Index (IDARE [idare] 1.0 API)

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

A

AbstractArrayContainer - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: A Basis class for container using ArrayNodeData.
AbstractArrayContainer(DataSet, NodeData) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer: Basic constructor with a source DataSet and the data used in this container.
AbstractArrayContainerLayout - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: The AbstractArrayContainerLayout provides basic features for any AbstractArrayContainerLayout, such as shape placements etc.
AbstractArrayContainerLayout() - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout: Basic constructor
AbstractArrayContainerLayout.LegendShapePosition - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: A AbstractArrayContainerLayout.LegendShapePosition extends a AbstractArrayContainerLayout.ShapePosition by additionally drawing a Label in the center of the shape.
AbstractArrayContainerLayout.ShapePosition - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: A Shapeposition combines a shape with positioning information.
AbstractArrayDataSetProperties - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: Basic properties for a ArrayDataSet.
AbstractArrayDataSetProperties() - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayDataSetProperties
acceptable() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Check whether the current selection is acceptable (i.e.
acceptable() - Method in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Check whether the current selection is acceptable (i.e.
actionPerformed(ActionEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DatasetMenu
actionPerformed(ActionEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
activate() - Method in class idare.imagenode.internal.GUI.Legend.LegendUpdater: Activate the legend updating method
activate() - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction: Activate this mapping.
activate() - Method in class idare.NodeDuplicator.Internal.NodeRegistry
ActiveNodeManager - Class in idare.imagenode.internal.ImageManagement
ActiveNodeManager(CyNetworkViewManager, VisualMappingManager) - Constructor for class idare.imagenode.internal.ImageManagement.ActiveNodeManager
addAllGenes(Set<Gene>) - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
addAltName(String, String) - Method in class idare.sbmlannotator.internal.gpr.Gene
addAltName(String, String) - Method in class idare.sbmlannotator.internal.gpr.Protein
addAltNames(HashMap<String, String>) - Method in class idare.sbmlannotator.internal.gpr.Gene
addAltNames(HashMap<String, String>) - Method in class idare.sbmlannotator.internal.gpr.Protein
addCell(boolean, String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow: Add a Cell with a specified value.
addChild(NetworkNode) - Method in class idare.subnetwork.internal.NetworkNode
addCobraInformationAnnotation() - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
addContainer(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Automatic.ImageBag: Add a DataSet, if there is sufficient space left in this bag.
addData(MultiArrayDataValue, String) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData: Add a new MultiArrayDataValue to this NodeData, for a specific SetID
addData(DataSet) - Method in class idare.imagenode.internal.DataManagement.ImageNodeModel: Add a DataSet to this node.
addDataSet(DataSet) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Add a Dataset to this Manager.
addDataset() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTaskFactory: Creates a new DataSetAdderTask.
addDataSet(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Automatic.ImageNodeContainer: Add A DataSet.
addDataSet(DataSetLayoutInfoBundle, Rectangle) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout: Add a dataset to this Layout.
addDataSetAboutToBeChangedListener(DataSetAboutToBeChangedListener) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Add a Listener that needs to be informed, if a dataset state is about to be changed, before the change actually happened
addDataSetChangeListener(DataSetChangeListener) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Add a Listener that needs to be informed, if a dataset state was changed
AddDataSetToManagerTask - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks
AddDataSetToManagerTask(IDAREWorkbook, DataSetReadingInfo) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.AddDataSetToManagerTask
AddDataSetToManuaLayoutTask - Class in idare.imagenode.internal.Layout.Manual.GUI.Tasks
AddDataSetToManuaLayoutTask(LayoutGUI) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.Tasks.AddDataSetToManuaLayoutTask
addErrorMessage(String) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
addFrame(DataSetFrame) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater: Add a frame to this layout
addGene(Gene) - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
addGenesByProtein(Protein, Set<Gene>) - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
addIDs(Collection<Long>) - Method in class idare.Properties.IDARESettingsManager: Add all IDs of the collection to this manager.
addImageLayoutChangedListener(GraphicsChangedListener) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Add a listener that listens to changed images (and updates accordingly)
addLayoutComponent(String, Component) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
addLayoutComponent(String, Component) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualNodeLayoutManager
addMergedRegion(CellRangeAddress) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
addNetworkToTree(CyNetwork, CyNetwork, String, String) - Method in class idare.subnetwork.internal.NetworkViewSwitcher: Add a subnetwork to the subnetwork hierarchy.
addNodeChangeListener(NodeChangedListener) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Add a listener that listens to changes in nodes in this manager.
addNodes(TaskMonitor) - Method in class idare.imagenode.internal.VisualStyle.StyleManager: Add nodes to the currently used Style, and update the TaskMonitor to indicate the current activity.
addNodes() - Method in class idare.imagenode.internal.VisualStyle.Tasks.AddNodesToStyleTaskFactory: Add Nodes to the current style
addNodeSelectionListener(ItemListener) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetLayoutToolBar
addNodesToStyle(VisualStyle) - Method in class idare.imagenode.internal.VisualStyle.Tasks.AddNodesToStyleTaskFactory
addNodesToStyleDuringLoad(TaskMonitor, VisualStyle) - Method in class idare.imagenode.internal.VisualStyle.StyleManager: Add nodes to the defined Style, and update the TaskMonitor to indicate the current activity.
AddNodesToStyleTaskFactory - Class in idare.imagenode.internal.VisualStyle.Tasks: A TaskFactory that adds nodes to Styles.
AddNodesToStyleTaskFactory(StyleManager, DialogTaskManager) - Constructor for class idare.imagenode.internal.VisualStyle.Tasks.AddNodesToStyleTaskFactory: Default Constructor
addPicture(byte[], int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
addPropertyOption(DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Add Property options to this Dataset, and indicate whether the addition was successful.
addSelectionListener(ItemListener) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ColorToolBarEntry
addSelectionListener(ItemListener) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetPropertyToolBarEntry
addSelectionListener(ItemListener) - Method in class idare.imagenode.internal.Layout.Manual.GUI.NodeIDSelectorToolBarEntry
addStyleUsingNodes(String) - Method in class idare.imagenode.internal.ImageManagement.ActiveNodeManager
addSubNetworkView(CyNetwork, CyNetworkView) - Method in class idare.subnetwork.internal.NetworkViewSwitcher: Add a new Network to the list of existing networks and also add its view.
addToolPack(UDFFinder) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
addValidationData(DataValidation) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
allFinished(FinishStatus) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTask
allHeaders - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
And - Class in idare.imagenode.internal.Services.JSBML: Wrapper for the And Node from the FBC Package of JSBML
And(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.And: Wraps the provided object
Annotation - Class in idare.imagenode.internal.Services.JSBML: Wrapper for the Annotation Object from JSBML which provides only a few operations.
Annotation(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Annotation: Wrap the provided Object (which should be an org.sbml.jsbml.Annotation object
apply(CyRow, View) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
apply(CyRow, View<? extends CyIdentifiable>) - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
apply(CyRow, View) - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
applyAll(CyNetworkView, Iterable<DelayedVizProp>) - Static method in class idare.ThirdParty.DelayedVizProp: Assign the visual properties stored in delayedProps to the given CyNetworkView.
applyStyleToNetwork(CyNetworkView) - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle: Apply the contained visualstyle to a given Networkview and update that view.
applyToAll() - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle: Check whether this style
area - Variable in class idare.imagenode.internal.Layout.Manual.Utilities.LayoutComparator
ArrayDataDescription - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: ItemDataDescription is a Panel, that manages the description of ArrayNodeData using the labels for these items.
ArrayDataDescription() - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
ArrayDataDescription.ItemDescriptionPane - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: A Pane enclosing the layout of a single item description (Label and Name)
ArrayDataDescription.ItemDescriptionResizeListener - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: Listener that updates the itemdescriptions based on the width of the enclosing legend.
ArrayDataSet - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: An Abstract basis class for item based datasets.
ArrayDataSet() - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Basic constructor using the default settings.
ArrayDataSet(String) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Basic constructor using a specific DataSetName
ArrayDataSet(int, boolean, Properties) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Constructor using an ID, indication for twoColumn use in the datafile, and a properties collection
ArrayNodeData - Class in idare.imagenode.Data.BasicDataTypes.ArrayData: NodeData that can be used for any ArrayDataSet
ArrayNodeData(DataSet) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData: Basic constructor using the dataset this is originating from
associateGenesToProtein(Protein, Set<Gene>) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
Association - Class in idare.imagenode.internal.Services.JSBML: Wrapper for the Association Object from the fbc package of JSBML
Association(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Association: A Wrapper that takes a hopefully) Association object
AutomaticNodeLayout - Class in idare.imagenode.internal.Layout.Automatic: Te NodeLAyout stores the localisation of different Containerlayouts and sets them up using the Datasets in this layout.
AutomaticNodeLayout() - Constructor for class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
AutomaticNodeLayout(Collection<DataSetLayoutInfoBundle>) - Constructor for class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout: Generate an automatic layout for a set of DataSetLayouts
autoresize - Variable in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
autoSizeColumn(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
autoSizeColumn(int, boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
availablecolors - Variable in class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale: A general field from which additional colors are generated.
availablecolors - Static variable in class idare.imagenode.internal.ColorManagement.ColorScales.PrismScale

B

BasicIDARECell - Class in idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation: Basic implementation of a Simple Cell for a BasicIDAREWorkbook.
BasicIDARECell(IDARECell.CellType, BasicIDARERow) - Constructor for class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell: Basic Constructor indicating the containing row and the type of the cell
BasicIDARECell(IDARECell.CellType, String, BasicIDARERow) - Constructor for class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell: Basic Constructor indicating the containing row and the type of the cell, along with the value to be stored.
BasicIDARERow - Class in idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation: A simple implementation of an IDARERow
BasicIDARERow(BasicIDARESheet) - Constructor for class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Simple constructor providing the parent sheet.
BasicIDARESheet - Class in idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation: This is a basic implementation of a IDARESheet for convenience.
BasicIDARESheet(String) - Constructor for class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet: Default constructor using the name of the sheet.
BasicIDAREWorkbook - Class in idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation: A simple implementation of an IDAREWorkbook
BasicIDAREWorkbook() - Constructor for class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
BlackYellowRed - Class in idare.imagenode.internal.ColorManagement.ColorScales: A Colorscale from Black via Yellow To Red
BlackYellowRed() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.BlackYellowRed
BLUEWHITERED - Static variable in class idare.imagenode.ColorManagement.ColorScaleFactory
BlueWhiteRedScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A Colorscale from Blue via White To Red
BlueWhiteRedScale() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.BlueWhiteRedScale
BlueYellowRed - Class in idare.imagenode.internal.ColorManagement.ColorScales: A Colorscale from Blue via Yellow To Red
BlueYellowRed() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.BlueYellowRed
BoundsPopupMenuListener - Class in idare.ThirdParty: This class will change the bounds of the JComboBox popup menu to support different functionality.
BoundsPopupMenuListener() - Constructor for class idare.ThirdParty.BoundsPopupMenuListener: Convenience constructore to allow the display of a horizontal scrollbar when required.
BoundsPopupMenuListener(boolean, boolean) - Constructor for class idare.ThirdParty.BoundsPopupMenuListener: Convenience constructor that allows you to display the popup wider and/or above the combo box.
BoundsPopupMenuListener(int) - Constructor for class idare.ThirdParty.BoundsPopupMenuListener: Convenience constructor that allows you to display the popup wider than the combo box and to specify the maximum width
BoundsPopupMenuListener(boolean, boolean, int, boolean) - Constructor for class idare.ThirdParty.BoundsPopupMenuListener: General purpose constructor to set all popup properties at once.
BufferedImageTranscoder - Class in idare.ThirdParty: Credits: http://bbgen.net/blog/2011/06/java-svg-to-bufferedimage/ Obtained from https://github.com/Data2Semantics/nodes/blob/master/nodes/src/main/java/org/nodes/util/BufferedImageTranscoder.java
BufferedImageTranscoder() - Constructor for class idare.ThirdParty.BufferedImageTranscoder
buildColorMapVisualisation(HashMap<Double, String>, JScrollPane) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Generate the Color Scale Layout and visual representation based on the Labels used for the respective positions.
buildResizer() - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
bundle - Variable in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
bundle - Variable in class idare.imagenode.internal.Layout.Manual.Utilities.LayoutComparator
bundlelayout - Variable in class idare.imagenode.internal.Layout.Manual.Utilities.LayoutComparator

