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

P

pack() - Method in class ucl.physiol.neuroconstruct.gui.CellMechanismEditor

paint(Graphics) - Method in class ucl.physiol.neuroconstruct.gui.plotter.PlotCanvas

paint(Graphics) - Method in class ucl.physiol.neuroconstruct.gui.view2d.ViewCanvas

PARALLEL_MODE_VAL - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PARAMETER_CONC_EXT - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_CONC_INT - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PARAMETER_GMAX - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_NAME_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_NAME_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PARAMETER_REV_POT - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_REV_POT_2 - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_VALUE_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PARAMETER_VALUE_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

parameterDescription - Variable in class ucl.physiol.neuroconstruct.project.InternalParameter

ParameterException - Exception in ucl.physiol.neuroconstruct.cell

A class representing an exception when dealing with parameterised expressions, e.g.

ParameterException(String) - Constructor for exception ucl.physiol.neuroconstruct.cell.ParameterException

parameterExists(String) - Method in class ucl.physiol.neuroconstruct.mechanisms.AbstractedCellMechanism

PARAMETERISED_GROUP - Static variable in class ucl.physiol.neuroconstruct.gui.ClickProjectHelper

PARAMETERISED_HH_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PARAMETERISED_HH_TYPE_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

ParameterisedGroup - Class in ucl.physiol.neuroconstruct.cell

A parameterisation of a group of sections, based on the Parameterized Domain specification in NEURON

ParameterisedGroup() - Constructor for class ucl.physiol.neuroconstruct.cell.ParameterisedGroup

ParameterisedGroup(String, String, ParameterisedGroup.Metric, ParameterisedGroup.ProximalPref, ParameterisedGroup.DistalPref, String) - Constructor for class ucl.physiol.neuroconstruct.cell.ParameterisedGroup

ParameterisedGroup.DistalPref - Enum in ucl.physiol.neuroconstruct.cell

ParameterisedGroup.Metric - Enum in ucl.physiol.neuroconstruct.cell

ParameterisedGroup.ProximalPref - Enum in ucl.physiol.neuroconstruct.cell

parameterList - Variable in class ucl.physiol.neuroconstruct.project.packing.CellPackingAdapter

parameterName - Variable in class ucl.physiol.neuroconstruct.project.InternalParameter

parameters - Variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismPlot

PARAMETERS_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

parametersEqual(Region) - Method in class ucl.physiol.neuroconstruct.project.Region

PARENT_FRACT_ALONG_V2 - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

PARENT_V2 - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

parse(File) - Method in class ucl.physiol.neuroconstruct.neuroml.hdf5.NetworkMLReader

parse1DDataset(Dataset, boolean, Properties) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parse2Ddataset(Dataset) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parse2DDataset(Dataset, boolean, Properties) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parseAttribute(Attribute, String, Properties, boolean) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parseDatasetForAttributes(Dataset) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parseExpression(String, Variable[]) - Static method in class ucl.physiol.neuroconstruct.utils.equation.Expression

parseForHyperlinks(String) - Static method in class ucl.physiol.neuroconstruct.utils.GeneralUtils

parseForSimConfigSpecifics(String, String) - Static method in class ucl.physiol.neuroconstruct.genesis.ScriptLocation

parseForSimConfigSpecifics(String, String) - Static method in class ucl.physiol.neuroconstruct.neuron.NativeCodeLocation

parseGroup(Group) - Method in class ucl.physiol.neuroconstruct.neuroml.hdf5.NetworkMLReader

parseGroupForAttributes(Group) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parseGroupForDatasets(Group, boolean) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parseGroupForDataStores(Group, boolean) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

parseNeuroML2File(File) - Static method in class ucl.physiol.neuroconstruct.neuroml.NeuroMLFileManager

