedSynapses() - Method in class org.simbrain.network.NetworkPanel: Returns selected Synapses.
getSelection() - Method in class org.simbrain.network.NetworkPanel: Return the selection as a collection of selected elements.
getSelection() - Method in class org.simbrain.network.NetworkSelectionEvent: Return the selection.
getSelection() - Method in class org.simbrain.network.NetworkSelectionModel: Return the selection as an unmodifiable collection of selected elements.
getSelectionColor() - Static method in class org.simbrain.network.NetworkPreferences: Network selection color.
getSelectionColor() - Static method in class org.simbrain.network.nodes.SelectionHandle
getSemiSaturationConstant() - Method in class org.simnet.neurons.NakaRushtonNeuron
getSendEnter() - Method in class org.simbrain.world.textworld.TextWorld
getSensorArray() - Method in class org.simnet.coupling.SensoryCoupling: Return the array of sensor names for this sensory coupling.
getSensorIdMenu(ActionListener, NeuronNode) - Method in class org.simbrain.workspace.Workspace: Returns a menu which shows what possible sources there are for sensory couplings in this workspace.
getSensorIdMenu(ActionListener) - Method in class org.simbrain.world.dataworld.DataWorld: Returns a menu with on id, "Column X" for each column.
getSensorIdMenu(ActionListener) - Method in class org.simbrain.world.odorworld.OdorWorld: Returns a menu with a sub-menu for each agent.
getSensorIdMenu(ActionListener) - Method in class org.simbrain.world.textworld.TextWorld
getSensorIdMenu(ActionListener) - Method in class org.simbrain.world.visionworld.VisionWorld
getSensorIdMenu(ActionListener) - Method in class org.simbrain.world.World: Return a menu of sensor ids for this world and register the specified action listener as an action listener for the menu items in the returned menu.
getSensoryCoupling() - Method in class org.simnet.interfaces.Neuron
getSetAutozoom() - Method in class org.simbrain.gauge.GaugeFrame
getSetAutoZoomMenuItem() - Method in class org.simbrain.network.NetworkActionManager: Return the set auto zoom check box menu item.
getSetNeuronPropertiesAction() - Method in class org.simbrain.network.NetworkActionManager: Return the neuron properties action.
getSetPropertiesAction() - Method in class org.simbrain.network.nodes.SubnetworkNode
getSetSynapsePropertiesAction() - Method in class org.simbrain.network.NetworkActionManager: Return the synapse properties action.
getSettings() - Method in class org.simbrain.gauge.graphics.GaugePanel
getShortLabel() - Method in class org.simnet.coupling.MotorCoupling: Return a short label for this motor coupling, that is the elements in the array of command names separated by spaces.
getShortLabel() - Method in class org.simnet.coupling.SensoryCoupling: Return a short label for this sensory coupling, that is the elements in the array of sensor names separated by spaces.
getShowClampToolBarMenuItem() - Method in class org.simbrain.network.NetworkActionManager: Return the show clamp tool bar menu item.
getShowDebugAction() - Method in class org.simbrain.network.NetworkActionManager
getShowEditToolBarMenuItem() - Method in class org.simbrain.network.NetworkActionManager: Return the show edit tool bar menu item.
getShowError() - Static method in class org.simbrain.gauge.GaugePreferences
getShowHelpAction() - Method in class org.simbrain.network.NetworkActionManager: Return the show help action.
getShowIOInfoMenuItem() - Method in class org.simbrain.network.NetworkActionManager: Return the show IO information check box menu item.
getShowMainToolBarMenuItem() - Method in class org.simbrain.network.NetworkActionManager: Return the show main tool bar menu item.
getShowNetworkPreferencesAction() - Method in class org.simbrain.network.NetworkActionManager: Return the show network preferences action.
getShowStatusBar() - Static method in class org.simbrain.gauge.GaugePreferences
getShowSubnetOutline() - Method in class org.simbrain.network.NetworkPanel
getShowTime() - Method in class org.simbrain.network.NetworkPanel
getSignalColor() - Method in class org.simbrain.network.NetworkPanel
getSignalColor() - Static method in class org.simbrain.network.NetworkPreferences: Network signal synapse color.