C

cancel() - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREReaderSetupTask
cancel() - Method in class idare.NodeDuplicator.Internal.NodeDuplicatorImpl
cancel() - Method in class idare.NodeDuplicator.Internal.NodeMergerImpl
cellIterator() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
cellIterator() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow: Obtain an Iterator over the IDARECells of this row.
cellIterator() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
cellIterator() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
changeItemCount(int) - Method in class idare.imagenode.Utilities.ColorScalePopupAdjuster: Change the number of items that are being adjusted by this adjuster
CircleContainer - Class in idare.imagenode.internal.Data.Array.CircleData: CircleContainer is a container for Circles representing the data items.
CircleContainer(DataSet, ArrayNodeData) - Constructor for class idare.imagenode.internal.Data.Array.CircleData.CircleContainer: Basic Constructor using the source dataset and an instance of the data.
CircleContainerLayout - Class in idare.imagenode.internal.Data.Array.CircleData: Layout for Circle items.
CircleContainerLayout() - Constructor for class idare.imagenode.internal.Data.Array.CircleData.CircleContainerLayout: Basic Constructor
CircleDataSetProperties - Class in idare.imagenode.internal.Data.Array.CircleData: Properties of an Array Dataset represented by Circles.
CircleDataSetProperties() - Constructor for class idare.imagenode.internal.Data.Array.CircleData.CircleDataSetProperties
CircleGridProperties - Class in idare.imagenode.internal.Data.Array.CircleGridData: Properties of a Gridded Circle Dataset.
CircleGridProperties() - Constructor for class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties
clear() - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction: Clear the mapping that is currently used
clearDataSets() - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Clear all Datasets, and inform any listeners that the sets are being removed.
clearTemporaryFolder() - Static method in class idare.imagenode.Utilities.IOUtils: Clear the Temporary folder.
cloneSheet(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
CobraUtil - Class in idare.ThirdParty: Contains some useful methods to manipulate 'COBRA SBML'
CobraUtil() - Constructor for class idare.ThirdParty.CobraUtil
colName - Variable in class idare.subnetwork.internal.NetworkNode
ColorMap - Class in idare.imagenode.ColorManagement: A ColorMap provides an interface to a DataSet to obtain colors for specific values present in the DataSet.
ColorMap(ColorScale) - Constructor for class idare.imagenode.ColorManagement.ColorMap: Generate a new ColorMap using the provided ColorScale
colormap - Variable in class idare.imagenode.internal.Layout.DataSetLayoutInfoBundle
colormaps - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
colormaps - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
ColorMenuItem - Class in idare.imagenode.internal.Layout.Manual.GUI
ColorMenuItem(ColorScalePane) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.ColorMenuItem
ColorPane - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
ColorPopup - Class in idare.imagenode.internal.Layout.Manual.GUI
ColorPopup() - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.ColorPopup
ColorScale - Interface in idare.imagenode.ColorManagement: A ColorScale provides Colors based on its properties for values between 0 and 1.
ColorScaleColors - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
ColorScaleFactory - Class in idare.imagenode.ColorManagement: The ColorScaleFactory can either generate individual ColorScales or sets of ColorScales which possess specific properties.
ColorScaleFactory() - Constructor for class idare.imagenode.ColorManagement.ColorScaleFactory
ColorScaleFractions - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
ColorScaleLegendLayout(Double[]) - Constructor for class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout: Generate a layout based on an array of fractions (these fractions have to rage from 0.0 to 1.0 in ascending order!
ColorScalePane - Class in idare.imagenode.ColorManagement: A Colorscale pane is a graphical representation of a ColorScale, that can be added to Swing Components.
ColorScalePane(ColorScale) - Constructor for class idare.imagenode.ColorManagement.ColorScalePane: Create a ColorScalePane using the provided ColorScale.
ColorScalePopupAdjuster - Class in idare.imagenode.Utilities: A PopupAdjuster for ColorScales, that updates the size of the colorscale being displayed, when selecting colors.
ColorScalePopupAdjuster(int) - Constructor for class idare.imagenode.Utilities.ColorScalePopupAdjuster: Default Constructor indicating how many panes to use.
ColorScaleProperties - Class in idare.imagenode.internal.ColorManagement.ColorScales: Properties of a colorscale.
ColorScaleProperties(Color[], float[]) - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.ColorScaleProperties
ColorSteps - Variable in class idare.imagenode.internal.ColorManagement.ColorScales.ColorScaleProperties
ColorSteps - Variable in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
ColorToolBarEntry - Class in idare.imagenode.internal.Layout.Manual.GUI
ColorToolBarEntry() - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.ColorToolBarEntry
ColorUtils - Class in idare.imagenode.ColorManagement: Color Utils provide some static convenience functions for Colors
ColorUtils() - Constructor for class idare.imagenode.ColorManagement.ColorUtils
colSelector - Variable in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI
Column_Identifiers - Static variable in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel
columncount - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
columnLabels - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: A Vector indicating the labels of each column
ColumnName - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
ColumnTypeChooser - Class in idare.imagenode.internal.GUI.NetworkSetup: ColumnTypeChoose is a JPanel that Provides multiple comboboxes depending on the number of options provided by a selected column.
ColumnTypeChooser(CyNetwork, Vector<String>) - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Default Constructor using the available columnNames
compareTo(NodeValue) - Method in class idare.imagenode.Interfaces.DataSets.NodeValue
compareTo(LayoutArea) - Method in class idare.imagenode.internal.Layout.Manual.Utilities.LayoutArea
compareTo(LayoutComparator) - Method in class idare.imagenode.internal.Layout.Manual.Utilities.LayoutComparator
ComponentLayout - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
componentMoved(ComponentEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
componentResized(ComponentEvent) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionResizeListener
componentResized(ComponentEvent) - Method in class idare.imagenode.GUI.Legend.Utilities.TextPaneResizer
componentResized(ComponentEvent) - Method in class idare.imagenode.internal.GUI.Legend.NodeResizer
componentResized(ComponentEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
CompoundID - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties
CompoundID - Variable in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnProperties
compoundTypeSelector - Variable in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser
compoundTypeSelector - Variable in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser
ContainerLayout - Class in idare.imagenode.Interfaces.Layout: Classes implementing this interface need to be able to generate a layout when provided with an area to generate the layout
ContainerLayout() - Constructor for class idare.imagenode.Interfaces.Layout.ContainerLayout
ContainerUnplaceableExcpetion - Exception in idare.imagenode.exceptions.layout: Exception indicating, that there was at least one unplaceable container in a given layout.
ContainerUnplaceableExcpetion(String) - Constructor for exception idare.imagenode.exceptions.layout.ContainerUnplaceableExcpetion
ContinousColorMap - Class in idare.imagenode.ColorManagement.ColorMapTypes: An Abstract class representing general continuous color maps and providing some functionality for such maps.
ContinousColorMap(double, double, ColorScale) - Constructor for class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Generate a continous color map based on a color scale and a minimal and maximal value.
ContinousColorMap.ColorScaleLegendLayout - Class in idare.imagenode.ColorManagement.ColorMapTypes: A Class that provides layout functionality for ColorScale Legends.
ContinousZeroBalancedMap - Class in idare.imagenode.ColorManagement.ColorMapTypes
ContinousZeroBalancedMap(double, double, ColorScale) - Constructor for class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap: A Constructor using a minimum and maximum value along with a given colorscale
convertBufferedImageToRectangle() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomImageLayer: Set the rectangle that contains the BufferedImage - or should contain it, according to x,y, width and height
CREATE_NULL_AS_BLANK - Static variable in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow: A Few Values to see how to handle missing or empty cells.
createAndShowGUI(DataSetSelectionModel, DataSetManager, IDAREImageNodeApp, CreateNodesTaskFactory) - Static method in class idare.imagenode.internal.Layout.Manual.LayoutGUI: Build the gui
createCell() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Create a Blank Cell at the end of this row.
createCell(IDARECell.CellType) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Create a Cell with a specified type at the end of this row This is the same as a call to createCell(type,getLastCellNum()-1)
createCell(int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Create a blank cell at a specified position, overwriting any cell existing at the provided position This is the same as the Call createCell(CellType.BLANK,pos)
createCell(IDARECell.CellType, int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Create a Cell of the specified type at the specified position.
createCell(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
createCell(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
createCellStyle() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
createColors(int, Color[]) - Static method in class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale: Create a color array given a number of colors necessary and the Colors available
createDataFormat() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
createDataSet(boolean, String, String, IDAREWorkbook) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Create a Dataset based on properties and a DataSetFile.
createDrawingPatriarch() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
createEmptyLayout() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer
createEmptyLayout() - Method in interface idare.imagenode.Interfaces.DataSets.DataContainer: Create a new Layout for this container.
createEmptyLayout() - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleContainer
createEmptyLayout() - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainer
createEmptyLayout() - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainer
createEmptyLayout() - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainer
createEmptyLayout() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainer
createFont() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
createFrame(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI: create A Frame for the given Bundle
createFreezePane(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
createFreezePane(int, int, int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
createImage(int, int) - Method in class idare.ThirdParty.BufferedImageTranscoder
createLayout(NodeData, Rectangle, String, DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.Layout.ContainerLayout: Create the Layout for a given set of data, in a specified area using a specified Label for the underlying Dataset.
createLayout() - Method in class idare.imagenode.internal.Layout.Automatic.ImageBag: Create the layout, if possible.
createLayout(JFrame) - Method in class idare.imagenode.internal.Layout.Automatic.ImageNodeContainer: Create the layout for the contained ImageBags and return the Panels generated from the ImageBags (mapped to the ImageBags and associated with their respective DataContainers.
createMarker(String, Point2D, double) - Static method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout: Plot a Marker for the given ID The chosen marker depends on the hash code of the itemID provided.
createMenuBar() - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
createName() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
CreateNodeImagesTaskFactory - Class in idare.imagenode.internal.GUI.Legend.Tasks
CreateNodeImagesTaskFactory(FileUtil, IDARELegend, NodeManager, CySwingApplication) - Constructor for class idare.imagenode.internal.GUI.Legend.Tasks.CreateNodeImagesTaskFactory
CreateNodeImageTask - Class in idare.imagenode.internal.GUI.Legend.Tasks
CreateNodeImageTask(IDARELegend, File, NodeManager, String) - Constructor for class idare.imagenode.internal.GUI.Legend.Tasks.CreateNodeImageTask: Default Constructor
CreateNodesTaskFactory - Class in idare.imagenode.internal.GUI.DataSetController: A TaskFactory that initializes the generation of Imagenodes.
CreateNodesTaskFactory(NodeManager, DataSetControlPanel, DialogTaskManager) - Constructor for class idare.imagenode.internal.GUI.DataSetController.CreateNodesTaskFactory: Default constructor with a TaskManager that can handle the created tasks, the NodeManager to generate the Layouts and the DataSetControlPanel to obtain the layoutinformation from.
createNullCell() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Create a Null cell at the end of this row.
createRow() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet: Create a row at the end of this sheet
createRow(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
createSelectedFrames(DataSetSelectionModel) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI: Create the selected Frames
createSelectionDescription(String, Color, Font) - Static method in class idare.imagenode.Utilities.GUIUtils: Create a JTextPane that is uneditable and uses background and font as desired.
createSelectionPanel(String, JComboBox, Color) - Static method in class idare.imagenode.Utilities.GUIUtils: Create a SelecionPanel, with a given String and a JCombobox as selector along with a given backrgound color.
createSheet(String) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook: Create a new Sheet in this Workbook.
createSheet() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
createSheet(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
createSplitPane(int, int, int, int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
createSubNetworkTableModel(CyNetwork) - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI: Create the TableModel for the SubSystem Selection
createSVGDoc() - Static method in class idare.imagenode.Utilities.LayoutUtils: Create an SVG Document using a default DOM implementation.
createTaskIterator() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTaskFactory
createTaskIterator() - Method in class idare.imagenode.internal.GUI.DataSetController.CreateNodesTaskFactory
createTaskIterator() - Method in class idare.imagenode.internal.GUI.Legend.Tasks.CreateNodeImagesTaskFactory
createTaskIterator(CyNetworkView) - Method in class idare.imagenode.internal.GUI.Legend.Tasks.CreateNodeImagesTaskFactory
createTaskIterator() - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTaskFactory
createTaskIterator(CyNetworkView) - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTaskFactory
createTaskIterator() - Method in class idare.imagenode.internal.VisualStyle.Tasks.AddNodesToStyleTaskFactory
createTaskIterator(CyNetworkView) - Method in class idare.imagenode.internal.VisualStyle.Tasks.AddNodesToStyleTaskFactory
createTaskIterator() - Method in class idare.imagenode.internal.VisualStyle.Tasks.RemoveNodesFromStyleTaskFactory
createTaskIterator(CyNetworkView) - Method in class idare.imagenode.internal.VisualStyle.Tasks.RemoveNodesFromStyleTaskFactory
createTaskIterator(View<CyNode>, CyNetworkView) - Method in class idare.NodeDuplicator.Internal.NodeDuplicatorFactory
createTaskIterator(View<CyNode>, CyNetworkView) - Method in class idare.NodeDuplicator.Internal.NodeMergerFactory
createTaskIterator() - Method in class idare.NodeDuplicator.Internal.NodeRegistry
createTaskIterator() - Method in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
createTaskIterator(CyNetworkView) - Method in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
createTaskIterator() - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFactory
createTaskIterator(CyNetworkView) - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFactory
createTaskIterator(View<CyNode>, CyNetworkView) - Method in class idare.subnetwork.internal.NetworkViewSwitcher
createTaskIterator() - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreatorTaskFactory
createTaskIterator(CyNetworkView) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreatorTaskFactory
createTemporaryFolder() - Static method in class idare.imagenode.Utilities.IOUtils: Create the Temporary folder (if it does not exist).
createTunableHandler(Field, Object, Tunable) - Method in class idare.imagenode.internal.GUI.DataSetAddition.DataSetParametersGUIHandlerFactory
createTunableHandler(Method, Method, Object, Tunable) - Method in class idare.imagenode.internal.GUI.DataSetAddition.DataSetParametersGUIHandlerFactory
createTunableHandler(Field, Object, Tunable) - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupGUIHandlerFactory
createTunableHandler(Method, Method, Object, Tunable) - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupGUIHandlerFactory
createTunableHandler(Field, Object, Tunable) - Method in class idare.imagenode.internal.Layout.Manual.GUI.Tasks.NetworkSetupGUIHandlerFactory
createTunableHandler(Method, Method, Object, Tunable) - Method in class idare.imagenode.internal.Layout.Manual.GUI.Tasks.NetworkSetupGUIHandlerFactory
createTunableHandler(Field, Object, Tunable) - Method in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkPropertyColumnGUIHandlerFactory
createTunableHandler(Method, Method, Object, Tunable) - Method in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkPropertyColumnGUIHandlerFactory
createTunableHandler(Field, Object, Tunable) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationGUIHandlerFactory
createTunableHandler(Method, Method, Object, Tunable) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationGUIHandlerFactory
cs - Variable in class idare.imagenode.ColorManagement.ColorMap
CSVCell - Class in idare.imagenode.internal.DataSetReaders.CSVReader: A implementation of a Cell for use in CSV files.
CSVCell(int, CSVRow) - Constructor for class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell: Create a new cell with of a specific type and in a specific row.
CSVReader - Class in idare.imagenode.internal.DataSetReaders.CSVReader: The CSV Reader assumes, that
CSVReader() - Constructor for class idare.imagenode.internal.DataSetReaders.CSVReader.CSVReader
CSVRow - Class in idare.imagenode.internal.DataSetReaders.CSVReader: An implementation of a Row in a CSV Sheet.
CSVRow(CSVSheet) - Constructor for class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow: Basic constructor with the enclosing sheet.
CSVSheet - Class in idare.imagenode.internal.DataSetReaders.CSVReader: A Sheet implementation to be used for CSV files.
CSVSheet(CSVWorkbook, String) - Constructor for class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet: Simple constructor.
CSVWorkbook - Class in idare.imagenode.internal.DataSetReaders.CSVReader: This class provides functionality to read text delimited files.
CSVWorkbook(File, String, int) - Constructor for class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook: Create a new Workbook using a specific file and a defined separator.
currentNetwork - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
currentNetworkView - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
customizePopup(BasicComboPopup) - Method in class idare.imagenode.Utilities.ColorScalePopupAdjuster: Costumize the Popup, by first adjusting the height according to the number of panes set for this ColorScalePopupAdjuster
customizePopup(BasicComboPopup) - Method in class idare.ThirdParty.BoundsPopupMenuListener
CVTerm - Class in idare.imagenode.internal.Services.JSBML
CVTerm(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.CVTerm
CVTerm.Qualifier - Enum in idare.imagenode.internal.Services.JSBML
CyActivator - Class in idare.internal
CyActivator() - Constructor for class idare.internal.CyActivator
cyAppMgr - Variable in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
cySwingApp - Variable in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
CytoscapeUtils - Class in idare.ThirdParty
CytoscapeUtils() - Constructor for class idare.ThirdParty.CytoscapeUtils