PASCAL - Static variable in class ucl.physiol.neuroconstruct.utils.units.Units

PassiveMembraneMechanism - Class in ucl.physiol.neuroconstruct.mechanisms

Cell Mechanism representing a leaky membrane

PassiveMembraneMechanism() - Constructor for class ucl.physiol.neuroconstruct.mechanisms.PassiveMembraneMechanism

PERCENTAGE_CELLS - Static variable in class ucl.physiol.neuroconstruct.project.cellchoice.PercentageOfCells

PERCENTAGE_CELLS_DESC - Static variable in class ucl.physiol.neuroconstruct.project.cellchoice.PercentageOfCells

PercentageOfCells - Class in ucl.physiol.neuroconstruct.project.cellchoice

Extension of CellChooser.

PercentageOfCells() - Constructor for class ucl.physiol.neuroconstruct.project.cellchoice.PercentageOfCells

PercentageOfCells(float) - Constructor for class ucl.physiol.neuroconstruct.project.cellchoice.PercentageOfCells

perUnitTimeVoltageUnits - Static variable in class ucl.physiol.neuroconstruct.utils.units.UnitConverter

perUnitVoltageUnits - Static variable in class ucl.physiol.neuroconstruct.utils.units.UnitConverter

PETA - Static variable in class ucl.physiol.neuroconstruct.utils.units.Prefix

PhysicalQuantity - Class in ucl.physiol.neuroconstruct.utils.units

Class for handling units.

PhysicalQuantity(double, Units) - Constructor for class ucl.physiol.neuroconstruct.utils.units.PhysicalQuantity

PHYSIOLOGICAL_UNITS - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PICO - Static variable in class ucl.physiol.neuroconstruct.utils.units.Prefix

PLOT_AND_SAVE - Static variable in class ucl.physiol.neuroconstruct.project.SimPlot

PLOT_ELEMENT_ROOT - Static variable in class ucl.physiol.neuroconstruct.genesis.GenesisFileManager

PLOT_ONLY - Static variable in class ucl.physiol.neuroconstruct.project.SimPlot

PLOT_SAVE - Static variable in class ucl.physiol.neuroconstruct.gui.ClickProjectHelper

PlotCanvas - Class in ucl.physiol.neuroconstruct.gui.plotter

Extenion of Canvas for plotting the graphs

PlotCanvas(PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotCanvas

PlotEquationDialog - Class in ucl.physiol.neuroconstruct.gui.plotter

Dialog to allow any equation to be placed on the PlotterFrame

PlotEquationDialog(Frame, String, boolean) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotEquationDialog

PlotEquationDialog(Frame, String, boolean, float, float, int) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotEquationDialog

PlotEquationDialog() - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotEquationDialog

plotFrameClosing(String) - Static method in class ucl.physiol.neuroconstruct.gui.plotter.PlotManager

PlotManager - Class in ucl.physiol.neuroconstruct.gui.plotter

Central point for controlling references to plot frames, to facilitate plotting multiple DataSets in each PlotFrame.

PlotManager() - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotManager

plotName - Variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismPlot

PlotSaveGenerator - Class in ucl.physiol.neuroconstruct.project

Thread to handle generation of what to plot/save during simulation run

PlotSaveGenerator(Project, GenerationReport) - Constructor for class ucl.physiol.neuroconstruct.project.PlotSaveGenerator

plotSaveGenerator - Variable in class ucl.physiol.neuroconstruct.project.ProjectManager

PLOTTED_VALUE_SEPARATOR - Static variable in class ucl.physiol.neuroconstruct.project.SimPlot

Used to separate the element from the field, e.g.

PlotterApp - Class in ucl.physiol.neuroconstruct.gui.plotter

Application for popping up a graph of a vector of points

PlotterApp() - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterApp

PlotterFrame - Class in ucl.physiol.neuroconstruct.gui.plotter

Main frame of application for popping up a graph of a vector of points

PlotterFrame(String, Project, boolean) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame

Create a new PlotterFrame.