getSlope() - Method in class org.simnet.neurons.LinearNeuron
getSlope() - Method in class org.simnet.neurons.SigmoidalNeuron
getSource() - Method in class org.simbrain.network.nodes.SynapseNode
getSource() - Method in class org.simnet.interfaces.Synapse
getSpaceHorizontalAction() - Method in class org.simbrain.network.NetworkActionManager: Return the space horizontal action.
getSpaceVerticalAction() - Method in class org.simbrain.network.NetworkActionManager: Return the space vertical action.
getSpikeResponder() - Method in class org.simnet.interfaces.Synapse
getSpikeResponderList() - Method in class org.simbrain.network.dialog.synapse.AbstractSpikeResponsePanel
getSpikeResponderList() - Method in class org.simbrain.network.dialog.synapse.SpikeResponsePanel
getSpikerTypeIndex(String) - Static method in class org.simnet.interfaces.SpikeResponder: Helper function for combo boxes.
getSpikingColor() - Method in class org.simbrain.network.NetworkPanel
getSpikingColor() - Static method in class org.simbrain.network.NetworkPreferences: Returns the current spiking synapse color.
getStandardDeviation() - Method in class org.simnet.util.RandomSource
getState() - Method in class org.simbrain.gauge.GaugedVariables: Converts gauged variable states into a double array to be sent to the hisee gauge.
getState() - Method in class org.simbrain.world.visionworld.Pixel
getState() - Method in class org.simnet.interfaces.Network: Returns the "state" of the network--the activation level of its neurons.
getSteepness() - Method in class org.simnet.neurons.NakaRushtonNeuron
getStimPanel() - Method in class org.simbrain.world.odorworld.DialogOdorWorldEntity
getStimPanel() - Method in class org.simbrain.world.odorworld.DialogOdorWorldWall
getStimulus(String[]) - Method in interface org.simbrain.world.Agent: Return the stimulus for this agent provided the specified sensor id.
getStimulus(String[]) - Method in class org.simbrain.world.dataworld.DataWorld: Returns the value in the given column of the table uses the current row.
getStimulus() - Method in class org.simbrain.world.odorworld.AbstractEntity
getStimulus(String[]) - Method in class org.simbrain.world.odorworld.OdorWorldAgent: Get the stimulus associated with the a given sensory id.
getStimulus() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getStimulus() - Method in class org.simbrain.world.odorworld.Stimulus: Return the stimulus.
getStimulus(double) - Method in class org.simbrain.world.odorworld.Stimulus: Calculate what impact the object will have on the creature's receptors (input nodes) based on its distance from this object and its features (whether it is a "noisy object", and how the stimulus decays.
getStimulus() - Method in class org.simbrain.world.odorworld.Wall: Return the stimulus.
getStimulus(String[]) - Method in class org.simbrain.world.visionworld.VisionWorld: Accepts a string in the form "x","y".
getStimulusDimension() - Method in class org.simbrain.world.odorworld.Stimulus: Return the dimension of the stimulus.
getStimulusS() - Method in class org.simbrain.world.odorworld.Stimulus: Return the stimulus string.
getStimulusVector() - Method in class org.simbrain.world.odorworld.Stimulus: Return the stimulus vector.
getStopNetworkAction() - Method in class org.simbrain.network.NetworkActionManager: Return the stop network action.
getStrength() - Method in class org.simnet.interfaces.Synapse
getStrength() - Static method in class org.simnet.NetworkPreferences: Return the strength preference setting.
getStringMatrix(File) - Static method in class org.simbrain.util.Utils: Read a csv (comma-separated-values) files.
getSubnet() - Method in class org.simnet.interfaces.NetworkEvent
getSubnetNodes() - Method in class org.simbrain.network.NetworkPanel: Return a collection of all subnet nodes.