D

data - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer
Data - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
data - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer: The NodeData this container is associated with
Data - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
DataContainer - Interface in idare.imagenode.Interfaces.DataSets: A DataContainer is a class that is able to provide a specific ContainerLayout for a node.
DataSet - Class in idare.imagenode.Interfaces.DataSets: A DataSet is a storage for data.
DataSet() - Constructor for class idare.imagenode.Interfaces.DataSets.DataSet
DataSet(int, boolean, Properties) - Constructor for class idare.imagenode.Interfaces.DataSets.DataSet
dataset - Variable in class idare.imagenode.internal.Layout.DataSetLayoutInfoBundle
DATASET_FILES - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
DATASET_PROPERTIES - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
DATASET_PROPERTIES_FILE_NAME - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES: IDS for File Lists to store and save Datasets in cytoscape
DataSetAboutToBeChangedListener - Interface in idare.imagenode.internal.DataManagement.Events: A Listener of this type will be informed, if DataSets are about to change.
DataSetAdderTask - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks
DataSetAdderTask(DataSetManager) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTask
DataSetAdderTaskFactory - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks: A Class to provide a factory method to create a Dataset
DataSetAdderTaskFactory(DataSetManager, DialogTaskManager, CySwingApplication) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTaskFactory
datasetChanged(DataSetChangedEvent) - Method in interface idare.imagenode.internal.DataManagement.Events.DataSetAboutToBeChangedListener: Inform that there will be a change in the DataSets
datasetChanged(DataSetChangedEvent) - Method in interface idare.imagenode.internal.DataManagement.Events.DataSetChangeListener: Inform that there was a change in the DataSets
datasetChanged(DataSetChangedEvent) - Method in class idare.imagenode.internal.DataManagement.NodeManager
datasetChanged(DataSetChangedEvent) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel
datasetChanged(DataSetChangedEvent) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
datasetChanged(DataSetChangedEvent) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout
datasetChanged(DataSetChangedEvent) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
datasetChanged(DataSetChangedEvent) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
DataSetChangedEvent - Class in idare.imagenode.internal.DataManagement.Events: An Event Indicating that Datasets are changing.
DataSetChangedEvent(DataSetManager, DataSet, boolean, boolean, boolean) - Constructor for class idare.imagenode.internal.DataManagement.Events.DataSetChangedEvent: Create a New Event with the changing set, the DataSetManager this event originates from and an indicator whether the set is added or removed.
DataSetChangeListener - Interface in idare.imagenode.internal.DataManagement.Events: A Listener of this kind will be informed if a Dataset HAS been changed.
DATASETCOLLECTION_FILE_NAME - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
DATASETCOLORSCALE - Static variable in class idare.imagenode.Interfaces.DataSets.DataSet
DataSetControlPanel - Class in idare.imagenode.internal.GUI.DataSetController: A Panel that controls the DataSets, and allows the management of said sets.
DataSetControlPanel(CySwingApplication, IDAREImageNodeApp) - Constructor for class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel: The Constructor for a DataSetControlPanel.
DATASETDESCRIPTION - Static variable in class idare.imagenode.Interfaces.DataSets.DataSet
DataSetFactory - Class in idare.imagenode.internal.DataManagement: A Class that loads different DataSets based on their classname
DataSetFactory() - Constructor for class idare.imagenode.internal.DataManagement.DataSetFactory: Default constructor
DataSetFrame - Class in idare.imagenode.internal.Layout.Manual.GUI
DataSetFrame(DataSetLayoutInfoBundle, String, JComponent) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
DataSetGenerationParameters - Class in idare.imagenode.internal.GUI.DataSetAddition
DataSetGenerationParameters() - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.DataSetGenerationParameters
dataSetID - Variable in class idare.imagenode.Interfaces.DataSets.DataSet
DataSetIDProvider - Class in idare.imagenode.internal.DataManagement: Generate IDs for DataSets, in order that sets have distinct IDs.
DataSetIDProvider() - Constructor for class idare.imagenode.internal.DataManagement.DataSetIDProvider: Initialize a new DataSetIDProvider
DataSetLayoutInfoBundle - Class in idare.imagenode.internal.Layout: A simple bundle struct for a DataSet and a ColorMap
DataSetLayoutInfoBundle() - Constructor for class idare.imagenode.internal.Layout.DataSetLayoutInfoBundle
DataSetLayoutProperties - Class in idare.imagenode.Interfaces.Layout: DataSetLayoutProperties allow the use of a specific class of DataSets for multiple different layouts.
DataSetLayoutProperties() - Constructor for class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties
DataSetLayoutToolBar - Class in idare.imagenode.internal.Layout.Manual.GUI
DataSetLayoutToolBar(ManualLayoutUpdater, Vector<String>) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.DataSetLayoutToolBar
DataSetLink - Interface in idare.imagenode.internal.Layout
DataSetManager - Class in idare.imagenode.internal.DataManagement: A class to manage Datasets
DataSetManager() - Constructor for class idare.imagenode.internal.DataManagement.DataSetManager: Default constructor initializing required fields.
DatasetMenu - Class in idare.imagenode.internal.Layout.Manual.GUI
DatasetMenu(DataSet, LayoutGUI) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.DatasetMenu
DataSetParametersGUIHandler - Class in idare.imagenode.internal.GUI.DataSetAddition
DataSetParametersGUIHandler(Method, Method, Object, Tunable, FileUtil, DataSetManager, CySwingApplication) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.DataSetParametersGUIHandler
DataSetParametersGUIHandler(Field, Object, Tunable, FileUtil, DataSetManager, CySwingApplication) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.DataSetParametersGUIHandler
DataSetParametersGUIHandlerFactory - Class in idare.imagenode.internal.GUI.DataSetAddition
DataSetParametersGUIHandlerFactory(FileUtil, DataSetManager, CySwingApplication) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.DataSetParametersGUIHandlerFactory
datasetProperties - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: The properties to be used for this dataset, need to be set during reading of data.
DataSetPropertyToolBarEntry - Class in idare.imagenode.internal.Layout.Manual.GUI
DataSetPropertyToolBarEntry() - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.DataSetPropertyToolBarEntry
DataSetProvider - Class in idare.imagenode.internal.DataManagement: A Simple Plugin that adds the Default properties and DataSets to IDARE
DataSetProvider() - Constructor for class idare.imagenode.internal.DataManagement.DataSetProvider
DataSetReaderProvider - Class in idare.imagenode.internal.DataSetReaders: This class provides the basic IDARE File Readers (XLS and TSV/CSV files).
DataSetReaderProvider() - Constructor for class idare.imagenode.internal.DataSetReaders.DataSetReaderProvider
DataSetReadingInfo - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks
DataSetReadingInfo(DataSetManager, DataSetGenerationParameters) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
datasetsChanged(DataSetsChangedEvent) - Method in interface idare.imagenode.internal.DataManagement.Events.DataSetAboutToBeChangedListener: Inform that a Collection of changes coming up in the DataSets.
datasetsChanged(DataSetsChangedEvent) - Method in interface idare.imagenode.internal.DataManagement.Events.DataSetChangeListener: Inform that a Collection of DataSets changed.
datasetsChanged(DataSetsChangedEvent) - Method in class idare.imagenode.internal.DataManagement.NodeManager
datasetsChanged(DataSetsChangedEvent) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel
datasetsChanged(DataSetsChangedEvent) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
datasetsChanged(DataSetsChangedEvent) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout
datasetsChanged(DataSetsChangedEvent) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
datasetsChanged(DataSetsChangedEvent) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
DataSetsChangedEvent - Class in idare.imagenode.internal.DataManagement.Events: An event indicating the change of the state of multiple Datasets.
DataSetsChangedEvent(DataSetManager, Collection<DataSet>, boolean, boolean, boolean) - Constructor for class idare.imagenode.internal.DataManagement.Events.DataSetsChangedEvent: Create a New Event with the changing sets, the DataSetManager this event originates from and an indicator whether the sets are added or removed.
DataSetSelectionModel - Class in idare.imagenode.internal.GUI.DataSetController: The DataSetSelectionModel provides specific renderers and Editors for the items in the current DataSetSelectionTable.
DataSetSelectionModel(DataSetManager) - Constructor for class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Create a new DataSetSelectionModel by providing the DataSetManager, which is used to build the model on.
DataSetSelectionTable - Class in idare.imagenode.internal.GUI.DataSetController: A DataSetSelectionTable, that is specific to the DataSetSelectionModel, using its unique renderers and editors.
DataSetSelectionTable(DataSetSelectionModel) - Constructor for class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionTable
DataSetType - Static variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
DataSetType - Variable in class idare.imagenode.internal.GUI.DataSetAddition.DataSetGenerationParameters
deactivate() - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction: Deactivate this mapping.
deactivate() - Method in class idare.NodeDuplicator.Internal.NodeRegistry
DebugException - Exception in idare.imagenode.internal.exceptions.debug: Class to be used with the PrintFDebugger
DebugException(String, Object) - Constructor for exception idare.imagenode.internal.exceptions.debug.DebugException
Debugging(Object, String) - Static method in class idare.imagenode.internal.Debug.PrintFDebugger
DEFAULT_SERIES_NAME - Static variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
defaultData - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
defaultEntry - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
DefaultLayoutProvider - Class in idare.imagenode.internal.ImageManagement
DefaultLayoutProvider() - Constructor for class idare.imagenode.internal.ImageManagement.DefaultLayoutProvider
DelayedVizProp - Class in idare.ThirdParty: DelayedVizProp, as suggested in the Cytoscape cookbook.
DelayedVizProp(CyIdentifiable, VisualProperty<?>, Object, boolean) - Constructor for class idare.ThirdParty.DelayedVizProp: Specify the desired visual property value for a node or edge.
deRegisterDataSetProperties(Class<? extends DataSet>, DataSetLayoutProperties) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Deregister DataSetProperties from a DataSet of the given Type.
deregisterDataSetReader(IDAREDatasetReader) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: DeRegister a IDAREDatasetReader.
deRegisterDataSetReader(IDAREDatasetReader) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Deregister an IDAREDatasetReader from being available in the app.
deRegisterDataSetType(String, Class<? extends DataSet>) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Remove a class from the available Datasetclasses.
deregisterDataSetType(DataSet) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Deregister a the an available DataSet class based on an instance of the class.
deRegisterLayout(ImageNodeLayout) - Method in class idare.imagenode.internal.Layout.io.LayoutIOManager: DeRegister a specific type of Layout, it will no longer be available.
deRegisterPlugin(IDAREPlugin) - Method in class idare.imagenode.IDAREImageNodeAppService: Deregister a plugin from the IDARE App;
deRegisterPlugin(IDAREPlugin) - Method in class idare.imagenode.internal.IDAREImageNodeApp: UnRegister a plugin.
deregisterPropertiesForDataSet(Class<? extends DataSet>, DataSetLayoutProperties) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Deregister Properties for a DataSet
description - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryDescriptionPane
Description - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: The Description of this Dataset.
DescriptionPanes - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
determineDisplayRange(Double[]) - Static method in class idare.imagenode.Interfaces.Layout.ContainerLayout: This function allows to get a Range of minimal and maximal values based on a valuerange to determine suitable axes.
determineNonEmptyColumns(IDAREWorkbook) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Determine the columns which are non empty, This can be derived from the Header column as all columns which are set have to contain a label.
DimensionMismatchException - Exception in idare.imagenode.exceptions.layout: Exception indicating, that a Container was too larger and could not be placed.
DimensionMismatchException(String) - Constructor for exception idare.imagenode.exceptions.layout.DimensionMismatchException
disable() - Method in class idare.imagenode.internal.GUI.Legend.LegendUpdater: Inactivate the updating method
DiscreteColorMap - Class in idare.imagenode.ColorManagement.ColorMapTypes: A Colormap that can provide colors for a discrete number of values (i.e.
DiscreteColorMap(Collection<Comparable>, ColorScale) - Constructor for class idare.imagenode.ColorManagement.ColorMapTypes.DiscreteColorMap: Generate a Colormap based on a set of values and a given colorscale.
DiscreteColorScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A Discrete color scale.
DiscreteColorScale(Color[]) - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale: Basic constructors using a set of colors and initializing the scale with as many colors.
DiscreteColorScale(Color[], int) - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale: A constructor for a scale with colorcount colors using the availablecolors array to generate these colors.
DiscreteColorScalePane - Class in idare.imagenode.ColorManagement: A Discrete color scale pane The difference to a normal colorscalepane is, that this pane will plot with discrete colors and will not use a linear gradient to walk between the colors.
DiscreteColorScalePane(ColorScale) - Constructor for class idare.imagenode.ColorManagement.DiscreteColorScalePane: A Basic DiscreteColorScalePane.
doc - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
doLayout() - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
doLayout() - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Produce the layout based on the added DataSets.
doLayout() - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
doLayout() - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
doUseTwoColumns() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
draw(SVGGraphics2D, Color) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.LegendShapePosition: Draw the shape at the specified position and then adding the label above it.
draw(SVGGraphics2D, Color) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.ShapePosition: Draw the shape in the given SVGGraphics2D context with the provided color
draw(SVGGraphics2D, Color) - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout.RectangleLegendShapePosition
draw(SVGGraphics2D, Color) - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout.RectangleShapePosition
draw(SVGGraphics2D) - Method in class idare.imagenode.Utilities.LegendLabel: Draw the Label in the given SVGGraphics2D context
draw(SVGGraphics2D, String) - Method in class idare.imagenode.Utilities.LegendLabel: Draw the Label in the given SVGGraphics2D context
ds - Variable in class idare.imagenode.internal.Layout.SimpleLink
DuplicateIDException - Exception in idare.imagenode.exceptions.io: Exception indicating that there was a duplicate ID.
DuplicateIDException(String, String) - Constructor for exception idare.imagenode.exceptions.io.DuplicateIDException
duplicateNodes - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties

E

EdgeType() - Constructor for class idare.Properties.IDAREProperties.EdgeType
emptycolumns - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
entry - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryDescriptionPane
EOOMarker - Class in idare.imagenode.Utilities: Helper Class for Serializable Input/OUTPUT Streams to mark the end of objects.
EOOMarker() - Constructor for class idare.imagenode.Utilities.EOOMarker
equals(Object) - Method in class idare.imagenode.Interfaces.DataSets.NodeValue
equals(Object) - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Two Datasetproperties are equal, if they have the same Type name.
equals(Object) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POICell
equals(Object) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
equals(Object) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
equals(Object) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
equals(Object) - Method in class idare.imagenode.internal.Layout.Manual.Utilities.LayoutComparator
equals(Object) - Method in class idare.imagenode.internal.Layout.SimpleLink
equals(Object) - Method in class idare.imagenode.internal.Services.JSBML.SBase
equals(Object) - Method in class idare.sbmlannotator.internal.gpr.Gene
equals(Object) - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
equals(Object) - Method in class idare.sbmlannotator.internal.gpr.Protein
ErrorMessage - Variable in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnProperties: An error Message if something besides an exception went wrong during the handling process.
eventHelper - Variable in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
execute(TaskMonitor) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREReaderSetupTask: Execute the Task.

F

FailureTask - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks
FailureTask(DataSetReadingInfo) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.FailureTask
FBCGPRParser - Class in idare.sbmlannotator.internal.gpr
FBCGPRParser(Association, Model, HashMap<SBase, Gene>, HashMap<SBase, Protein>, HashMap<String, SBase>) - Constructor for class idare.sbmlannotator.internal.gpr.FBCGPRParser
fileTypeAccepted(File) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: Test, whether the file can potentially be read by this reader.
fileTypeAccepted(File) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVReader
fileTypeAccepted(File) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.TSVReader
fileTypeAccepted(File) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIReader
fileutil - Variable in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
findFont(short, short, short, String, boolean, boolean, short, byte) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
flagcolors - Static variable in class idare.imagenode.internal.ColorManagement.ColorScales.FlagScale
FlagScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A Discrete ColorScale with Red, white blue and black as colors.
FlagScale() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.FlagScale
Flexible - Variable in class idare.imagenode.Properties.Localisation
fractions - Variable in class idare.imagenode.internal.ColorManagement.ColorScales.ColorScaleProperties
fractions - Variable in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
fUtil - Variable in class idare.imagenode.internal.Services.JSBML.SBMLManagerHolder