PlotterFrame.ApAnalysisMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.ApAnalysisMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.ApAnalysisMenuListener

PlotterFrame.DataSetAbsAreaMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetAbsAreaMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetAbsAreaMenuListener

PlotterFrame.DataSetAreaMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetAreaMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetAreaMenuListener

PlotterFrame.DataSetAutocorrMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetAutocorrMenuListener(DataSet, Component) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetAutocorrMenuListener

PlotterFrame.DataSetColourMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetColourMenuListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetColourMenuListener

PlotterFrame.DataSetDetachMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetDetachMenuListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetDetachMenuListener

PlotterFrame.DataSetDistHistMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetDistHistMenuListener(DataSet, int) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetDistHistMenuListener

PlotterFrame.DataSetEditPointsMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetEditPointsMenuListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetEditPointsMenuListener

PlotterFrame.DataSetExportMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetExportMenuListener(DataSet, PlotterFrame, File) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetExportMenuListener

PlotterFrame.DataSetFormatMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetFormatMenuListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetFormatMenuListener

PlotterFrame.DataSetInfoMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetInfoMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetInfoMenuListener

PlotterFrame.DataSetISIHistMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetISIHistMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetISIHistMenuListener

PlotterFrame.DataSetListPointsMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetListPointsMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetListPointsMenuListener

PlotterFrame.DataSetMoveMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetMoveMenuListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetMoveMenuListener

PlotterFrame.DataSetPeaksMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetPeaksMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetPeaksMenuListener

PlotterFrame.DataSetPhasePlanePlotMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetPhasePlanePlotMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetPhasePlanePlotMenuListener

PlotterFrame.DataSetQuickStatsMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetQuickStatsMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetQuickStatsMenuListener

PlotterFrame.DataSetRemoveMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetRemoveMenuListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetRemoveMenuListener

PlotterFrame.DataSetSaveInProjMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetSaveInProjMenuListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetSaveInProjMenuListener

PlotterFrame.DataSetSimpDerivMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetSimpDerivMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetSimpDerivMenuListener

PlotterFrame.DataSetSpikeMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetSpikeMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetSpikeMenuListener

PlotterFrame.DataSetSyncIndexMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetSyncIndexMenuListener(DataSet, Component) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetSyncIndexMenuListener

PlotterFrame.DataSetTransformListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetTransformListener(DataSet, PlotterFrame) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetTransformListener

PlotterFrame.DataSetZerosMenuListener - Class in ucl.physiol.neuroconstruct.gui.plotter

PlotterFrame.DataSetZerosMenuListener(DataSet) - Constructor for class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame.DataSetZerosMenuListener

PLUS - Static variable in class ucl.physiol.neuroconstruct.utils.equation.BinaryOperation

POINT_DIAM_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

POINT_PROCESS - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanism

POINT_X_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

POINT_Y_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

POINT_Z_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

pointToString(int) - Method in class ucl.physiol.neuroconstruct.dataset.DataSet

POP_NAME_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POPULATION_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POPULATIONS_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POS_X_AXIS - Static variable in class ucl.physiol.neuroconstruct.j3D.Utils3D

POS_X_DIRECTION - Static variable in class ucl.physiol.neuroconstruct.j3D.Utils3D

POS_Y_AXIS - Static variable in class ucl.physiol.neuroconstruct.j3D.Utils3D

POS_Y_DIRECTION - Static variable in class ucl.physiol.neuroconstruct.j3D.Utils3D

POS_Z_AXIS - Static variable in class ucl.physiol.neuroconstruct.j3D.Utils3D

POS_Z_DIRECTION - Static variable in class ucl.physiol.neuroconstruct.j3D.Utils3D

POSITION_DATA_FILE - Static variable in class ucl.physiol.neuroconstruct.simulation.SimulationData

PositionedCell - Class in ucl.physiol.neuroconstruct.project

Class for holding the position of a cell, and its cell group

PositionedCell(Point3f, String, String) - Constructor for class ucl.physiol.neuroconstruct.project.PositionedCell

positionOfSoma - Variable in class ucl.physiol.neuroconstruct.project.PositionedCell