getSubnetwork() - Method in class org.simbrain.network.nodes.SubnetworkNode: Return the subnetwork for this subnetwork node.
getSubnetworkNodeFilter() - Static method in class org.simbrain.network.filters.Filters: Return the subnetwork node filter.
getSumDistances() - Method in class org.simbrain.gauge.core.Dataset
getSummedIncomingWeights() - Method in class org.simnet.interfaces.Neuron: Returns the sum of the strengths of the weights attaching to this neuron.
getSynapse() - Method in class org.simbrain.network.nodes.SynapseNode
getSynapse(String) - Method in class org.simnet.interfaces.Network: Find a synapse with a given string id.
getSynapse() - Method in class org.simnet.interfaces.NetworkEvent
getSynapseList() - Method in class org.simbrain.network.dialog.synapse.AbstractSynapsePanel
getSynapseNodeFilter() - Static method in class org.simbrain.network.filters.Filters: Return the synapse node filter.
getSynapseNodes() - Method in class org.simbrain.network.NetworkPanel: Return a collection of all synapse nodes.
getSynapseTypeIndex(String) - Static method in class org.simnet.interfaces.Synapse: Helper function for combo boxes.
getTabbedPane() - Method in class org.simbrain.world.odorworld.PanelStimulus
getTable() - Method in class org.simbrain.world.dataworld.DataWorld
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.simbrain.world.dataworld.ButtonEditor
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.simbrain.world.dataworld.ButtonRenderer
getTabPaint() - Method in class org.simbrain.network.nodes.SubnetworkNode: Return the tab paint for this subnetwork node.
getTabStroke() - Method in class org.simbrain.network.nodes.SubnetworkNode: Return the tab stroke for this subnetwork node.
getTabStrokePaint() - Method in class org.simbrain.network.nodes.SubnetworkNode: Return the tab stroke paint for this subnetwork node.
getTarget() - Method in class org.simbrain.network.nodes.SynapseNode
getTarget() - Method in class org.simnet.interfaces.Synapse
getTextString() - Method in class org.simbrain.world.textworld.Entry
getTextVector() - Method in class org.simbrain.world.textworld.Entry
getTfLowBound() - Method in class org.simbrain.network.dialog.RandomPanel
getTfMean() - Method in class org.simbrain.network.dialog.RandomPanel
getTfStandardDeviation() - Method in class org.simbrain.network.dialog.RandomPanel
getTfUpBound() - Method in class org.simbrain.network.dialog.RandomPanel
getTheHeight() - Method in class org.simbrain.gauge.GaugeFrame
getTheHeight() - Method in class org.simbrain.network.NetworkFrame: Return the "theHeight" for this network frame.
getTheHeight() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getTheHeight() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getTheImage() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getTheSettings() - Method in class org.simbrain.gauge.core.Projector
getTheToolBar() - Method in class org.simbrain.gauge.graphics.GaugePanel
getTheWidth() - Method in class org.simbrain.gauge.GaugeFrame
getTheWidth() - Method in class org.simbrain.network.NetworkFrame: Return the "theWidth" for this network frame.
getTheWidth() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getTheWidth() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getThreshold() - Method in class org.simnet.neurons.BinaryNeuron
getThreshold() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getTime() - Method in class org.simnet.interfaces.Network: Returns the current time.
getTimeConstant() - Method in class org.simnet.neurons.ExponentialDecayNeuron
getTimeConstant() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getTimeConstant() - Method in class org.simnet.neurons.NakaRushtonNeuron
getTimeLabel() - Method in class org.simnet.interfaces.Network
getTimeStep() - Static method in class org.simbrain.network.NetworkPreferences: Netowork time step.
getTimeStep() - Method in class org.simnet.interfaces.Network
getTimeStep() - Method in class org.simnet.synapses.spikeresponders.RiseAndDecay
getTimeType() - Method in class org.simnet.interfaces.Network
getTimeType() - Method in class org.simnet.interfaces.Neuron
getTimeType() - Method in class org.simnet.neurons.AdditiveNeuron
getTimeType() - Method in class org.simnet.neurons.BinaryNeuron
getTimeType() - Method in class org.simnet.neurons.ClampedNeuron: TODO: Not really true...