G

Gene - Class in idare.sbmlannotator.internal.gpr
Gene(HashMap<String, String>) - Constructor for class idare.sbmlannotator.internal.gpr.Gene
Gene(String, String) - Constructor for class idare.sbmlannotator.internal.gpr.Gene
GENE_BASE - Static variable in class idare.sbmlannotator.internal.gpr.GPRManager
geneAnnotationDataBase - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
GeneID - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties
GeneProduct - Class in idare.imagenode.internal.Services.JSBML
GeneProduct(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.GeneProduct
GeneProductRef - Class in idare.imagenode.internal.Services.JSBML
GeneProductRef(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.GeneProductRef
generateGeneNodes - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
generateGraphicsForID(String, boolean) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Get the Graphic for the respective ID
generateGraphicsForIDs(Collection<String>) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Generate the Graphics for the respective IDs
generateLayoutForDataSets(Collection<DataSetLayoutInfoBundle>) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout: Generate a Layout for a given set of DataSets.
generateLayoutsForNodes(Set<DataSet>, ImageNodeLayout, TaskMonitor) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Generate Layouts for All nodes in the DataSets present in the DataSetLayoutInfoBundles provided.
generateLayoutsForNodes(Set<DataSet>, ImageNodeLayout) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Generate Layouts for All nodes in the DataSets present in the DataSetLayoutInfoBundles provided.
geneTypeSelector - Variable in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser
getActions() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the actions used in this app
getActiveIDs() - Method in class idare.imagenode.internal.DataManagement.NodeManager: Get a Collection of IDs for which layouts exist and which are active.
getActiveNodeIDs() - Method in class idare.imagenode.internal.ImageManagement.ActiveNodeManager: Get the set of active Nodes
getActiveNodeManager() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the ActiveNodeManager created by this App
getActiveSheetIndex() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getAll() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getAll() - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
getAll() - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
getAllPictures() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getAnnotation() - Method in class idare.imagenode.internal.Services.JSBML.SBase
getArrayFormulaRange() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getAssociation() - Method in class idare.imagenode.internal.Services.JSBML.Reaction
getAutobreaks() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getAvailableDataSetTypes() - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Get the Types of Datasets available to this Manager.
getAvailableReaders() - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Get all IDAREDatasetReaders currently registered with IDARE.
getBiologicalQualifierType() - Method in class idare.imagenode.internal.Services.JSBML.CVTerm: Get the Qualifier associated with this CVTerm
getBooleanCellValue() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getBounds2D() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomImageLayer
getBufferedImage() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomImageLayer: Get the BufferedImage used in this GraphicLayer
getBufferedImage() - Method in class idare.ThirdParty.BufferedImageTranscoder
getCachedFormulaResultType() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getCell(int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
getCell(int, int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
getCell(int) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow: Get the IDARECell in the specified column from this Row.
getCell(int, int) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow: Get the IDARECell in the specified column from this Row, using the specified policy to handle non existing or blank cells.
getCell(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getCell(int, Row.MissingCellPolicy) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getCell(int) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
getCell(int, int) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
getCellComment() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getCellComment(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getCellEditor(int, int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionTable
getCellFormula() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getCellIndex(BasicIDARECell) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Get the position/index of a given Cell
getCellRenderer(int, int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionTable
getCellStyle() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getCellStyleAt(short) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getCellType() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell
getCellType() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell: Get the Cell Type of
getCellType() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getCellType() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POICell
getCenterPosition() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Get the central position of the color map (on a 0-1 range).
getCenterPosition() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap
getCenterValue() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Get the center value (i.e.
getCenterValue() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap
getCharacters() - Method in class idare.imagenode.internal.Services.JSBML.XMLNode
getChild(int) - Method in class idare.imagenode.internal.Services.JSBML.XMLNode
getChildCount() - Method in class idare.imagenode.internal.Services.JSBML.XMLNode
getChildElement(String, String) - Method in class idare.imagenode.internal.Services.JSBML.XMLNode
getChildElements(String, String) - Method in class idare.imagenode.internal.Services.JSBML.XMLNode
getChildNetworks() - Method in class idare.subnetwork.internal.NetworkNode
getChildren() - Method in class idare.subnetwork.internal.NetworkNode
getCodingGenes() - Method in class idare.sbmlannotator.internal.gpr.Protein
getColor(Comparable) - Method in class idare.imagenode.ColorManagement.ColorMap: Get the Color that is associated with the Comparable object provided.
getColor(Comparable) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
getColor(Comparable) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap
getColor(Comparable) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.DiscreteColorMap
getColor(double) - Method in interface idare.imagenode.ColorManagement.ColorScale: get a color
getColor(double) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
getColorForValue(double) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale
getColorForValue(double) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale: Get the color associated with the provided value
getColorMapComponent(JScrollPane) - Method in class idare.imagenode.ColorManagement.ColorMap: Get a Component that represents this ColorMap
getColorMapComponent(JScrollPane) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap
getColorMapComponent(JScrollPane) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.DiscreteColorMap
getColorMapOptions() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getColorMapOptions() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getColorMapOptions() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the ColorMaps available for this DataSet The objects in this vector should always be the same (i.e.
getColorScale(String) - Static method in class idare.imagenode.ColorManagement.ColorScaleFactory: Get a ColorScale based on a given class name
getColorScaleEditor(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Get the Editor for the appropriate ColorScalePane renderer.
getColorScalePane() - Method in class idare.imagenode.ColorManagement.ColorMap: Get a visual representation of the ColorScale used in this map.
getColorScalePane() - Method in interface idare.imagenode.ColorManagement.ColorScale: Get a ColorScalePane as a description for this ColorScale
getColorScalePane() - Method in class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale
getColorScalePane() - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
getColorScaleProperties() - Method in interface idare.imagenode.ColorManagement.ColorScale: Get the Properties of this ColorScale.
getColorScaleProperties() - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
getColorScaleRenderer(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Get the renderer for the ColorScalePane in the specified row.
getColorsForDataSet(DataSetLink) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
getColorsForDataSet(DataSetLink) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Get the ColorMap associated with this DataSet in this AutomaticNodeLayout.
getColorsForDataSet(DataSetLink) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
getColorsForDataSet(DataSetLink) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
getColumnBreaks() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getColumnClass(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel
getColumnIndex() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell
getColumnIndex() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell: Get the index of the column of this cell.
getColumnIndex() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getColumnIndex() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POICell
getColumnLabel(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Get the Label for a specific Column in the data, or null if it does not exist, or there is no clear label.
getColumnNumber(Cell) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow: Get the Column number of a specific cell.
getColumnProperties() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertyColumnChooser: Get the properties selected in this Panel.
getColumnStyle(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getColumnWidth(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getCompartment() - Method in class idare.imagenode.internal.Services.JSBML.Species
getComponent() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel
getComponent() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend
getCompoundID() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Get The ID to use for Compounds
getCompoundID() - Method in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Get The ID to use for Compounds
getContainerForID(String) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getContainerForID(String) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getContainerForID(String) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the appropriate DataContainer for an ID.
getContinousColorScales() - Static method in class idare.imagenode.ColorManagement.ColorScaleFactory: Get a set of continuous ColorScales.
getContrastingColor(Color) - Static method in class idare.imagenode.ColorManagement.ColorUtils: Obtain the contrasting black/white color for a original color.
getCreationHelper() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getCurrentlyUsedNode() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend: Get the id representing the currently used node in the Legend.
getCytoPanelName() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel
getCytoPanelName() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend
getData() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer
getData(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData: Since ArrayDataSets have ordered rows of data, this function can be used to get the position-th item in this data.
getData() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer
getData(String) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData: Get the Data stored for a specific Sheetname, returns null if this sheetname does have no associated data.
getData() - Method in interface idare.imagenode.Interfaces.DataSets.DataContainer: Get the NodeData associated with this Container
getData() - Method in class idare.imagenode.internal.DataManagement.ImageNodeModel: Get all NodeData associated with this Node.
getDataBaseName(String) - Method in class idare.sbmlannotator.internal.gpr.Gene
getDataBaseName(String) - Method in class idare.sbmlannotator.internal.gpr.Protein
getDataForID(String) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getDataForID(String) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getDataForID(String) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the NodeData for a specific ID.
getDataSet() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer
getDataSet() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer
getDataSet() - Method in interface idare.imagenode.Interfaces.DataSets.DataContainer: Get the source Dataset this Container was build from.
getDataSet() - Method in class idare.imagenode.Interfaces.DataSets.NodeData: Get the originating DataSet this NodeData belongs to.
getDataSet(String) - Static method in class idare.imagenode.internal.DataManagement.DataSetFactory: Generate a new instance for a class of a specific classname.
getDataSet() - Method in class idare.imagenode.internal.Layout.DataSetLayoutInfoBundle
getDataSet() - Method in interface idare.imagenode.internal.Layout.DataSetLink: Get the DataSet this link refers to
getDataSet() - Method in class idare.imagenode.internal.Layout.SimpleLink
getDataSetDescription() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
getDataSetDescriptionPane(JScrollPane, String, ColorMap, DataSet) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayDataSetProperties
getDataSetDescriptionPane(JScrollPane, String, ColorMap) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get a Description of this DataSet in the form of a JPanel.
getDataSetDescriptionPane(JScrollPane, String, ColorMap, DataSet) - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Plot the Legend for this Dataset.
getDataSetDescriptionPane(JScrollPane, String, ColorMap, DataSet) - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
getDataSetDescriptionPane(JScrollPane, String, ColorMap, DataSet) - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
getDataSetDescriptionPane(JScrollPane, String, ColorMap, DataSet) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
getDataSetEditor(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Get the Editor for the appropriate DataSet renderer.
getDataSetForID(Integer) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Get the dataset with the specified ID from this manager.
getDataSetLabel(DataSetLink) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
getDataSetLabel(DataSetLink) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Get the label for a specific DataSet used in this layout;
getDataSetLabel(DataSetLink) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
getDataSetLabel(DataSetLink) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
getDataSetManager() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
getDatasetManager() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the DataSetManager created by this App
getDataSetPanel() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Obtain the DataSetControlPanel generated by this instance of IDARE.
getDataSetParameters() - Method in class idare.imagenode.internal.GUI.DataSetAddition.TunableDataSetAdderGUI
getDataSets() - Method in class idare.imagenode.internal.DataManagement.DataSetManager
getDatasetsInOrder() - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
getDatasetsInOrder() - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Get the DataSets used in this Layout in the order of labeling
getDatasetsInOrder() - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
getDatasetsInOrder() - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
getDataSetType() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
getDataSetTypeName() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getDataSetTypeName() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getDataSetTypeName() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the general Name for this Type of DataSet
getDataValidationHelper() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getDateCellValue() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getDefaultColor() - Method in class idare.imagenode.ColorManagement.ColorMap
getDefaultColumnWidth() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getDefaultData() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getDefaultData() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getDefaultData() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get a default NodeData object for this dataset
getDefaultProperties() - Static method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Get the Default Properties (Description/Colorscale etc) for this dataset.
getDefaultProperties() - Static method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Get the default properties for a MultiArrayDataSet.
getDefaultProperties() - Static method in class idare.imagenode.Interfaces.DataSets.DataSet
getDefaultRowHeight() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getDefaultRowHeightInPoints() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getDescriptionPane(Color, String) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDescription: Get a Description Pane for the current Entry Description, with the given color and given ID
getDescriptionPane(Color, String) - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.LineDescription
getDescriptionPane(Color, String) - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.LineDescription
getDescriptionPane(Color, String) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.MarkerDataDescription
getDifferentSubSystems(CyTable, String) - Static method in class idare.subnetwork.internal.SubNetworkUtils: Get a Vector of SubSystem Identifiers from the given CyTable and the given Column name (i.e.
getDiscreetColorScales(int) - Static method in class idare.imagenode.ColorManagement.ColorScaleFactory: Get a set of discreet ColorScales.
getDiscreteColorScale(int) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale: Get a discrete Version of this color scale.
getDisplayGuts() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getDisplayName() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
getDisplayStrings(Double[]) - Static method in class idare.imagenode.ColorManagement.ColorMap: Provides appropriate (not too long) representations of the values provided.
getEntry(Color) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryDescriptionPane: Depending on the implementation, this function should return a SetEntryPanel that represents the Entry using a color (e.g.
getEntryData() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataValue: Get the Line Data stored in this value
getErrorCellValue() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getErrorMessages() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
getExistingNetworks() - Method in class idare.subnetwork.internal.NetworkViewSwitcher
getExistingNetworksForColumn(String) - Method in class idare.subnetwork.internal.NetworkViewSwitcher: Get the subnetworks that currently exist for the provided column present in any parent network
getFactories() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the Task Factories used in the App.
getFBCExtension() - Method in class idare.imagenode.internal.Services.JSBML.Reaction
getFinalLayout() - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
getFirstCellNum() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getFirstRowNum() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getFirstVisibleTab() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getFitRatio() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
getFitToPage() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getFontAt(short) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getFooter() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getForceFormulaRecalculation() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getForceFormulaRecalculation() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getFormattedCellValue() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell
getFormattedCellValue() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell: Get a string representation of the value of this cell (regardless what this cell actually represents).
getFormattedCellValue() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POICell
getGene(String) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getGene(HashMap<String, String>) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getGeneID() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Get the identifier to use for Genes ( if it is available)
getGeneProduct() - Method in class idare.imagenode.internal.Services.JSBML.GeneProductRef
getGenes() - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
getGenesWithoutProteins() - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
getGPRAssoc(Protein) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getGPRAssociation() - Method in class idare.sbmlannotator.internal.gpr.FBCGPRParser
getGPRAssociations() - Method in class idare.sbmlannotator.internal.gpr.GPRListTokenizer
getGPRAssociations() - Method in class idare.sbmlannotator.internal.gpr.GPRTokenizer
getGraphicForID(String) - Method in class idare.imagenode.internal.ImageManagement.GraphicsChangedEvent: get The CyCustomGraphics object for the requested ID, or null if it is not part of this event.
getGroupExtension() - Method in class idare.imagenode.internal.Services.JSBML.Model
getHeader() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getHeaders() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getHeaders() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Get all values present in the headers of this DataSet
getHeaders() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the Headers in this DataSet
getHeadersForSheet(String) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Get the Headers (Either String or Double, so handle with care) for a specific sheet in this Dataset, based on the sheet name.
getHeight() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getHeight() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
getHeightInPoints() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getHorizontallyCenter() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getHyperlink() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getIcon() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel
getIcon() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend
getID() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getID() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getID() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the ID of this set.
getID() - Method in class idare.imagenode.Interfaces.DataSets.NodeData: Get the ID of this nodeData.
getId() - Method in class idare.imagenode.internal.Services.JSBML.SBase
getIDCol() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertyColumnChooser: Get the Column Name for the ID Columnn
getIdentifier() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
getIdRef() - Method in class idare.imagenode.internal.Services.JSBML.Member
getIDs() - Method in class idare.imagenode.internal.ImageManagement.GraphicsChangedEvent: Get the updated IDs.
getImage(int, int) - Method in class idare.imagenode.ColorManagement.ColorScalePane: Get an image that represents this ColorScalePane, with the given width and height
getImageNodeApp() - Method in class idare.internal.IDAREApp: Since the IDAREImageNodeApp provides a couple of services itself, this function allows to obtain the used copy
getimagenodeImageForItem(String) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Get the BufferedImage associated with a specific ID The Image will be generated if necessar (and possible)
getImageStorage() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the ImageStorage created by this App
getInputFile() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
getInstance(URL) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getInstance(String) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getItemFlexibility() - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Get information whether this dataset can be layouted flexibly or whether it has to obay the precisoe dimensions provided.
getItemFlexibility() - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleDataSetProperties
getItemFlexibility() - Method in class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties
getItemFlexibility() - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleDataSetProperties
getItemFlexibility() - Method in class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties
getItemFlexibility() - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
getItemFlexibility() - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
getItemFlexibility() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
getLabel() - Method in class idare.imagenode.Interfaces.DataSets.NodeData: Get the label of this NodeData (which can be used for display purposes.
getLabel() - Method in class idare.imagenode.internal.Services.JSBML.GeneProduct
getLabel() - Method in class idare.imagenode.Properties.LabelGenerator: Get the next label
GetLabelForNumbers(HashMap<Double, Double>) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Create Strings Representations for the values in a Map which are Doubles.
getLabelsForData(Vector<Comparable>) - Static method in class idare.imagenode.Utilities.LayoutUtils: Get alphanumeric unique labels for a set of entries (i.e.
getLabelSize() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.LargeScatterProperties
getLabelSize() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties: Get the size of labels for these Properties.
getLabelSize() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.SmallScatterProperties
getLastCellNum() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
getLastCellNum() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow: Gets the index of the last cell contained in this row PLUS ONE.!
getLastCellNum() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getLastCellNum() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
getLastRowNum() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet
getLastRowNum() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARESheet: Get the index of the last Row
getLastRowNum() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getLastRowNum() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
getLayers(CyNetworkView, View) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
getLayoutArea() - Method in class idare.imagenode.Interfaces.Layout.ContainerLayout: Get the area assigned to this layout container (in the IMAGENODEPROPERTIES.IMAGEWIDTH // IMAGENODEPROPERTIES.IMAGEHEIGHT) range.
getLayoutContainer(DataSetLayoutProperties) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getLayoutContainer(DataSetLayoutProperties) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getLayoutContainer(DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get a sample container for Layout purposes
getLayoutContainerUsedFor(DataSet) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout: Get the Container used for the provided dataset
getLayoutedIDs() - Method in class idare.imagenode.internal.DataManagement.NodeManager: Get a Collection of IDs for which layouts exist.
getLayoutForNode(String) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Get the layout for a specific id
getLayoutIOManager() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get The LayoutIOManager
getLeftCol() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getLegend() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the IDARELegend generated by this instance of IDARE.
getLegendShape(Rectangle2D, String) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout: Get the ShapePosition representing the current Legend using the label indicated, and the Dimension provided.
getLegendShape(Rectangle2D, String) - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleContainerLayout
getLegendShape(Rectangle2D, String) - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout
getListOfAssociations() - Method in class idare.imagenode.internal.Services.JSBML.Association
getListOfCVTerms() - Method in class idare.imagenode.internal.Services.JSBML.Annotation: Get the List of CVTerms
getListOfGeneProducts() - Method in class idare.imagenode.internal.Services.JSBML.Model
getListOfGroups() - Method in class idare.imagenode.internal.Services.JSBML.GroupModelPlugin
getListOfMembers() - Method in class idare.imagenode.internal.Services.JSBML.Group
getListOfReactions() - Method in class idare.imagenode.internal.Services.JSBML.Model
getListOfSpecies() - Method in class idare.imagenode.internal.Services.JSBML.Model
getLocalisationPreference() - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Get the preferred Localisation Localisation.Position.CENTER, Localisation.Position.EDGE, Localisation.Position.FREE of this dataset.
getLocalisationPreference() - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleDataSetProperties
getLocalisationPreference() - Method in class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties
getLocalisationPreference() - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleDataSetProperties
getLocalisationPreference() - Method in class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties
getLocalisationPreference() - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
getLocalisationPreference() - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
getLocalisationPreference() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
getMappedValue(CyRow) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getMappedValue(CyRow) - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
getMappedValue(CyRow) - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
getMappingColumnName() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getMappingColumnName() - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
getMappingColumnName() - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
getMappingColumnType() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getMappingColumnType() - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
getMappingColumnType() - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
getMapValue(String) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getMapValue(String) - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
getMapValue(String) - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
getMargin(short) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getMaximumWidth() - Method in class idare.ThirdParty.BoundsPopupMenuListener: Return the maximum width of the popup.
getMergedRegion(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getMinimalSize() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer
getMinimalSize() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer
getMinimalSize() - Method in interface idare.imagenode.Interfaces.DataSets.DataContainer: A container should provide information on its size This dimension is assumed to simultaneously represent the number of items (i.e.
getMinSize() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionPane: Get the minimal width necessary for this item.
getMinSize(JLabel) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionPane: Get the minimial width necessary for a specific JLabel.
getMissingCellPolicy() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getModel() - Method in class idare.imagenode.internal.Services.JSBML.SBMLDocument
getName(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getName() - Method in class idare.imagenode.internal.Services.JSBML.GeneProduct
getName() - Method in class idare.imagenode.internal.Services.JSBML.SBase
getName() - Method in class idare.sbmlannotator.internal.gpr.Gene
getName(String) - Method in class idare.sbmlannotator.internal.gpr.Protein
getName() - Method in class idare.sbmlannotator.internal.gpr.Protein
getNameAt(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getNameIndex(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getNetwork() - Method in class idare.subnetwork.internal.NetworkNode
getNetworkID() - Method in class idare.subnetwork.internal.NetworkNode
getNetworkIDAREIDs(CyNetwork, String) - Static method in class idare.Properties.IDARESettingsManager: Get the set of nodeIDs present in the provided network
getNetworkSetupProperties() - Method in class idare.imagenode.internal.GUI.NetworkSetup.NetworkSetupTunableGUI: Get the properties selected in this GUI
getNetworkSetupProperties() - Method in class idare.imagenode.internal.Layout.Manual.GUI.Tasks.LayoutPropertiesGUI: Get the properties selected in this GUI
getNextGeneID() - Method in class idare.Properties.IDARESettingsManager: Get the next gene ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
getNextID() - Method in class idare.imagenode.internal.DataManagement.DataSetIDProvider: Get the next ID.
getNextNetworkID() - Method in class idare.Properties.IDARESettingsManager: Get the next network ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
getNextNodeID() - Method in class idare.Properties.IDARESettingsManager: Get the next ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
getNextProteinComplexID() - Method in class idare.Properties.IDARESettingsManager: Get the nextprotein Complex ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
getNextProteinID() - Method in class idare.Properties.IDARESettingsManager: Get the next protein ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
getNode(String) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Get the Node corresponding to the given ID
getNodeID() - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
getNodeIDs() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
getNodeIDs() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
getNodeIDs() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the set of Node IDs contained in this DataSet.
getNodeManager() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the NodeManager created by this App
getNodesForLayout(ImageNodeLayout) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Create a Collection of IDs that are associated with a specific Layout.
getNodesToDuplicate() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI: Get the CyNode which should not link to other networks
getNodesToRemove() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI: Get All Nodes that are to be ignored in the SubNetwork Generation
getNodesToSkip() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI: Get the CyNode which should not link to other networks
getNodesWithData() - Method in class idare.imagenode.internal.DataManagement.NodeManager: Get all nodes, that have associated data.
getNodesWithValue(CyNetwork, CyTable, String, Object) - Static method in class idare.ThirdParty.CytoscapeUtils: From the APP Developer Cookbook: Get all the nodes with a given attribute value.
getNodeTableColumnNames(CyNetwork) - Static method in class idare.subnetwork.internal.SubNetworkUtils: Get all Columns present in the node Table of the provided network
getNodeView() - Method in class idare.subnetwork.internal.NodeViewLink: Get the View of the Node
getNonWhiteDiscreteColorScales(int) - Static method in class idare.imagenode.ColorManagement.ColorScaleFactory
getNotes() - Method in class idare.imagenode.internal.Services.JSBML.SBase
getNotesString() - Method in class idare.imagenode.internal.Services.JSBML.SBase
getNumberOfFonts() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getNumberOfNames() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getNumberOfSheets() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
getNumberOfSheets() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDAREWorkbook: Get the number of individual data sheets present in this workbook
getNumberOfSheets() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getNumberOfSheets() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIWorkBook
getNumCellStyles() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getNumericCellValue() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell
getNumericCellValue() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell: Get the Numeric Value of this cell, if it can be converted to numeric.
getNumericCellValue() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getNumericCellValue() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POICell
getNumMergedRegions() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getObjClassame() - Method in exception idare.imagenode.internal.exceptions.debug.DebugException: Get the class name of the Object
getPaint(Rectangle2D) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomImageLayer
getPane() - Method in class idare.imagenode.internal.Layout.Manual.GUI.ColorMenuItem
getPaneInformation() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getPhysicalNumberOfCells() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getPhysicalNumberOfRows() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet
getPhysicalNumberOfRows() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARESheet: Get the total number of non null rows in this Sheet.
getPhysicalNumberOfRows() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getPhysicalNumberOfRows() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
getPreferredposition() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the preferred layout localisation of this dataset
getPreferredSize(Dimension, IMAGENODEPROPERTIES.LayoutStyle) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer: The common Item container will use a flexible adjustment of its height/width to best fill the availablearea.
getPreferredSize(Dimension, IMAGENODEPROPERTIES.LayoutStyle) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer
getPreferredSize(Dimension, IMAGENODEPROPERTIES.LayoutStyle) - Method in interface idare.imagenode.Interfaces.DataSets.DataContainer: Get the preferred size (as a rectangle with Integer width and height, based on the available area provided The resulting Rectangle width must be smaller or equal to the provided Rectangle.
getPreferredSize(JTextComponent, Dimension, int) - Static method in class idare.imagenode.Utilities.GUIUtils: Get the preferred size of a JTextComponent given a specific minimal width and its current dimension
getPrefix() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getPrintArea(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getPrintSetup() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getProblemMessage() - Method in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Get the problem that causes this selection to be not acceptable.
getProperties() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI: Get the Properties for the Subnetwork generation task as defined in this GUI
getPropertiesEditor(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Get the Editor for the appropriate DataSetLayoutProperties renderer.
getPropertiesRenderer(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Get the renderer for the properties in the specified row.
getPropertyOptions() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the selection of different properties available for this dataset
getProtect() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getProtein(GPRAssociation) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getProtein(String) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getProtein(HashMap<String, String>) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getProteinBuildingGenes(Protein) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getProteinID() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Get The ID to use for Proteins ( if it is available)
getProteins() - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
getProteins(Collection<GPRAssociation>) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getReactionID() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Get The ID to use for Reactions
getReactionID() - Method in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Get The ID to use for Reactions
getRenderedImage() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
getResources() - Method in class idare.imagenode.internal.Services.JSBML.CVTerm: Get the REssources as a List of String
getResults(Class<? extends R>) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.ObservableIDARETask
getRichStringCellValue() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getRow(int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet
getRow(int) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARESheet: Get the Row with the provided row index
getRow() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getRow(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getRow(int) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
getRowBreaks() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getRowIndex(BasicIDARERow) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet: Get the index of a given Row
getRowIndex() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getRowNum() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
getRowNum() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow: Get the position of this row in the enclosing IDARESheet;
getRowNum() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getRowNum() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
getRowNumber(Row) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet: get the row position of a row.
getRowsAndCols(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription: Get the rows and columns for this panel based on the available width.
getRowStyle() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getRowSumsBelow() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getRowSumsRight() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getSBMLStatus() - Method in class idare.imagenode.internal.Services.JSBML.SBMLManagerHolder
getSBOTerm() - Method in class idare.imagenode.internal.Services.JSBML.SBase
getScaledBounds() - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
getScenarioProtect() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getScrollBarWidth(BasicComboPopup, JScrollPane) - Method in class idare.ThirdParty.BoundsPopupMenuListener
getScrollPane(BasicComboPopup) - Method in class idare.ThirdParty.BoundsPopupMenuListener
getSelectedDataSets() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Get the selected DataSets along with the currently used ColorMaps
getSelectedFrame() - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
getSelectedItems() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Get the items used in the comboboxes, excluding those provided.
getSelectedItems(JComboBox<String>) - Method in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Get the items used in the comboboxes, excluding those provided.
getSelectedMap() - Method in class idare.imagenode.internal.Layout.Manual.GUI.ColorToolBarEntry: Get the Colormap corresponding to the selected scale
getSelectedProperties() - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetPropertyToolBarEntry: Get the Colormap corresponding to the selected scale
getSeparator() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVReader: Get the column separator used in this reader
getSeparator() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.TSVReader
getServices() - Method in interface idare.imagenode.Interfaces.Plugin.IDAREPlugin: Provide all instances of IDAREInterfaces this plugin shall provide to the app.
getServices() - Method in class idare.imagenode.internal.DataManagement.DataSetProvider
getServices() - Method in class idare.imagenode.internal.DataSetReaders.DataSetReaderProvider
getServices() - Method in class idare.imagenode.internal.ImageManagement.DefaultLayoutProvider
getSet() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetChangedEvent: Get the DataSet that is changing
getSet() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetsChangedEvent: Get the Collection of datasets that are changing.
getSetNames() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Get the names of the Sheets represented in this DataSet
getSettingsManager() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the IDARESettingsManager created by this App
getSettingsManager() - Method in class idare.internal.IDAREApp: Get the IDARESettingsManager used in this app
getSetupTask(File, boolean) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: The Reader should provide a Task that can be used to set up the reader for future use on the given inputFile.
getSetupTask(File, boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVReader
getSetupTask(File, boolean) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIReader
getShape(Dimension) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout: Get the Shape to be used for individual items in the specified area.
getShape(double, double, double, double) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryPanel: Get the shape that represents this entry.
getShape(Dimension) - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleContainerLayout
getShape(Dimension) - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout
getShapePosition(Shape, Rectangle2D) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout: Generate a AbstractArrayContainerLayout.ShapePosition from a Rectangle and a given Shape.
getShapePosition(Shape, Rectangle2D) - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout
getSheet(String) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
getSheet(String) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDAREWorkbook: Get the sheet with the specified name
getSheet() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getSheet() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
getSheet(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getSheet(String) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIWorkBook
getSheetAt(int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
getSheetAt(int) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDAREWorkbook: Get the Sheet at the requested position, or null if it does not exist-
getSheetAt(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getSheetAt(int) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIWorkBook
getSheetConditionalFormatting() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getSheetIndex(String) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
getSheetIndex(IDARESheet) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
getSheetIndex(String) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDAREWorkbook: Get the 0-based index of a sheet with the provided name
getSheetIndex(IDARESheet) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDAREWorkbook: Get the index of the provided IDARESheet.
getSheetIndex(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getSheetIndex(Sheet) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getSheetIndex(String) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIWorkBook
getSheetIndex(IDARESheet) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIWorkBook
getSheetName() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet
getSheetName(int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
getSheetName() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARESheet: Get the Name of this Sheet.
getSheetName(int) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDAREWorkbook: Get the name of the sheet at the provided position
getSheetName() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getSheetName(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
getSheetName() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
getSheetName(int) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIWorkBook
getSingleGeneProtein(Gene) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getSource() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetChangedEvent: Get the DataSetManager this event originates from.
getSource() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetsChangedEvent: Get the DataSetManager this event originates from.
getSourceNetwork() - Method in class idare.subnetwork.internal.NodeViewLink: Get the source CyNetwork
getStatusMessage() - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: Informs about the status of the reader.
getStringCellValue() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell
getStringCellValue() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell: Get the string cell value, if the cell is a string cell.
getStringCellValue() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
getStringCellValue() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POICell
getStyleManager() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Obtain the StyleManager generated by this instance of IDARE.
getSubNetworkName(CyNetwork) - Method in class idare.subnetwork.internal.NetworkViewSwitcher: Get the internal name of the network (i.e.
getSubNetworkType(String) - Method in class idare.Properties.IDARESettingsManager: Get the IDAREType associated with a specific Target Type for the subnetwork generation.
getSubNetworkWorksForNetwork(CyNetwork, String) - Method in class idare.subnetwork.internal.NetworkViewSwitcher: Get the Names of all subnetworks for a specific parent network and a specific column.
getSupportedClass() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getSVGFontMetrics(Font) - Static method in class idare.imagenode.Utilities.LayoutUtils
getTargetNetwork() - Method in class idare.subnetwork.internal.NodeViewLink: Get the target CyNetwork
getTargetNetworkView() - Method in class idare.subnetwork.internal.NodeViewLink: Get the Target CyNetworkView for this Link.
getTargetNode() - Method in class idare.subnetwork.internal.NodeViewLink: Get the CyNode
getTemporaryFile(String, String) - Static method in class idare.imagenode.Utilities.IOUtils: Get a Temporary file with a given Filename and a given Extension.
getTitle() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel
getTitle() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend
getTopRow() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getType() - Method in class idare.imagenode.Interfaces.DataSets.NodeValue: Get the Type of NodeValue (numeric, String, Vector)
getType(String) - Method in class idare.Properties.IDAREProperties
getType(String) - Method in class idare.Properties.IDARESettingsManager: Get the Type associated with a specific Name.
getTypeCol() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertyColumnChooser: Get the Column NAme for the Type Columnn
getTypeName() - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Get the type of DataSet (this can be used for display purposes
getTypeName() - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleDataSetProperties
getTypeName() - Method in class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties
getTypeName() - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleDataSetProperties
getTypeName() - Method in class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties
getTypeName() - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
getTypeName() - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
getTypeName() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.LargeScatterProperties
getTypeName() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
getTypeName() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.SmallScatterProperties
getUnassociatedGene(String) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getUnassociatedProtein(String) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
getupdatedIDs() - Method in class idare.imagenode.internal.DataManagement.Events.NodeUpdateEvent: Get all IDs of updated nodes
getValue() - Method in class idare.imagenode.Interfaces.DataSets.NodeValue: Get the value of this NodeValue
getValueCount() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData: Return the number of Elements for one set of Data e.g.
getVerticallyCenter() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getViewFactory() - Method in class idare.ThirdParty.TextPaneEditorKit
getVisualProperty() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
getVisualProperty() - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
getVisualProperty() - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
getVisualStyle() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Get the IDAREVisualStyle created by this App
getWidth() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
getWorkbook() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
getWorkbook() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
getWorkingClassTypes() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayDataSetProperties
getWorkingClassTypes() - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Get the DataSet class Types these Properties are supposed to work with.
getWorkingClassTypes() - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
getWorkingClassTypes() - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
getWorkingClassTypes() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
getYAxisLimits() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the limits (minimum and maximum value) if this is a numeric dataset.
GetYPosition(int, int, double, double) - Method in class idare.sbmlannotator.internal.SBMLAnnotaterTask: Get the Y Position for the number-th of code Nodes
GetYPosition(int, int, double, double) - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask: Get the Y Position for the number-th of code Nodes
getZeroHeight() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
GPRAssociation - Class in idare.sbmlannotator.internal.gpr
GPRAssociation(GPRAssociation, GPRAssociation) - Constructor for class idare.sbmlannotator.internal.gpr.GPRAssociation
GPRAssociation() - Constructor for class idare.sbmlannotator.internal.gpr.GPRAssociation
GPRListTokenizer - Class in idare.sbmlannotator.internal.gpr
GPRListTokenizer(String, GPRManager) - Constructor for class idare.sbmlannotator.internal.gpr.GPRListTokenizer
GPRManager - Class in idare.sbmlannotator.internal.gpr
GPRManager(IDARESettingsManager) - Constructor for class idare.sbmlannotator.internal.gpr.GPRManager
GPRTokenizer - Class in idare.sbmlannotator.internal.gpr
GPRTokenizer(String, GPRManager) - Constructor for class idare.sbmlannotator.internal.gpr.GPRTokenizer
GraphContainer - Class in idare.imagenode.internal.Data.MultiArray.GraphData: Container Class for GraphData
GraphContainer(DataSet, NodeData) - Constructor for class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainer
GraphContainerLayout - Class in idare.imagenode.internal.Data.MultiArray.GraphData: ContainerLayout Class for Graph Data, storing common information like the location fo axes, labels and frames.
GraphContainerLayout() - Constructor for class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout: Default Constructor
GraphDataSetProperties - Class in idare.imagenode.internal.Data.MultiArray.GraphData
GraphDataSetProperties() - Constructor for class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
GraphicsChangedEvent - Class in idare.imagenode.internal.ImageManagement: An event that informs about changes in graphics for specific IDs.
GraphicsChangedListener - Interface in idare.imagenode.internal.ImageManagement: A GraphicsChangedListener will listen to changes in the graphics controlled by the IDARE app.
GreenBlackRed - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale from Green via black to red
GreenBlackRed() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.GreenBlackRed
GreenYellow - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale from green to yellow
GreenYellow() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.GreenYellow
Group - Class in idare.imagenode.internal.Services.JSBML
Group(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Group
groupColumn(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
GroupModelPlugin - Class in idare.imagenode.internal.Services.JSBML
GroupModelPlugin(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.GroupModelPlugin
groupRow(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
GUIUtils - Class in idare.imagenode.Utilities: Class proviing static utilitits for multiple GUI classes.
GUIUtils() - Constructor for class idare.imagenode.Utilities.GUIUtils