PositionRecord - Class in ucl.physiol.neuroconstruct.project

Single position record

PositionRecord(int, float, float, float) - Constructor for class ucl.physiol.neuroconstruct.project.PositionRecord

PositionRecord(String) - Constructor for class ucl.physiol.neuroconstruct.project.PositionRecord

POST_CELL_ID_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POST_CONN_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POST_DELAY_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POST_FRACT_ALONG_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POST_SEGMENT_ID_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PostSynapticObject - Class in ucl.physiol.neuroconstruct.project

Helper class for specifying a single post synaptic mechanism instance corresponding e.g.

PostSynapticObject(String, String, int, int, int) - Constructor for class ucl.physiol.neuroconstruct.project.PostSynapticObject

PostSynapticTerminalLocation - Class in ucl.physiol.neuroconstruct.cell

Location of a synaptic endpoint on a dendritic section

PostSynapticTerminalLocation(int, float) - Constructor for class ucl.physiol.neuroconstruct.cell.PostSynapticTerminalLocation

POT_SYN_LOC_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POT_SYN_LOC_ELEMENT_preV1_7_1 - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

POWER - Static variable in class ucl.physiol.neuroconstruct.utils.equation.BinaryOperation

PRE_CELL_ID_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PRE_CONN_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PRE_DELAY_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PRE_FRACT_ALONG_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PRE_SEGMENT_ID_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PREF_MAX_ELECT_LEN - Static variable in class ucl.physiol.neuroconstruct.simulation.SimulationParameters

PREF_MIN_ELECT_LEN - Static variable in class ucl.physiol.neuroconstruct.simulation.SimulationParameters

prefConfig - Static variable in class ucl.physiol.neuroconstruct.hpc.mpi.MpiSettings

PREFIX - Static variable in class ucl.physiol.neuroconstruct.neuroml.BiophysicsConstants

PREFIX - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PREFIX - Static variable in class ucl.physiol.neuroconstruct.neuroml.MetadataConstants

PREFIX - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

PREFIX - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

Prefix - Class in ucl.physiol.neuroconstruct.utils.units

Class for handling units.

Prefix() - Constructor for class ucl.physiol.neuroconstruct.utils.units.Prefix

Here to support saving of Units via XMLEncoder

PrePostAllowedLocs - Class in ucl.physiol.neuroconstruct.project

Helper class for storing which of axon, dendrite, soma are allowed for pre or post connections

PrePostAllowedLocs() - Constructor for class ucl.physiol.neuroconstruct.project.PrePostAllowedLocs

PreSynapticTerminalLocation - Class in ucl.physiol.neuroconstruct.cell

Location of a synaptic endpoint on an axonal section

PreSynapticTerminalLocation(int, float) - Constructor for class ucl.physiol.neuroconstruct.cell.PreSynapticTerminalLocation

printContents() - Method in class ucl.physiol.neuroconstruct.utils.ToolTipHelper

printDetails(Cell, Project) - Static method in class ucl.physiol.neuroconstruct.cell.utils.CellTopologyHelper

printDetails(Cell, Project, boolean) - Static method in class ucl.physiol.neuroconstruct.cell.utils.CellTopologyHelper

printDetails(Cell, Project, boolean, boolean, boolean) - Static method in class ucl.physiol.neuroconstruct.cell.utils.CellTopologyHelper

printDetails(Cell, Project, boolean, boolean, boolean, boolean) - Static method in class ucl.physiol.neuroconstruct.cell.utils.CellTopologyHelper

printDetails() - Method in class ucl.physiol.neuroconstruct.mechanisms.AbstractedCellMechanism

printDetails() - Method in class ucl.physiol.neuroconstruct.project.RegionsInfo

printDetails(SimpleCompartment[]) - Static method in class ucl.physiol.neuroconstruct.utils.compartment.CompartmentHelper