getTimeType() - Method in class org.simnet.neurons.DecayNeuron
getTimeType() - Method in class org.simnet.neurons.ExponentialDecayNeuron: TODO: Not really true...
getTimeType() - Method in class org.simnet.neurons.IACNeuron
getTimeType() - Method in class org.simnet.neurons.IntegrateAndFireNeuron
getTimeType() - Method in class org.simnet.neurons.IzhikevichNeuron
getTimeType() - Method in class org.simnet.neurons.LinearNeuron
getTimeType() - Method in class org.simnet.neurons.LMSNeuron
getTimeType() - Method in class org.simnet.neurons.LogisticNeuron
getTimeType() - Method in class org.simnet.neurons.NakaRushtonNeuron
getTimeType() - Method in class org.simnet.neurons.RandomNeuron
getTimeType() - Method in class org.simnet.neurons.RunningAverageNeuron
getTimeType() - Method in class org.simnet.neurons.SigmoidalNeuron
getTimeType() - Method in class org.simnet.neurons.SinusoidalNeuron: TODO: As with clamped, no real time type...
getTimeType() - Method in class org.simnet.neurons.StochasticNeuron
getTimeType() - Method in class org.simnet.neurons.TemporalDifferenceNeuron: TODO: Not really true...
getTimeType() - Method in class org.simnet.neurons.ThreeValuedNeuron
getTimeType() - Method in class org.simnet.neurons.TraceNeuron
getTimeUnits() - Static method in class org.simbrain.network.NetworkPreferences: Network time units.
getTolerance() - Method in class org.simbrain.gauge.core.Projector
getTolerance() - Method in class org.simbrain.gauge.core.Settings
getTolerance() - Static method in class org.simbrain.gauge.GaugePreferences
getToolTipText() - Method in class org.simbrain.network.nodes.NeuronNode
getToolTipText() - Method in class org.simbrain.network.nodes.ScreenElement: Return a String to use as tool tip text for this screen element.
getToolTipText() - Method in class org.simbrain.network.nodes.subnetworks.BackpropNetworkNode
getToolTipText() - Method in class org.simbrain.network.nodes.subnetworks.CompetitiveNetworkNode
getToolTipText() - Method in class org.simbrain.network.nodes.subnetworks.ElmanNetworkNode
getToolTipText() - Method in class org.simbrain.network.nodes.subnetworks.HopfieldNetworkNode
getToolTipText() - Method in class org.simbrain.network.nodes.subnetworks.LMSNetworkNode
getToolTipText() - Method in class org.simbrain.network.nodes.subnetworks.StandardNetworkNode
getToolTipText() - Method in class org.simbrain.network.nodes.subnetworks.WTANetworkNode
getToolTipText() - Method in class org.simbrain.network.nodes.SynapseNode
getToolTipText() - Method in class org.simbrain.network.nodes.ToolTipTextUpdater: Return a string to use as tool tip text.
getToolTipText() - Method in class org.simnet.interfaces.Neuron: Returns string for tool tip or short description.