H

handle() - Method in class idare.imagenode.internal.GUI.DataSetAddition.DataSetParametersGUIHandler
handle() - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupGUIHandler
handle() - Method in class idare.imagenode.internal.Layout.Manual.GUI.Tasks.LayoutPropertiesGUIHandler
handle() - Method in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkPropertyColumnGUIHandler
handle() - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationGUIHandler
handleEvent(SessionLoadedEvent) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Handle A SessionLoadedevent, since order is relevant this object is not directly a listener but gets the command from a listener.
handleEvent(SessionAboutToBeSavedEvent) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Handle A SessionAboutToBeSavedEvent, ad add data of the DataManger to this Event.
handleEvent(SessionAboutToBeSavedEvent, IDAREImageNodeApp) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Handle a SessionAboutToBeSavedEvent.
handleEvent(SessionLoadedEvent, IDAREImageNodeApp) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Restore the data of this nodemanager.
handleEvent(RowsSetEvent) - Method in class idare.imagenode.internal.GUI.Legend.LegendUpdater
handleEvent(SessionAboutToBeSavedEvent) - Method in class idare.imagenode.internal.IDAREImageNodeApp
handleEvent(VisualStyleSetEvent) - Method in class idare.imagenode.internal.ImageManagement.ActiveNodeManager
handleEvent(SessionLoadedEvent) - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle
handleEvent(SessionLoadedEvent) - Method in class idare.imagenode.internal.VisualStyle.StyleManager
handleEvent(SessionAboutToBeSavedEvent) - Method in class idare.imagenode.internal.VisualStyle.StyleManager
handleEvent(SessionLoadedEvent) - Method in class idare.internal.IDAREApp
handleEvent(RowsSetEvent) - Method in class idare.NodeDuplicator.Internal.NodeRegistry
handleEvent(NetworkAboutToBeDestroyedEvent) - Method in class idare.subnetwork.internal.NetworkViewSwitcher
handleEvent(RowsSetEvent) - Method in class idare.subnetwork.internal.NetworkViewSwitcher: Check whether the set row is a network row and if, check whether it refers to a network, we are listening to and update all links accordingly
handleEvent(SessionAboutToBeSavedEvent) - Method in class idare.subnetwork.internal.NetworkViewSwitcher
handleNodeUpdate(NodeUpdateEvent) - Method in interface idare.imagenode.internal.DataManagement.Events.NodeChangedListener: Handle a NodeUpdateEvent, that informs that certain nodes were updated.
handleNodeUpdate(NodeUpdateEvent) - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend
handleNodeUpdate(NodeUpdateEvent) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
handleSessionLoadedEvent(SessionLoadedEvent) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Handle a session load event.
handleSessionLoadedEvent(SessionLoadedEvent) - Method in class idare.Properties.IDARESettingsManager: Handle the loading of a session
handleSessionLoadedEvent(SessionLoadedEvent) - Method in class idare.subnetwork.internal.SubnetworkSessionManager
hashCode() - Method in class idare.imagenode.Interfaces.DataSets.NodeValue: This class is only a representation of its value, so its hash is the same as its value.
hashCode() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POICell
hashCode() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
hashCode() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
hashCode() - Method in class idare.imagenode.internal.Layout.Manual.Utilities.LayoutComparator
hashCode() - Method in class idare.imagenode.internal.Layout.SimpleLink
hashCode() - Method in class idare.imagenode.internal.Services.JSBML.SBase
hashCode() - Method in class idare.sbmlannotator.internal.gpr.Gene
hashCode() - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
hashCode() - Method in class idare.sbmlannotator.internal.gpr.Protein
hasName(String, String) - Method in class idare.sbmlannotator.internal.gpr.Gene
hasName(String, String) - Method in class idare.sbmlannotator.internal.gpr.Protein
hasNext() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARECellIterator
hasNext() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARERowIterator
HeaderDescription - Class in idare.imagenode.internal.Data.MultiArray.ScatterData
HeaderDescription() - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.HeaderDescription
Headerlines - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
HGAP - Static variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
horizontalScrollBarWillBeVisible(BasicComboPopup, JScrollPane) - Method in class idare.ThirdParty.BoundsPopupMenuListener
HSVScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale ranging from red via yellow, green, cyan, blue and pink again to red
HSVScale() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.HSVScale