printDetails() - Method in class ucl.physiol.neuroconstruct.utils.RecentFiles

printGroup(Group, String) - Static method in class ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

printMemory(boolean) - Static method in class ucl.physiol.neuroconstruct.utils.GeneralUtils

printShortDetails(Cell) - Static method in class ucl.physiol.neuroconstruct.cell.utils.CellTopologyHelper

printThemeInfo() - Method in class ucl.physiol.neuroconstruct.gui.CustomLookAndFeel

printTransform3DDetails(Transform3D, String) - Static method in class ucl.physiol.neuroconstruct.j3D.Utils3D

printTransformGroupDetails(TransformGroup, String) - Static method in class ucl.physiol.neuroconstruct.j3D.Utils3D

ProcessFeedback - Interface in ucl.physiol.neuroconstruct.hpc.utils

Simple interface for giving feedback from processes

processingInstruction(String, String) - Method in class ucl.physiol.neuroconstruct.utils.xml.SimpleXMLReader

ProcessManager - Class in ucl.physiol.neuroconstruct.hpc.utils

Simple class for spawning external processes

ProcessManager() - Constructor for class ucl.physiol.neuroconstruct.hpc.utils.ProcessManager

ProcessManager - Class in ucl.physiol.neuroconstruct.nmodleditor.processes

nmodlEditor application software

ProcessManager(File) - Constructor for class ucl.physiol.neuroconstruct.nmodleditor.processes.ProcessManager

ProcessOutputCatcher - Class in ucl.physiol.neuroconstruct.hpc.utils

Listens for feedback from processes

ProcessOutputCatcher(InputStream, String, ProcessFeedback, int) - Constructor for class ucl.physiol.neuroconstruct.hpc.utils.ProcessOutputCatcher

ProcessOutputWatcher - Class in ucl.physiol.neuroconstruct.nmodleditor.processes

nmodlEditor application software

ProcessOutputWatcher(InputStream, String) - Constructor for class ucl.physiol.neuroconstruct.nmodleditor.processes.ProcessOutputWatcher

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.CellChooserDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.CellGroupDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.CellMechanismEditor

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.CellPackingPatternDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.DataSetManager

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.FieldPotentialFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.HelpFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.InformationDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.MainFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.MainFrame_AboutBox

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.NetworkConnectionDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.NeuronImportDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.NewProjectDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.NumberGeneratorDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.OptionsFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.plotter.PlotterFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.RegionsInfoDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.SequenceGeneratorDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.SimpleTextInput

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.SimpleViewer

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.SimPlotDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.SimulationBrowser

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.SimulationRerunFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.SlicerFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.StimDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.view2d.View2DPlane

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.gui.VolBasedConnDialog

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.hpc.condor.CondorFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.hpc.condor.CondorFrame_AboutBox

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.hpc.mpi.MpiFrame

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.hpc.mpi.MpiFrame_AboutBox

processWindowEvent(WindowEvent) - Method in class ucl.physiol.neuroconstruct.j3D.FullScreen3D

PRODUCT - Static variable in class ucl.physiol.neuroconstruct.utils.equation.BinaryOperation

proj3Dproperties - Variable in class ucl.physiol.neuroconstruct.project.Project

PROJ_NAME_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PROJ_PREFERENCES - Static variable in class ucl.physiol.neuroconstruct.gui.OptionsFrame

PROJ_QUICK_SAVE - Static variable in class ucl.physiol.neuroconstruct.project.ProjectStructure

PROJ_SVN_SAVE - Static variable in class ucl.physiol.neuroconstruct.project.ProjectStructure

Project - Class in ucl.physiol.neuroconstruct.project

Main class holding references to the important data objects of the project

PROJECT_EDITED_NOT_SAVED - Static variable in class ucl.physiol.neuroconstruct.project.Project

PROJECT_IS_VALID - Static variable in class ucl.physiol.neuroconstruct.gui.ValidityStatus