getToolTipText() - Method in class org.simnet.neurons.NakaRushtonNeuron
getToolTipText() - Method in class org.simnet.neurons.TraceNeuron
getTotalInput() - Method in class org.simnet.interfaces.Neuron
getTrace() - Method in class org.simnet.neurons.TraceNeuron
getTraceHistory() - Method in class org.simnet.neurons.TraceNeuron
getTrainingINFile() - Method in class org.simnet.networks.Backprop
getTrainingINFile() - Method in class org.simnet.networks.LMSNetwork
getTrainingInputs() - Method in class org.simnet.networks.Backprop
getTrainingInputs() - Method in class org.simnet.networks.LMSNetwork
getTrainingOUTFile() - Method in class org.simnet.networks.Backprop
getTrainingOUTFile() - Method in class org.simnet.networks.LMSNetwork
getTrainingOutputs() - Method in class org.simnet.networks.Backprop
getTrainingOutputs() - Method in class org.simnet.networks.LMSNetwork
getTRUE() - Static method in class org.simbrain.util.TristateDropDown
getTsClipping() - Method in class org.simbrain.network.dialog.RandomPanel
getTurnIncrement() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getType() - Method in class org.simbrain.network.dialog.network.HopfieldDialog
getType() - Method in class org.simbrain.network.dialog.network.HopfieldPropertiesDialog
getType() - Method in class org.simbrain.world.dataworld.DataWorld
getType() - Method in class org.simbrain.world.odorworld.OdorWorld
getType() - Method in class org.simbrain.world.textworld.TextWorld
getType() - Method in class org.simbrain.world.visionworld.VisionWorld
getType() - Method in class org.simbrain.world.World: Return the type of this world.
getType() - Method in class org.simnet.interfaces.Network
getType() - Method in class org.simnet.interfaces.Neuron
getType() - Method in class org.simnet.interfaces.SpikeResponder
getType() - Method in class org.simnet.interfaces.Synapse
getTypeList() - Static method in class org.simnet.interfaces.Neuron
getTypeList() - Static method in class org.simnet.interfaces.SpikeResponder
getTypeList() - Static method in class org.simnet.interfaces.Synapse
getUnits() - Static method in class org.simnet.interfaces.Network
getUpdateNetwork() - Method in class org.simbrain.gauge.graphics.GaugeThread
getUpdateOrder() - Method in class org.simnet.networks.Hopfield
getUpdateWhileDragging() - Method in class org.simbrain.world.odorworld.OdorWorld
getUpperBound() - Method in class org.simbrain.world.dataworld.DataWorld
getUpperBound() - Method in class org.simnet.interfaces.Neuron
getUpperBound() - Method in class org.simnet.interfaces.Synapse
getUpperBound() - Method in class org.simnet.util.RandomSource
getUpperThreshold() - Method in class org.simnet.neurons.ThreeValuedNeuron
getUpperValue() - Method in class org.simnet.neurons.ThreeValuedNeuron
getUpstairs() - Method in class org.simbrain.gauge.core.Gauge: Convenience method to get upstairs dataset.
getUpstairs() - Method in class org.simbrain.gauge.core.Projector
getUpstairsText() - Method in class org.simbrain.gauge.graphics.ToolTipTextUpdater: Get the high dimensional coordinates of a point.
getUseAdaptation() - Method in class org.simnet.neurons.NakaRushtonNeuron
getUseLeakyLearning() - Method in class org.simnet.networks.Competitive: Return the leaky learning value.
getUseLocalBounds() - Method in class org.simbrain.world.odorworld.OdorWorld
getUseSlidingOutputThreshold() - Method in class org.simnet.synapses.HebbianThresholdSynapse
getUsingIndent() - Static method in class org.simbrain.network.NetworkPreferences: Network files indenting.
getUsingTabs() - Method in class org.simbrain.network.NetworkPanel
getValue() - Method in class org.simnet.interfaces.SpikeResponder
getValue() - Method in class org.simnet.interfaces.Synapse: For spiking source neurons, returns the spike-responder's value times the synapse strength For non-spiking neurons, returns the pre-synaptic activation times the synapse strength.
getValue() - Method in class org.simnet.synapses.SignalSynapse
getValues() - Method in class org.simbrain.world.odorworld.DialogOdorWorld: Set projector values based on fields.
getVectorString(double[], String) - Static method in class org.simbrain.util.Utils: Convert an array of doubles into a String.
getVectorString(String, String) - Static method in class org.simbrain.util.Utils: Convert a delimeted string of doubles into an array of doubles.
getWallColor() - Method in class org.simbrain.world.odorworld.OdorWorld
getWallItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getWallPropsItem() - Method in class org.simbrain.world.odorworld.OdorWorldMenu
getWeight(int) - Method in class org.simnet.interfaces.Network
getWeight(Neuron, Neuron) - Static method in class org.simnet.interfaces.Network: Returns a reference to the synapse connecting two neurons, or null if there is none.