I

id - Variable in class idare.imagenode.Interfaces.DataSets.NodeData
idare.imagenode - package idare.imagenode: This package contains the Service of the IDAREApp that allows the addition of plugins to the app.
idare.imagenode.ColorManagement - package idare.imagenode.ColorManagement: This Package contains classes used for Displaying and defining ColorMaps available in IDARE.
idare.imagenode.ColorManagement.ColorMapTypes - package idare.imagenode.ColorManagement.ColorMapTypes: This Package contains the ColorMapTypes available in IDARE.
idare.imagenode.Data.BasicDataTypes.ArrayData - package idare.imagenode.Data.BasicDataTypes.ArrayData: This package contains the basic Dataset assuming that the data consists of one sheet of information.
idare.imagenode.Data.BasicDataTypes.MultiArrayData - package idare.imagenode.Data.BasicDataTypes.MultiArrayData: This package contains the a Dataset specification for datasets with multiple sheets of containing multiple related sets of information..
idare.imagenode.exceptions.io - package idare.imagenode.exceptions.io: This Package contains exceptions supposed to be thrown, when problems during data parsing occur.
idare.imagenode.exceptions.layout - package idare.imagenode.exceptions.layout: This Package contains exceptions supposed to be thrown, when problems during layouting occur.
idare.imagenode.GUI.Legend.Utilities - package idare.imagenode.GUI.Legend.Utilities: This package contains classes for use with the IDARELegend.
idare.imagenode.Interfaces.DataSetReaders - package idare.imagenode.Interfaces.DataSetReaders: A Package that defines interfaces that have to be used by Readers for additional DataSet Formats.
idare.imagenode.Interfaces.DataSetReaders.WorkBook - package idare.imagenode.Interfaces.DataSetReaders.WorkBook: This package contains the Interfaces necessary for DataSet parsing.
idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation - package idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation: This package contains a basic implementation of an IDAREWorkbook compatible with the IDARE Interface.
idare.imagenode.Interfaces.DataSets - package idare.imagenode.Interfaces.DataSets: A Package that defines interfaces and abstract basis classes for all components necessary to represent a DataSet.
idare.imagenode.Interfaces.Layout - package idare.imagenode.Interfaces.Layout: A Package that defines interfaces and abstract basis classes for all components necessary to generate a Layout for n individual DataSet
idare.imagenode.Interfaces.Plugin - package idare.imagenode.Interfaces.Plugin: A Package that defines interfaces hich have to be implemented by Plugins to Cytoscape.
idare.imagenode.internal - package idare.imagenode.internal
idare.imagenode.internal.ColorManagement.ColorScales - package idare.imagenode.internal.ColorManagement.ColorScales
idare.imagenode.internal.Data.Array.CircleData - package idare.imagenode.internal.Data.Array.CircleData
idare.imagenode.internal.Data.Array.CircleGridData - package idare.imagenode.internal.Data.Array.CircleGridData
idare.imagenode.internal.Data.Array.RectangleData - package idare.imagenode.internal.Data.Array.RectangleData
idare.imagenode.internal.Data.Array.TimeSeriesData - package idare.imagenode.internal.Data.Array.TimeSeriesData
idare.imagenode.internal.Data.MultiArray.GraphData - package idare.imagenode.internal.Data.MultiArray.GraphData
idare.imagenode.internal.Data.MultiArray.IndividualGraph - package idare.imagenode.internal.Data.MultiArray.IndividualGraph
idare.imagenode.internal.Data.MultiArray.ScatterData - package idare.imagenode.internal.Data.MultiArray.ScatterData
idare.imagenode.internal.DataManagement - package idare.imagenode.internal.DataManagement
idare.imagenode.internal.DataManagement.Events - package idare.imagenode.internal.DataManagement.Events
idare.imagenode.internal.DataSetReaders - package idare.imagenode.internal.DataSetReaders: This package contains Readers for Excel and CSV File formats implementing the IDAREDatasetReader interface
idare.imagenode.internal.DataSetReaders.CSVReader - package idare.imagenode.internal.DataSetReaders.CSVReader
idare.imagenode.internal.DataSetReaders.POIReader - package idare.imagenode.internal.DataSetReaders.POIReader: This package contains a wrapper to wrap POI Workbooks to IDAREWorkbooks
idare.imagenode.internal.Debug - package idare.imagenode.internal.Debug
idare.imagenode.internal.exceptions.debug - package idare.imagenode.internal.exceptions.debug
idare.imagenode.internal.GUI.DataSetAddition - package idare.imagenode.internal.GUI.DataSetAddition
idare.imagenode.internal.GUI.DataSetAddition.Tasks - package idare.imagenode.internal.GUI.DataSetAddition.Tasks
idare.imagenode.internal.GUI.DataSetController - package idare.imagenode.internal.GUI.DataSetController
idare.imagenode.internal.GUI.Legend - package idare.imagenode.internal.GUI.Legend
idare.imagenode.internal.GUI.Legend.Tasks - package idare.imagenode.internal.GUI.Legend.Tasks
idare.imagenode.internal.GUI.NetworkSetup - package idare.imagenode.internal.GUI.NetworkSetup
idare.imagenode.internal.GUI.NetworkSetup.Tasks - package idare.imagenode.internal.GUI.NetworkSetup.Tasks
idare.imagenode.internal.ImageManagement - package idare.imagenode.internal.ImageManagement
idare.imagenode.internal.Layout - package idare.imagenode.internal.Layout
idare.imagenode.internal.Layout.Automatic - package idare.imagenode.internal.Layout.Automatic
idare.imagenode.internal.Layout.io - package idare.imagenode.internal.Layout.io
idare.imagenode.internal.Layout.Manual - package idare.imagenode.internal.Layout.Manual
idare.imagenode.internal.Layout.Manual.GUI - package idare.imagenode.internal.Layout.Manual.GUI
idare.imagenode.internal.Layout.Manual.GUI.Tasks - package idare.imagenode.internal.Layout.Manual.GUI.Tasks
idare.imagenode.internal.Layout.Manual.Utilities - package idare.imagenode.internal.Layout.Manual.Utilities
idare.imagenode.internal.Services - package idare.imagenode.internal.Services
idare.imagenode.internal.Services.JSBML - package idare.imagenode.internal.Services.JSBML
idare.imagenode.internal.Services.POI - package idare.imagenode.internal.Services.POI
idare.imagenode.internal.VisualStyle - package idare.imagenode.internal.VisualStyle
idare.imagenode.internal.VisualStyle.Tasks - package idare.imagenode.internal.VisualStyle.Tasks
idare.imagenode.Properties - package idare.imagenode.Properties: This package contains Properties and Static Variables used in the ImageNode Generation App.
idare.imagenode.Utilities - package idare.imagenode.Utilities: This package contains simple helper functions and functionalities that might be useful e.g.
idare.imagenode.Utilities.GUI - package idare.imagenode.Utilities.GUI
idare.internal - package idare.internal: This package contains the basic app object that is available to all parts of the app.
idare.NodeDuplicator.Internal - package idare.NodeDuplicator.Internal
idare.NodeDuplicator.Internal.Tasks - package idare.NodeDuplicator.Internal.Tasks
idare.Properties - package idare.Properties: This package contains Properties and Static Variables used in multiple parts of the IDARE App.
idare.sbmlannotator.internal - package idare.sbmlannotator.internal
idare.sbmlannotator.internal.gpr - package idare.sbmlannotator.internal.gpr
idare.sbmlannotator.internal.Tasks - package idare.sbmlannotator.internal.Tasks
idare.subnetwork.internal - package idare.subnetwork.internal
idare.subnetwork.internal.GUI - package idare.subnetwork.internal.GUI
idare.subnetwork.internal.Tasks - package idare.subnetwork.internal.Tasks
idare.subnetwork.internal.Tasks.propertySelection - package idare.subnetwork.internal.Tasks.propertySelection
idare.subnetwork.internal.Tasks.SubsystemGeneration - package idare.subnetwork.internal.Tasks.SubsystemGeneration
idare.ThirdParty - package idare.ThirdParty: This package contains Classes and Code obtained from third party sites.
IDARE_DISPLAYMANAGERINFO_SESSION_ID - Static variable in class idare.Properties.IDAREProperties
IDARE_DUPLICATED_NODE - Static variable in class idare.Properties.IDAREProperties
IDARE_EDGE_PROPERTY - Static variable in class idare.Properties.IDAREProperties: IDARE Column Headers
IDARE_GENE - Static variable in class idare.Properties.IDAREProperties.NodeType
IDARE_GENE_EDGE_ID - Static variable in class idare.Properties.IDAREProperties
IDARE_IMAGE_SESSION_ID - Static variable in class idare.Properties.IDAREProperties: The Field ID of IDARE information in stored sessions.
IDARE_imagenode - Static variable in class idare.Properties.IDAREProperties.NodeType
IDARE_LINK - Static variable in class idare.Properties.IDAREProperties.NodeType
IDARE_LINK_TARGET - Static variable in class idare.Properties.IDAREProperties: This field should only be set if the corresponding node is a Link Node (i.e.
IDARE_LINK_TARGET_SUBSYSTEM - Static variable in class idare.Properties.IDAREProperties: This is an awkward way to restore the correct linking behaviour since there is otherwise no way to know which SubsystemView a link targeted.
IDARE_NETWORK_ID - Static variable in class idare.Properties.IDAREProperties
IDARE_NODE_DISPLAY_HEIGHT - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
IDARE_NODE_DISPLAY_SHAPE - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
IDARE_NODE_DISPLAY_WIDTH - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES: Visual Properties of IMAGENODEs
IDARE_NODE_NAME - Static variable in class idare.Properties.IDAREProperties
IDARE_NODE_TYPE - Static variable in class idare.Properties.IDAREProperties
IDARE_NODE_UID - Static variable in class idare.Properties.IDAREProperties: The ID for this node if it is the target of a link.
IDARE_ORIGINAL_NODE - Static variable in class idare.Properties.IDAREProperties
IDARE_PROTEIN - Static variable in class idare.Properties.IDAREProperties.NodeType
IDARE_PROTEINCOMPLEX - Static variable in class idare.Properties.IDAREProperties.NodeType
IDARE_REACTION - Static variable in class idare.Properties.IDAREProperties.NodeType
IDARE_SPECIES - Static variable in class idare.Properties.IDAREProperties.NodeType
IDARE_STYLE_TITLE - Static variable in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle
IDARE_SUBNETWORK_TYPE - Static variable in class idare.Properties.IDAREProperties
IDAREApp - Class in idare.internal: This is a class that manages the behaviour of the IDAREapp upon loading a session.
IDAREApp() - Constructor for class idare.internal.IDAREApp: A Default constructor that initializes the IDARESettingsManager used in this app.
IDARECell - Interface in idare.imagenode.Interfaces.DataSetReaders.WorkBook: A general class of cells in a Workbook used for IDARE.
IDARECell.CellType - Enum in idare.imagenode.Interfaces.DataSetReaders.WorkBook: Different Types of Cells that can be available.
IDARECellIterator - Class in idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation: This class provides a simple Iterator that can be used for all types of Workbooks that implement the IDARE interfaces Since it is likely necessary to provide this, it is directly supplied here.
IDARECellIterator(Iterator<? extends IDARECell>) - Constructor for class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARECellIterator
IDARECustomGraphics - Class in idare.imagenode.internal.ImageManagement: A class for Custom graphics in the Cytoscape visualisation of IDARE
IDARECustomGraphics(BufferedImage, int, int) - Constructor for class idare.imagenode.internal.ImageManagement.IDARECustomGraphics: Default constructor with an Image and initial Heights and width
IDARECustomImageLayer - Class in idare.imagenode.internal.ImageManagement: An implementation of a ImageCustomGraphicLayer for imagenode Display
IDARECustomImageLayer(BufferedImage, int, int, int, int) - Constructor for class idare.imagenode.internal.ImageManagement.IDARECustomImageLayer: Standard constructor with position and width/height information
IDAREDatasetReader - Class in idare.imagenode.Interfaces.DataSetReaders: A IDAREDatasetReader must be able to read a Datafile into a
IDAREDatasetReader() - Constructor for class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader
IDAREDependentMapper<S> - Class in idare.imagenode.internal.VisualStyle: A Visual Mapping function that provides its mapping dependent on IDARE
IDAREDependentMapper(String, VisualProperty<S>, NodeManager, S) - Constructor for class idare.imagenode.internal.VisualStyle.IDAREDependentMapper: Standard constructor of the Mapper
IDAREImageNodeApp - Class in idare.imagenode.internal: The core class of the app, generates necessary objects for the class and provides them to external requests.
IDAREImageNodeApp(CyServiceRegistrar, IDARESettingsManager) - Constructor for class idare.imagenode.internal.IDAREImageNodeApp: Basic constructor that gets the IDareSettingsManager along with a CyServiceRegistrar to obtain all necessary services.
IDAREImageNodeAppService - Class in idare.imagenode: The IDAREImageNodeAppService is the interaction point for plugins that want to provide additional features for the IDARE image generation tool.
IDAREImageNodeAppService(IDAREImageNodeApp) - Constructor for class idare.imagenode.IDAREImageNodeAppService: Default constructor obtaining an IDAREImageNodeApp.
IDARELegend - Class in idare.imagenode.internal.GUI.Legend: An LegendPanel for IDARE, should be displayed in the Results Panel of Cytoscape.
IDARELegend(JPanel, NodeManager) - Constructor for class idare.imagenode.internal.GUI.Legend.IDARELegend: Default constructor given a ContentPane to wrap this scrollerpane around and the NodeManager to obtain layouts for updated nodes.
IDAREMappingFunction - Class in idare.imagenode.internal.VisualStyle: A Mapping Function That is dependent on IDARE.
IDAREMappingFunction(ImageStorage, VisualProperty) - Constructor for class idare.imagenode.internal.VisualStyle.IDAREMappingFunction: Default constructor
IDARENodeManager - Interface in idare.imagenode
IDAREPlugin - Interface in idare.imagenode.Interfaces.Plugin
IDAREProperties - Class in idare.Properties: Class containing all static Fields for the IDARE Columns.
IDAREProperties() - Constructor for class idare.Properties.IDAREProperties
IDAREProperties.EdgeType - Class in idare.Properties
IDAREProperties.NodeType - Class in idare.Properties
IDAREReaderSetupTask - Class in idare.imagenode.Interfaces.DataSetReaders: An Abstract Basis Class that defines a Task that is necessary to set up a reader for dataset parsing.
IDAREReaderSetupTask(IDAREDatasetReader) - Constructor for class idare.imagenode.Interfaces.DataSetReaders.IDAREReaderSetupTask: Default constructor using the reader this Task is supposed to set up.
IDAREReaderTask - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks
IDAREReaderTask(IDAREDatasetReader, DataSetReadingInfo) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.IDAREReaderTask
IDARERow - Interface in idare.imagenode.Interfaces.DataSetReaders.WorkBook: An IDARERow is a row in a data sheet.
IDARERowIterator - Class in idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation: This class provides a simple Iterator that can be used for all types of Workbooks that implement the IDARE interfaces Since it is likely necessary to provide this, it is directly supplied here.
IDARERowIterator(Iterator<? extends IDARERow>) - Constructor for class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARERowIterator
IDAREService - Interface in idare.imagenode.internal: An Interface to indicate services that can be added to the IDARE app.
IDARESettingsManager - Class in idare.Properties: Class to keep track of IDARE IDs and complain (throw exceptions) if duplicate IDs are found.
IDARESettingsManager() - Constructor for class idare.Properties.IDARESettingsManager: Initialize the IDare Manager
IDARESheet - Interface in idare.imagenode.Interfaces.DataSetReaders.WorkBook: An IDARESheet is a sheet containing multiple rows (i.e.
IDAREVisualStyle - Class in idare.imagenode.internal.VisualStyle: A Visual Style using information from the IDARE columns (defined in IDAREProperties) for better visibility of the networks.
IDAREVisualStyle(VisualStyleFactory, VisualMappingManager, VisualMappingFunctionFactory, VisualMappingFunctionFactory, CyEventHelper, ImageStorage, CyNetworkViewManager, NodeManager, ActiveNodeManager) - Constructor for class idare.imagenode.internal.VisualStyle.IDAREVisualStyle: Create a new Visual Style and Activator.
IDAREWorkbook - Interface in idare.imagenode.Interfaces.DataSetReaders.WorkBook: An IDAREWorkbook contains one or multiple sets of data in individual IDARESheets
IDCol - Variable in class idare.imagenode.internal.GUI.NetworkSetup.NetworkSetupTunableGUI
IDCol - Variable in class idare.subnetwork.internal.GUI.SubnetworkPropertyColumnChooser
IDCol - Variable in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnProperties
IDColID - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties
IDFont - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
IDPanel - Class in idare.imagenode.internal.Layout.Manual.GUI
IDPanel() - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.IDPanel
ignoredNodes - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
ImageBag - Class in idare.imagenode.internal.Layout.Automatic: An ImageBag is a class that represents on part of the layout of an image node.
ImageBag(ImageBag.BAGPOSITON, ImageNodeContainer) - Constructor for class idare.imagenode.internal.Layout.Automatic.ImageBag: Default Constructor linking to the parent using this bag and providing the position of this bag.
ImageBag.BAGPOSITON - Enum in idare.imagenode.internal.Layout.Automatic
IMAGEHEIGHT - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
IMAGENODE_TEMP_FOLDER - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
ImageNodeContainer - Class in idare.imagenode.internal.Layout.Automatic: An ImageNodeContainer encapsulates the parts of the Layout (right center and left bag) and can layout the respective bags according to their provided Panel-Container layouts.
ImageNodeContainer() - Constructor for class idare.imagenode.internal.Layout.Automatic.ImageNodeContainer: Generate a new, and empty imageContainer.
ImageNodeLayout - Interface in idare.imagenode.internal.Layout
ImageNodeModel - Class in idare.imagenode.internal.DataManagement: A Class storing which Datasets are associated with a specific StringID.
ImageNodeModel(String) - Constructor for class idare.imagenode.internal.DataManagement.ImageNodeModel: Default constructor using the ID of this Node
IMAGENODEPROPERTIES - Class in idare.imagenode.Properties: Class that stores the Static properties used by imagenodeS.
IMAGENODEPROPERTIES() - Constructor for class idare.imagenode.Properties.IMAGENODEPROPERTIES
IMAGENODEPROPERTIES.LayoutStyle - Enum in idare.imagenode.Properties
ImageStorage - Class in idare.imagenode.internal.ImageManagement: The ImageStorage functions as both CyCustomGraphicsFactory and management for images used by IDARE.
ImageStorage(VisualProperty<CyCustomGraphics<CustomGraphicLayer>>) - Constructor for class idare.imagenode.internal.ImageManagement.ImageStorage: Default Constructor defining the VisualProperty that this VisualMappingFunction maps to.
imageUpdated(GraphicsChangedEvent) - Method in interface idare.imagenode.internal.ImageManagement.GraphicsChangedListener: Update according to the updated images provided in this event.
imageUpdated(GraphicsChangedEvent) - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
imageUpdated(GraphicsChangedEvent) - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle
imageUpdated(GraphicsChangedEvent) - Method in class idare.imagenode.internal.VisualStyle.StyleManager
IMAGEWIDTH - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
IndividualGraphContainer - Class in idare.imagenode.internal.Data.MultiArray.IndividualGraph: Container Class for GraphData
IndividualGraphContainer(DataSet, NodeData) - Constructor for class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainer
IndividualGraphContainerLayout - Class in idare.imagenode.internal.Data.MultiArray.IndividualGraph: ContainerLayout Class for Graph Data, storing common information like the location fo axes, labels and frames.
IndividualGraphContainerLayout() - Constructor for class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout: Default Constructor
IndividualGraphDataSetProperties - Class in idare.imagenode.internal.Data.MultiArray.IndividualGraph
IndividualGraphDataSetProperties() - Constructor for class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
initColors() - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale: Initialize the colors.
initNetwork(CyNetwork) - Static method in class idare.Properties.IDARESettingsManager: Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types
inputFile - Variable in class idare.imagenode.internal.GUI.DataSetAddition.DataSetGenerationParameters
InteractionID - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties
internalFrameActivated(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
internalFrameActivated(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
internalFrameClosed(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
internalFrameClosed(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
internalFrameClosing(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
internalFrameClosing(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
internalFrameDeactivated(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
internalFrameDeactivated(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
internalFrameDeiconified(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
internalFrameDeiconified(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
internalFrameIconified(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
internalFrameIconified(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
internalFrameOpened(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
internalFrameOpened(InternalFrameEvent) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
invalidate(String) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Invalidate a specific ID (i.e.
invalidate(Collection<String>) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Invalidate all Images associated with the provided Strings.
InvalidSelectionException - Exception in idare.subnetwork.internal.Tasks
InvalidSelectionException(String) - Constructor for exception idare.subnetwork.internal.Tasks.InvalidSelectionException
IOUtils - Class in idare.imagenode.Utilities: A few useful IO Functions
IOUtils() - Constructor for class idare.imagenode.Utilities.IOUtils
IS_READY - Static variable in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader
IS_SET_UP - Static variable in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader
isActive() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend: Determine whether the Legend is currently displaying information.
isCellEditable(int, int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel
isColumnBroken(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isColumnHidden(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isColumnSet(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Check whether a specific column is set or empty.
isDataSetAdded() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
isdiscreet - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: An Indicator whether this is a discreet data set (i.e.
isDisplayFormulas() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isDisplayGridlines() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isDisplayRowColHeadings() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isDisplayZeros() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isempty() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData
isempty() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData
isempty() - Method in class idare.imagenode.Interfaces.DataSets.NodeData: Check whether this Data is empty (i.e.
isempty() - Method in class idare.imagenode.internal.Layout.Automatic.ImageBag: Test, whether this Bag is emptys
isempty(CyRow, String) - Static method in class idare.subnetwork.internal.SubNetworkUtils: Check whether the entry of Column ColName in CyRow row is empty.
isempty(Object) - Static method in class idare.subnetwork.internal.SubNetworkUtils: Check whether a given Object is either empty or an empty String
isempty(CyRow, String) - Static method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask: Check whether the entry of Column ColName in CyRow row is empty.
isempty(Object) - Static method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask: Check whether a given Object is either empty or an empty String
isFBCPackageEnabled() - Method in class idare.imagenode.internal.Services.JSBML.Model
isFlexibility() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Return the flexibility of this dataset for layout purposes.
isFormatted() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
isHidden() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
isNodeActive(String) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Check whether the node with the given ID is layouted and needs an image.
isNodeLayouted(String) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Check whether a tge node with the given ID is layouted
isNull() - Method in class idare.imagenode.internal.Services.JSBML.Association
isNull() - Method in class idare.imagenode.internal.Services.JSBML.SBase
isnumeric - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: An Indicator whether the dataset uses numeric representation
isNumeric(String) - Static method in class idare.imagenode.Utilities.StringUtils: Test, whether a string is numeric (i.e.
isPartOfArrayFormulaGroup() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
isPopupAbove() - Method in class idare.ThirdParty.BoundsPopupMenuListener: Determine if the popup should be displayed above the combo box.
isPopupWider() - Method in class idare.ThirdParty.BoundsPopupMenuListener: Determine if the popup might be displayed wider than the combo box
isPrintGridlines() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isProteinComplex() - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
isReady() - Method in class idare.imagenode.internal.GUI.Legend.Tasks.CreateNodeImagesTaskFactory
isReady(CyNetworkView) - Method in class idare.imagenode.internal.GUI.Legend.Tasks.CreateNodeImagesTaskFactory
isReady(CyNetworkView) - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTaskFactory: This factory is in general ready if there is a network selected.
isReady() - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTaskFactory: This factory is in general ready if there is a network selected.
isReady(CyNetworkView) - Method in class idare.imagenode.internal.VisualStyle.Tasks.AddNodesToStyleTaskFactory
isReady(CyNetworkView) - Method in class idare.imagenode.internal.VisualStyle.Tasks.RemoveNodesFromStyleTaskFactory
isReady(View<CyNode>, CyNetworkView) - Method in class idare.NodeDuplicator.Internal.NodeDuplicatorFactory
isReady(View<CyNode>, CyNetworkView) - Method in class idare.NodeDuplicator.Internal.NodeMergerFactory
isReady() - Method in class idare.NodeDuplicator.Internal.NodeRegistry
isReady() - Method in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
isReady(CyNetworkView) - Method in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
isReady() - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFactory
isReady(CyNetworkView) - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFactory
isReady(CyNetworkView) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreatorTaskFactory: If we obtain a view, this has to be possible, as we are obviously in a view.
isReversible() - Method in class idare.imagenode.internal.Services.JSBML.Reaction
isRightToLeft() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isRowBroken(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isSBMLManagerPresent() - Method in class idare.imagenode.internal.Services.JSBML.SBMLManagerHolder
isScrollBarRequired() - Method in class idare.ThirdParty.BoundsPopupMenuListener: Determine if the horizontal scroll bar might be required for the popup
isSelected() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
isSetAnnotation() - Method in class idare.imagenode.internal.Services.JSBML.SBase
isSetName() - Method in class idare.sbmlannotator.internal.gpr.Gene
isSetName() - Method in class idare.sbmlannotator.internal.gpr.Protein
isSetNotes() - Method in class idare.imagenode.internal.Services.JSBML.SBase
isSetSBOTerm() - Method in class idare.imagenode.internal.Services.JSBML.SBase
isSetupNetwork(CyNetwork) - Static method in class idare.Properties.IDARESettingsManager: Test whether a Network has the table Columns required for usage in IDARE
isSheetHidden(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
isSheetVeryHidden(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
isstring - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: An Indicator whether the dataset uses numeric representation
isValid() - Method in class idare.imagenode.internal.DataManagement.ImageNodeModel: Check whether this node still has associated DataSets.
isValid() - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
isValid() - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Check whether this AutomaticNodeLayout is valid.
isValid() - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
isValid() - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
isValidForIDARE() - Method in class idare.imagenode.internal.Layout.Automatic.ImageNodeContainer: Check whether this layoutcontainer is still valid.
isValueSet(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData: Check whether the element at a specific position is set.
ItemDescriptionPane(String, String) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionPane: Set up the Descriptionpane using a IDString and a description string.
ItemDescriptionResizeListener(ArrayDataDescription) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionResizeListener
Itemdescriptions - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
itemStateChanged(ItemEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetLayoutToolBar
itemStateChanged(ItemEvent) - Method in class idare.imagenode.Utilities.GUI.JSVGGlassCanvas
itemxPositions - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
iterator() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
iterator() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet
iterator() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
iterator() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
iterator() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
iterator() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet

J

JetScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale ranging from a dark blue via blue, cyan, yellow and red to a dark red
JetScale() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.JetScale
JSVGGlassCanvas - Class in idare.imagenode.Utilities.GUI
JSVGGlassCanvas(Container) - Constructor for class idare.imagenode.Utilities.GUI.JSVGGlassCanvas

K

keepoldLinks - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask

L

label - Variable in class idare.imagenode.Interfaces.DataSets.NodeData
label - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout.LabelAndPosition
Label - Variable in class idare.imagenode.internal.Layout.DataSetLayoutInfoBundle
Label - Variable in class idare.imagenode.Utilities.LegendLabel
LabelAndPosition(Double, String) - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout.LabelAndPosition: Default constructor using the String Label and a x position
LabelForDataSet - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LabelForDataSet - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LabelForDataSet - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LabelGenerator - Class in idare.imagenode.Properties: A Class to produce continuous labels in an alphanumeric fashion.
LabelGenerator() - Constructor for class idare.imagenode.Properties.LabelGenerator
LABELHEIGHT - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
labelSize - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LargeScatterProperties - Class in idare.imagenode.internal.Data.MultiArray.ScatterData
LargeScatterProperties() - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.LargeScatterProperties
LAYOUT_FILE_NAME - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
LAYOUT_FILES - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
layoutAlgorithm - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
layoutarea - Variable in class idare.imagenode.Interfaces.Layout.ContainerLayout
LayoutArea - Class in idare.imagenode.internal.Layout.Manual.Utilities: This is a comparable rectangle where the order is further left to right and top to bottom.
LayoutArea(Rectangle) - Constructor for class idare.imagenode.internal.Layout.Manual.Utilities.LayoutArea
LayoutComparator - Class in idare.imagenode.internal.Layout.Manual.Utilities: LayoutComparator.
LayoutComparator(LayoutArea, DataSetLayoutInfoBundle) - Constructor for class idare.imagenode.internal.Layout.Manual.Utilities.LayoutComparator
layoutContainer(Container) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
layoutContainer(Container) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualNodeLayoutManager
layoutData() - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
LayoutDataForNode(NodeData, SVGGraphics2D, boolean, ColorMap) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout
LayoutDataForNode(NodeData, SVGGraphics2D, boolean, ColorMap) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainerLayout
LayoutDataForNode(NodeData, SVGGraphics2D, boolean, ColorMap) - Method in class idare.imagenode.Interfaces.Layout.ContainerLayout: Layout the Data according to the previously generated layout
LayoutDataForNode(NodeData, SVGGraphics2D, boolean, ColorMap) - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LayoutDataForNode(NodeData, SVGGraphics2D, boolean, ColorMap) - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LayoutDataForNode(NodeData, SVGGraphics2D, boolean, ColorMap) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LayoutGUI - Class in idare.imagenode.internal.Layout.Manual
LayoutGUI(DataSetManager, IDAREImageNodeApp, CreateNodesTaskFactory) - Constructor for class idare.imagenode.internal.Layout.Manual.LayoutGUI
LayoutIOManager - Class in idare.imagenode.internal.Layout.io
LayoutIOManager() - Constructor for class idare.imagenode.internal.Layout.io.LayoutIOManager
layoutLegendNode(Collection<NodeData>, SVGGraphics2D) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
layoutLegendNode(Collection<NodeData>, SVGGraphics2D) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Lay out the legend for a specific set of node data
layoutLegendNode(Collection<NodeData>, SVGGraphics2D) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
layoutLegendNode(Collection<NodeData>, SVGGraphics2D) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
layoutNode(Collection<NodeData>, SVGGraphics2D) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
layoutNode(Collection<NodeData>, SVGGraphics2D) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Layout a specific node in a given context.
layoutNode(Collection<NodeData>, SVGGraphics2D) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
layoutNode(Collection<NodeData>, SVGGraphics2D) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
LayoutPropertiesGUI - Class in idare.imagenode.internal.Layout.Manual.GUI.Tasks
LayoutPropertiesGUI(DataSetManager) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.Tasks.LayoutPropertiesGUI: Generate the Requesting fields using the given dataset
LayoutPropertiesGUIHandler - Class in idare.imagenode.internal.Layout.Manual.GUI.Tasks
LayoutPropertiesGUIHandler(Method, Method, Object, Tunable, DataSetManager) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.Tasks.LayoutPropertiesGUIHandler
LayoutPropertiesGUIHandler(Field, Object, Tunable, DataSetManager) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.Tasks.LayoutPropertiesGUIHandler
LayoutPropertyBundle - Class in idare.imagenode.internal.Layout.Manual
LayoutPropertyBundle() - Constructor for class idare.imagenode.internal.Layout.Manual.LayoutPropertyBundle
layoutSelector - Variable in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI
LayoutUtils - Class in idare.imagenode.Utilities: Class that provides several utility function to handle SVG Objects (like DOM initialization etc pp
LayoutUtils() - Constructor for class idare.imagenode.Utilities.LayoutUtils
LEGEND_DESCRIPTION_OPTIMAL_WIDTH - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
LegendAxes - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LegendAxes - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LegendAxes - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LegendFrame - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LegendFrame - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LegendFrame - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LegendLabel - Class in idare.imagenode.Utilities: Class that represents a LegendLabel, which can be drawn in a specific graphics context.
LegendLabel(Font, Point, String) - Constructor for class idare.imagenode.Utilities.LegendLabel: Default Constructor providing the Font, position and String used when writing this label.
LegendLineArea - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LegendLineArea - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LegendLineArea - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LegendShapePosition(Shape, Rectangle2D, String, Point2D, Font) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.LegendShapePosition: Create a AbstractArrayContainerLayout.LegendShapePosition.
LegendSizeListener - Interface in idare.imagenode.GUI.Legend.Utilities
LegendUpdater - Class in idare.imagenode.internal.GUI.Legend: A Class to keep the legend up to date with the current Row Selection.
LegendUpdater(IDARELegend, NodeManager, CyApplicationManager, VisualMappingManager, StyleManager) - Constructor for class idare.imagenode.internal.GUI.Legend.LegendUpdater: Default contstructor using the target IDARELegend, the NodeManager to check whether there are layouts for the node, The Style Manager to determine, whether a Style is using ImageNodes and Cytoscape managers to deterine the properties of visual styles and nodes.
LegendZeroLine - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LegendZeroLine - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LegendZeroLine - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LineArea - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LineArea - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LineArea - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
linecolors - Static variable in class idare.imagenode.internal.ColorManagement.ColorScales.LineScale
LineDescription - Class in idare.imagenode.internal.Data.MultiArray.GraphData
LineDescription(JScrollPane) - Constructor for class idare.imagenode.internal.Data.MultiArray.GraphData.LineDescription
LineDescription - Class in idare.imagenode.internal.Data.MultiArray.IndividualGraph
LineDescription(JScrollPane) - Constructor for class idare.imagenode.internal.Data.MultiArray.IndividualGraph.LineDescription
LineHeaders - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
LineHeaders - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
LineHeaders - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
LineScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A DiscreteColorScale with multiple colors fitting for lines
LineScale() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.LineScale
loadWorkBook(IDAREWorkbook) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: This function loads calls the implementing classes function setupWorkBook to interpret the Workbook provided and tests, whether there are viable DataSetLayoutProperties in IDARE that can be used with this DataSet and the given Workbook.
loc - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer
loc - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer: The localisation information of this DataContainer
Localisation - Class in idare.imagenode.Properties: A Class encapsulating the Localisation information (i.e.
Localisation(Localisation.Position, boolean) - Constructor for class idare.imagenode.Properties.Localisation: DEfault constructor using a position and a flexibility indicator
Localisation.Position - Enum in idare.imagenode.Properties