PROJECT_NOT_INITIALISED - Static variable in class ucl.physiol.neuroconstruct.project.Project

PROJECT_NOT_YET_EDITED - Static variable in class ucl.physiol.neuroconstruct.project.Project

PROJECT_PROPERTIES_MODE - Static variable in class ucl.physiol.neuroconstruct.gui.OptionsFrame

PROJECT_SAVED - Static variable in class ucl.physiol.neuroconstruct.project.Project

ProjectEventListener - Interface in ucl.physiol.neuroconstruct.project

Interface to add to Main Frame which, when altered, change the info of the project

ProjectEventListner - Interface in ucl.physiol.neuroconstruct.project

Interface to add to components in the Main Frame which, when altered, change the info of the project

ProjectFileParsingException - Exception in ucl.physiol.neuroconstruct.project

Exception thrown when the parsing of a project file goes bad

ProjectFileParsingException() - Constructor for exception ucl.physiol.neuroconstruct.project.ProjectFileParsingException

ProjectFileParsingException(String) - Constructor for exception ucl.physiol.neuroconstruct.project.ProjectFileParsingException

ProjectFileParsingException(String, Throwable) - Constructor for exception ucl.physiol.neuroconstruct.project.ProjectFileParsingException

ProjectFileParsingException(Throwable) - Constructor for exception ucl.physiol.neuroconstruct.project.ProjectFileParsingException

ProjectFileUpdate - Class in ucl.physiol.neuroconstruct.project

Class used to update project files when there is a change in the names of classes used, e.g.

ProjectFileUpdate() - Constructor for class ucl.physiol.neuroconstruct.project.ProjectFileUpdate

PROJECTION_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PROJECTIONS_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

projectLoaded() - Method in class ucl.physiol.neuroconstruct.project.ProjectManager

ProjectManager - Class in ucl.physiol.neuroconstruct.project

A class for handling interaction with the project All non gui functionality will (eventually) be transferred here, to reduce the size of MainFrame, and to give access to the core functionality via the command line interface

ProjectManager() - Constructor for class ucl.physiol.neuroconstruct.project.ProjectManager

ProjectManager(GenerationReport, ProjectEventListener) - Constructor for class ucl.physiol.neuroconstruct.project.ProjectManager

ProjectProperties - Class in ucl.physiol.neuroconstruct.project

A class to contain non 3D related project specific settings

ProjectProperties() - Constructor for class ucl.physiol.neuroconstruct.project.ProjectProperties

ProjectStructure - Class in ucl.physiol.neuroconstruct.project

Class defining, and if necessary creating, project directories, etc.

ProjectStructure() - Constructor for class ucl.physiol.neuroconstruct.project.ProjectStructure

projManager - Variable in class ucl.physiol.neuroconstruct.gui.MainFrame

projProperties - Variable in class ucl.physiol.neuroconstruct.project.Project

PROP_CELL_MECH_DEFAULT_NAME - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_CELL_MECH_DESCRIPTION - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_CELL_MECH_MODEL - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_CELL_MECH_NAME - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_CELL_MECH_TYPE - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_CHANNELML_FILE - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_DELAY_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PROP_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.MetadataConstants

PROP_IMPL_METHOD - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_MAPPING_SUFFIX - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_NEEDS_COMP_SUFFIX - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_PLOT_INFO_FILE - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_SBML_FILE - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_SIMENV_SUFFIX - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

PROP_TAG_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.MetadataConstants

PROP_TAG_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.MetadataConstants

PROP_VALUE_ATTR - Static variable in class ucl.physiol.neuroconstruct.neuroml.MetadataConstants

PROP_VALUE_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.MetadataConstants

PROPERTIES_FILENAME - Static variable in class ucl.physiol.neuroconstruct.mechanisms.CellMechanismHelper

props - Variable in class ucl.physiol.neuroconstruct.project.GeneratedNetworkConnections.SingleSynapticConnection