getWeight(int, int) - Method in class org.simnet.interfaces.Network: Gets the weight at particular point.
getWeightCount() - Method in class org.simnet.interfaces.Network
getWeightedInputs() - Method in class org.simnet.interfaces.Neuron: Sums the weighted signals that are sent to this node.
getWeightedInputs() - Method in class org.simnet.neurons.LMSNeuron: Overrides superclass implementation by ignoring inputs from targetValue synapses.
getWeightList() - Method in class org.simnet.interfaces.Network
getWeights(Network, Network) - Static method in class org.simnet.util.ConnectNets: Returns a matrix representation of the connections between two subnetworks.
getWeightValues() - Static method in class org.simbrain.network.NetworkPreferences: Network weight values.
getWhiskerAngle() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getWhiskerLength() - Method in class org.simbrain.world.odorworld.OdorWorldAgent
getWidth() - Method in class org.simbrain.world.odorworld.AbstractEntity
getWidth() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getWidth() - Method in class org.simbrain.world.odorworld.Wall: Return the width.
getWinValue() - Method in class org.simnet.networks.Competitive: Return the winner value.
getWinValue() - Method in class org.simnet.networks.WinnerTakeAll
getWorkspace() - Method in class org.simbrain.gauge.GaugeFrame
getWorkspace() - Method in class org.simbrain.network.NetworkFrame: Return the workspace for this network frame.
getWorkspace() - Method in class org.simbrain.network.NetworkPanel: Returns a reference to the workspace.
getWorkspace() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getWorkspace() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getWorkspace() - Method in class org.simnet.interfaces.Network
getWorld() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getWorld() - Method in class org.simbrain.world.odorworld.OdorWorldFrame: Return the odor world.
getWorld() - Method in class org.simbrain.world.textworld.TextWorldFrame: Gets a particular instance of TextWorld.
getWorld() - Method in class org.simbrain.world.visionworld.VisionWorldFrame
getWorld() - Method in class org.simnet.coupling.Coupling: Return the world for this coupling, that is the parent world of this coupling's agent, or null if this coupling's agent is null.
getWorldFrameList() - Method in class org.simbrain.workspace.Workspace
getWorldHeight() - Method in class org.simbrain.world.odorworld.OdorWorld
getWorldList() - Method in class org.simbrain.workspace.Workspace
getWorldName() - Method in class org.simbrain.world.dataworld.DataWorld
getWorldName() - Method in class org.simbrain.world.odorworld.OdorWorld
getWorldName() - Method in class org.simbrain.world.textworld.TextWorld
getWorldName() - Method in class org.simbrain.world.visionworld.VisionWorld
getWorldName() - Method in class org.simbrain.world.World: Return the name of this world.
getWorldName() - Method in class org.simnet.coupling.Coupling: Return the world name for this coupling.
getWorldToNetworkInteractionModeAction() - Method in class org.simbrain.network.NetworkActionManager: Return the world to network interaction mode action.
getWorldType() - Method in class org.simnet.coupling.Coupling: Return the world type for this coupling.
getWorldWidth() - Method in class org.simbrain.world.odorworld.OdorWorld
getWTASubnetwork() - Method in class org.simbrain.network.nodes.subnetworks.WTANetworkNode
getWtIncrement() - Static method in class org.simnet.NetworkPreferences: Return the weight increment preference setting.
getWtLowerBound() - Static method in class org.simnet.NetworkPreferences: Return the weight lower bound preference setting.
getWtUpperBound() - Static method in class org.simnet.NetworkPreferences: Return the weight increment preference setting.
getX() - Method in class org.simbrain.world.odorworld.AbstractEntity
getX() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getX() - Method in class org.simbrain.world.odorworld.Wall: Return the x.