PROPS_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.MetadataConstants

PROPS_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.MorphMLConstants

PROTOCOL - Static variable in class ucl.physiol.neuroconstruct.gui.ClickProjectHelper

PSICS - Static variable in class ucl.physiol.neuroconstruct.simulation.SimEnvHelper

PSICS_SING_CHAN_COND_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PSICS_SING_CHAN_COND_NAME - Static variable in class ucl.physiol.neuroconstruct.neuroml.ChannelMLConstants

PsicsException - Exception in ucl.physiol.neuroconstruct.psics

General exception when dealing with/generating PSICS files

PsicsException() - Constructor for exception ucl.physiol.neuroconstruct.psics.PsicsException

PsicsException(String) - Constructor for exception ucl.physiol.neuroconstruct.psics.PsicsException

PsicsException(String, Throwable) - Constructor for exception ucl.physiol.neuroconstruct.psics.PsicsException

PsicsException(Throwable) - Constructor for exception ucl.physiol.neuroconstruct.psics.PsicsException

psicsFileManager - Variable in class ucl.physiol.neuroconstruct.project.Project

PsicsFileManager - Class in ucl.physiol.neuroconstruct.psics

Main file for generating the PSICS files

PsicsFileManager(Project) - Constructor for class ucl.physiol.neuroconstruct.psics.PsicsFileManager

psicsLogFile - Static variable in class ucl.physiol.neuroconstruct.simulation.SimulationsInfo

PsicsMorphologyGenerator - Class in ucl.physiol.neuroconstruct.psics

A single PSICS morphology file from a Cell object

PsicsMorphologyGenerator(Cell, Project, File) - Constructor for class ucl.physiol.neuroconstruct.psics.PsicsMorphologyGenerator

psicsSettings - Variable in class ucl.physiol.neuroconstruct.project.Project

PsicsSettings - Class in ucl.physiol.neuroconstruct.psics

The general parameters needed for PSICS simulations

PsicsSettings() - Constructor for class ucl.physiol.neuroconstruct.psics.PsicsSettings

PULSE_ELEMENT_ROOT - Static variable in class ucl.physiol.neuroconstruct.genesis.GenesisFileManager

PULSEINPUT_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PULSEINPUT_INSTANCE_ELEMENT - Static variable in class ucl.physiol.neuroconstruct.neuroml.NetworkMLConstants

PurkinjeCell - Class in ucl.physiol.neuroconstruct.cell.examples

A simple cell in the cerebellum, used for testing purposes

PurkinjeCell() - Constructor for class ucl.physiol.neuroconstruct.cell.examples.PurkinjeCell

PurkinjeCell(String) - Constructor for class ucl.physiol.neuroconstruct.cell.examples.PurkinjeCell

PynnException - Exception in ucl.physiol.neuroconstruct.pynn

General exception when dealing with/generating PyNN files

PynnException() - Constructor for exception ucl.physiol.neuroconstruct.pynn.PynnException

PynnException(String) - Constructor for exception ucl.physiol.neuroconstruct.pynn.PynnException

PynnException(String, Throwable) - Constructor for exception ucl.physiol.neuroconstruct.pynn.PynnException

PynnException(Throwable) - Constructor for exception ucl.physiol.neuroconstruct.pynn.PynnException

pynnFileManager - Variable in class ucl.physiol.neuroconstruct.project.Project

PynnFileManager - Class in ucl.physiol.neuroconstruct.pynn

Main file for generating the PyNN files

PynnFileManager(Project) - Constructor for class ucl.physiol.neuroconstruct.pynn.PynnFileManager

PynnFileManager.PynnSimulator - Enum in ucl.physiol.neuroconstruct.pynn

pynnUtilsDir - Static variable in class ucl.physiol.neuroconstruct.project.ProjectStructure

PythonUtils - Class in ucl.physiol.neuroconstruct.utils.python

Utilities for Python files

PythonUtils() - Constructor for class ucl.physiol.neuroconstruct.utils.python.PythonUtils