getX() - Method in class org.simnet.interfaces.Neuron
getXI() - Method in class org.simbrain.gauge.core.ProjectSammon
getXJ() - Method in class org.simbrain.gauge.core.ProjectSammon
getXpos() - Method in class org.simbrain.gauge.GaugeFrame
getXpos() - Method in class org.simbrain.network.NetworkFrame: Return the "xpos" for this network frame.
getXpos() - Method in class org.simbrain.network.nodes.NeuronNode
getXpos() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getXpos() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getY() - Method in class org.simbrain.world.odorworld.AbstractEntity
getY() - Method in class org.simbrain.world.odorworld.OdorWorldEntity
getY() - Method in class org.simbrain.world.odorworld.Wall: Return the y.
getY() - Method in class org.simnet.interfaces.Neuron
getYArray() - Method in class org.simbrain.gauge.core.ProjectSammon
getYI() - Method in class org.simbrain.gauge.core.ProjectSammon
getYJ() - Method in class org.simbrain.gauge.core.ProjectSammon
getYM() - Method in class org.simbrain.gauge.core.ProjectSammon
getYN() - Method in class org.simbrain.gauge.core.ProjectSammon
getYNew() - Method in class org.simbrain.gauge.core.ProjectSammon
getYpos() - Method in class org.simbrain.gauge.GaugeFrame
getYpos() - Method in class org.simbrain.network.NetworkFrame: Return the "ypos" for this network frame.
getYpos() - Method in class org.simbrain.network.nodes.NeuronNode
getYpos() - Method in class org.simbrain.world.dataworld.DataWorldFrame
getYpos() - Method in class org.simbrain.world.odorworld.OdorWorldFrame
getZeroWeightColor() - Method in class org.simbrain.network.NetworkPanel
getZeroWeightColor() - Static method in class org.simbrain.network.NetworkPreferences: Network zero weight color.
getZoomInEditModeAction() - Method in class org.simbrain.network.NetworkActionManager: Return the zoom in edit mode action.
goStraightBackward(double) - Method in class org.simbrain.world.odorworld.OdorWorldAgent: Moves agent backward.
goStraightForward(double) - Method in class org.simbrain.world.odorworld.OdorWorldAgent: Moves agent forward.
GridLayout - Class in org.simnet.layouts: Lay neurons out in a line.
GridLayout(double, double, int) - Constructor for class org.simnet.layouts.GridLayout: Create a layout.
GridLayoutPanel - Class in org.simbrain.network.dialog.network.layout: LayoutPanel allows the user to define the layout of a network.
GridLayoutPanel() - Constructor for class org.simbrain.network.dialog.network.layout.GridLayoutPanel: Default constructor.

H

handlePreferenceDialogs() - Method in class org.simbrain.gauge.graphics.GaugePanel: Open preference dialog based on which projector is currently selected.
hasChanged() - Method in class org.simbrain.gauge.GaugeFrame: Checks to see if anything has changed and then offers to save if true.
hasChangedSinceLastSave() - Method in class org.simbrain.network.NetworkPanel
hasContextMenu() - Method in class org.simbrain.network.nodes.NeuronNode
hasContextMenu() - Method in class org.simbrain.network.nodes.ScreenElement: Return true if this screen element has a context menu.
hasContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.BackpropNetworkNode
hasContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.CompetitiveNetworkNode
hasContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.ElmanNetworkNode
hasContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.HopfieldNetworkNode
hasContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.LMSNetworkNode
hasContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.StandardNetworkNode
hasContextMenu() - Method in class org.simbrain.network.nodes.subnetworks.WTANetworkNode
hasContextMenu() - Method in class org.simbrain.network.nodes.SynapseNode
hasDialog() - Method in class org.simbrain.gauge.core.ProjectCoordinate
hasDialog() - Method in class org.simbrain.gauge.core.Projector
hasDialog() - Method in class org.simbrain.gauge.core.ProjectPCA
hasDialog() - Method in class org.simbrain.gauge.core.ProjectSammon
hasPropertyDialog() - Method in class org.simbrain.network.nodes.