M

ManualLayout - Class in idare.imagenode.internal.Layout.Manual
ManualLayout() - Constructor for class idare.imagenode.internal.Layout.Manual.ManualLayout
ManualLayoutUpdater - Class in idare.imagenode.internal.Layout.Manual.GUI
ManualLayoutUpdater(ManualLayout, IDARELegend, LayoutGUI, NodeManager) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
ManualNodeLayout - Class in idare.imagenode.internal.Layout.Manual: This is a very simplistic Node Layout that originates from a Manual layout generation.
ManualNodeLayout() - Constructor for class idare.imagenode.internal.Layout.Manual.ManualNodeLayout: Create an empty layout.
ManualNodeLayoutManager - Class in idare.imagenode.internal.Layout.Manual.GUI
ManualNodeLayoutManager(JComponent, JComponent, Dimension, Dimension) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.ManualNodeLayoutManager
MarkerDataDescription - Class in idare.imagenode.internal.Data.MultiArray.ScatterData: Class to Generate Descriptions for Lines
MarkerDataDescription(JScrollPane) - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.MarkerDataDescription: Create a new LineDataDescription, which is contained in a JScrollPane.
maxCenterFixDimensionHeight - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxCenterFixDimensionWidth - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxCenterFixItems - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxCenterFlexItems - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxEdgeFixDimensionHeight - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxEdgeFixDimensionWidth - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxEdgeFixItems - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxEdgeFlexItems - Static variable in class idare.imagenode.internal.Layout.Automatic.ImageBag
maxitemwidth - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
maxval - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
MaxValue - Variable in class idare.imagenode.Interfaces.DataSets.DataSet
Member - Class in idare.imagenode.internal.Services.JSBML
Member(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Member
menuCanceled(MenuEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DatasetMenu
menuDeselected(MenuEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DatasetMenu
menuSelected(MenuEvent) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DatasetMenu
mgr - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties: The managers necessary to keep track/update IDs etc pp
minheight - Static variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer: The minimal height (out of 10) of the container.
MINIMAL_FONT_SIZE - Static variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
minimumLayoutSize(Container) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
minimumLayoutSize(Container) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualNodeLayoutManager
minval - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
MinValue - Variable in class idare.imagenode.Interfaces.DataSets.DataSet
minwidth - Static variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer: The minimal width (out of 10) of the container
mixedheaders - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Mixed headers can appear due to e.g.
Model - Class in idare.imagenode.internal.Services.JSBML
Model(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Model
mouseDragged(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseDraggingListener
mouseDragged(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseResizerListener
MouseDraggingListener<T extends JComponent> - Class in idare.imagenode.Utilities.GUI
MouseDraggingListener(JDesktopPane, Class<T>) - Constructor for class idare.imagenode.Utilities.GUI.MouseDraggingListener
mouseMoved(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseDraggingListener
mouseMoved(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseResizerListener
mousePressed(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseDraggingListener
mousePressed(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseResizerListener
mouseReleased(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseDraggingListener
mouseReleased(MouseEvent) - Method in class idare.imagenode.Utilities.GUI.MouseResizerListener
MouseResizerListener<T extends JComponent> - Class in idare.imagenode.Utilities.GUI
MouseResizerListener(JDesktopPane, Class<T>) - Constructor for class idare.imagenode.Utilities.GUI.MouseResizerListener
moveBundleToFront(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout: Move a specific bundle to the front (i.e.
moveEntryDown() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionTable: Move the selected entry (we assume single selection) down one row.
moveEntryUp() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionTable: Move the selected entry (we assume single selection) down one row.
movePointOnScale(float, float) - Method in interface idare.imagenode.ColorManagement.ColorScale: Move a point in the 0-1 scale to the target value.
movePointOnScale(float, float) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
moveRowDown(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Move a DataSet down in the table (supplying the row of the dataset to move down
moveRowUp(int) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Move a DataSet up in the table (supplying the row of the dataset to move up
MultiArrayContainer - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: A Container for a MultiArrayDataSet
MultiArrayContainer(DataSet, NodeData) - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer: Standard Constructor using the Source Dataset and a NodeData
MultiArrayContainerLayout - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: Abstract class providing some functionalities for Layouts of Value Sets
MultiArrayContainerLayout() - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainerLayout: Basic Constructor
MultiArrayDataProperties - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: A basic class for all MultiArrayDataProperties
MultiArrayDataProperties() - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataProperties
MultiArrayDataSet - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: Class to provide a basic setting for MultiArray Datasets.
MultiArrayDataSet() - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Basic Constructor, generating an empty dataset.
MultiArrayDataSet(int, boolean, Properties) - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Constructor using an id, a two column indicator and the dataset properties.
MultiArrayDataValue - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: A NodeValue for MultiArrayDataSet The Value of a NodeValue is always the String representing the Sheet it is contained in.
MultiArrayDataValue(Comparable) - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataValue: Generate a new NodeValue based on a specific ColorValue (likely the sheet name).
MultiArrayDescription - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: Abstract class that provides an entry to building basic Descriptions in a Legend for given shapes.
MultiArrayDescription(JScrollPane) - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDescription: Create a new LineDataDescription, which is contained in a JScrollPane.
MultiArrayEntryDescriptionPane - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: Abstract description of an Entry (i.e.
MultiArrayEntryDescriptionPane(Color, String) - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryDescriptionPane: Default constructor receiving the color for this entry along with a descriptive String.
MultiArrayEntryPanel - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: A SetEntryPanel is a simple abstract representation of a marker or shape along with the color of a specific entry.
MultiArrayEntryPanel(Color) - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryPanel: Default Constructor using a given color for representation.
MultiArrayNodeData - Class in idare.imagenode.Data.BasicDataTypes.MultiArrayData: NodeData for MultiArrayDataSets
MultiArrayNodeData(DataSet) - Constructor for class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData: Basic constructor providing a source DataSet
MultiArrayTypeName - Static variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
MultiColorScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale is a color scale, that contains multiple colors and commonly has gradients between those colors that will be used to obtain the colors for plotting It will provide a discrete number of colors, to reduce computational cost in calculating the color at each request.
MultiColorScale(Color[], float[], int) - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale: General constructor using a set of colors, a float array for the positions of the colors on a 0-1 scale and the number of discrete colors to generate.
MultiColorScale(Color[], float[]) - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale: A Constructor generating a colorscale using the given colors and the given fractions.

N

network - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties: The Target network to set up
network - Variable in class idare.subnetwork.internal.NodeAndNetworkStruct
networkID - Variable in class idare.subnetwork.internal.NetworkNode
networkIDAREID - Variable in class idare.subnetwork.internal.NetworkNode
NetworkNode - Class in idare.subnetwork.internal
NetworkNode(NetworkNode, CyNetwork, String, String, IDARESettingsManager) - Constructor for class idare.subnetwork.internal.NetworkNode
NetworkNode(CyNetwork, IDARESettingsManager) - Constructor for class idare.subnetwork.internal.NetworkNode
NetworkSetupGUIHandler - Class in idare.imagenode.internal.GUI.NetworkSetup.Tasks
NetworkSetupGUIHandler(Method, Method, Object, Tunable, IDARESettingsManager, NodeManager, CyNetwork) - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupGUIHandler
NetworkSetupGUIHandler(Field, Object, Tunable, IDARESettingsManager, NodeManager, CyNetwork) - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupGUIHandler
NetworkSetupGUIHandlerFactory - Class in idare.imagenode.internal.GUI.NetworkSetup.Tasks
NetworkSetupGUIHandlerFactory(NodeManager, IDARESettingsManager, CyApplicationManager) - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupGUIHandlerFactory
NetworkSetupGUIHandlerFactory - Class in idare.imagenode.internal.Layout.Manual.GUI.Tasks
NetworkSetupGUIHandlerFactory(DataSetManager, IDARESettingsManager, CyApplicationManager) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.Tasks.NetworkSetupGUIHandlerFactory
NetworkSetupProperties - Class in idare.imagenode.internal.GUI.NetworkSetup.Tasks
NetworkSetupProperties() - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties
NetworkSetupTask - Class in idare.imagenode.internal.GUI.NetworkSetup.Tasks
NetworkSetupTask() - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTask
NetworkSetupTaskFactory - Class in idare.imagenode.internal.GUI.NetworkSetup.Tasks
NetworkSetupTaskFactory(CyApplicationManager) - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTaskFactory
NetworkSetupTunableGUI - Class in idare.imagenode.internal.GUI.NetworkSetup
NetworkSetupTunableGUI(CyNetwork) - Constructor for class idare.imagenode.internal.GUI.NetworkSetup.NetworkSetupTunableGUI: Generate the Requesting fields using the given network
NetworkViewSwitcher - Class in idare.subnetwork.internal: A Class that acts as switcher between networks.
NetworkViewSwitcher(CyServiceRegistrar, IDARESettingsManager) - Constructor for class idare.subnetwork.internal.NetworkViewSwitcher: Constructs a NetworkView Switcher for the current application.
NetworkViewSwitchTask - Class in idare.subnetwork.internal: Simple Task to switch between two network views
NetworkViewSwitchTask(CyServiceRegistrar, CyNode, CyNetwork) - Constructor for class idare.subnetwork.internal.NetworkViewSwitchTask: A Task switching the current view to the View in the TargetView and focusing on the NodeView listed.
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Create a new Container for a specific DataSet and a given NodeData.
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleDataSetProperties
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleDataSetProperties
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
next() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARECellIterator
next() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARERowIterator
nm - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties
noBranchNodes - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
node - Variable in class idare.subnetwork.internal.NodeAndNetworkStruct
NodeAndNetworkStruct - Class in idare.subnetwork.internal: Helper Struct to bundle a Node and its containing network since it seems, that the network pointer in a node is not always set...
NodeAndNetworkStruct(CyNode, CyNetwork) - Constructor for class idare.subnetwork.internal.NodeAndNetworkStruct: Default constructor using a CyNode and a CyNetwork
NodeAxes - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
NodeAxes - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
NodeAxes - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
NodeChangedListener - Interface in idare.imagenode.internal.DataManagement.Events: A Listener that listens to the change in Nodes.
NodeData - Class in idare.imagenode.Interfaces.DataSets: A Data Entry will always only have numbers stored in it as it is used for data representation on color scales or in graphs.
NodeData(DataSet) - Constructor for class idare.imagenode.Interfaces.DataSets.NodeData: Generic contstructor using the source DataSet.
NodeDuplicationTask - Class in idare.NodeDuplicator.Internal.Tasks
NodeDuplicationTask() - Constructor for class idare.NodeDuplicator.Internal.Tasks.NodeDuplicationTask
NodeDuplicatorFactory - Class in idare.NodeDuplicator.Internal
NodeDuplicatorFactory(CyServiceRegistrar) - Constructor for class idare.NodeDuplicator.Internal.NodeDuplicatorFactory
NodeDuplicatorImpl - Class in idare.NodeDuplicator.Internal
NodeDuplicatorImpl(CyNode, CyNetwork, CyServiceRegistrar, boolean) - Constructor for class idare.NodeDuplicator.Internal.NodeDuplicatorImpl: Default Constructor using a CyNode with its associated CyNetwork along with a CyServiceRegistrar
NodeIDSelectorToolBarEntry - Class in idare.imagenode.internal.Layout.Manual.GUI
NodeIDSelectorToolBarEntry(Vector<String>) - Constructor for class idare.imagenode.internal.Layout.Manual.GUI.NodeIDSelectorToolBarEntry
NodeLabels - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
NodeManager - Class in idare.imagenode.internal.DataManagement: NodeManager manages the nodes used in the IDARE App.
NodeManager(CyNetworkManager, ActiveNodeManager) - Constructor for class idare.imagenode.internal.DataManagement.NodeManager
NodeMergerFactory - Class in idare.NodeDuplicator.Internal
NodeMergerFactory(CyServiceRegistrar) - Constructor for class idare.NodeDuplicator.Internal.NodeMergerFactory
NodeMergerImpl - Class in idare.NodeDuplicator.Internal
NodeMergerImpl(CyNode, CyNetwork, CyServiceRegistrar) - Constructor for class idare.NodeDuplicator.Internal.NodeMergerImpl
NodeRegistry - Class in idare.NodeDuplicator.Internal
NodeRegistry(CyServiceRegistrar) - Constructor for class idare.NodeDuplicator.Internal.NodeRegistry
NodeResizer - Class in idare.imagenode.internal.GUI.Legend: The NOde Resizer will resize the Canvas containing the layouted node.
NodeResizer(NodeSVGCanvas) - Constructor for class idare.imagenode.internal.GUI.Legend.NodeResizer
NodeSVGCanvas - Class in idare.imagenode.internal.GUI.Legend: This class is mainly a hack to only allow preferredsize changes when they are requested by the IDAREapp.
NodeSVGCanvas() - Constructor for class idare.imagenode.internal.GUI.Legend.NodeSVGCanvas
NodeType() - Constructor for class idare.Properties.IDAREProperties.NodeType
NodeUpdateEvent - Class in idare.imagenode.internal.DataManagement.Events: An Event to indicate that specific nodes were updated.
NodeUpdateEvent(Collection<String>) - Constructor for class idare.imagenode.internal.DataManagement.Events.NodeUpdateEvent: Default constructor with a provided set of IDs.
NodeValue - Class in idare.imagenode.Interfaces.DataSets: A NodeValue represents the Value at a specific node.
NodeValue(Double) - Constructor for class idare.imagenode.Interfaces.DataSets.NodeValue: Create a NodeValue using a Double value.
NodeValue(boolean) - Constructor for class idare.imagenode.Interfaces.DataSets.NodeValue: Create a NodeValue indicating whether it is a numeric or non numeric value.
NodeValue(String) - Constructor for class idare.imagenode.Interfaces.DataSets.NodeValue: Create a NodeValue as a String.
NodeValueType - Enum in idare.imagenode.Properties: Enumerator for different types of NodeValues.
NodeViewLink - Class in idare.subnetwork.internal: A Struct class to bundle information for a target node.
NodeViewLink(View<CyNode>, CyNetworkView, CyNetwork, CyNode, CyNetwork) - Constructor for class idare.subnetwork.internal.NodeViewLink: Default Constructor to Combine the View of a target CyNode wth the respective CyNetwork, CyNetworkView and the CyNode
NoNetworksToCreateException - Exception in idare.subnetwork.internal: A Exception indicating, that there were no Networks to create.
NoNetworksToCreateException() - Constructor for exception idare.subnetwork.internal.NoNetworksToCreateException
numericheaders - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Indicator whether numeric headers are used
numericHeaders - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
numericstrings - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: an indicator whether the dataset uses numeric data represented by strings

O

ObservableIDARETask - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks
ObservableIDARETask() - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.ObservableIDARETask
oddrange - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
oldsize - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
Or - Class in idare.imagenode.internal.Services.JSBML
Or(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Or
origin - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer
origin - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer: The DataSet this container is associated with
overwrite - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties: Whether to overwrite data

P

paintComponent(Graphics) - Method in class idare.imagenode.ColorManagement.ColorScalePane
paintComponent(Graphics) - Method in class idare.imagenode.ColorManagement.DiscreteColorScalePane
paintComponent(Graphics) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryPanel
paintComponent(Graphics) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ColorMenuItem
paintComponent(Graphics) - Method in class idare.imagenode.Utilities.GUI.JSVGGlassCanvas
paintScale(Graphics, int, int) - Method in class idare.imagenode.ColorManagement.ColorScalePane: This helper function paints a LinearGradientPaint on a graphics object.
paintScale(Graphics, int, int) - Method in class idare.imagenode.ColorManagement.DiscreteColorScalePane: This helper function paints a LinearGradientPaint on a graphics object.
params - Variable in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTask
params - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTask: Tunables that get the desired properties.
params - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask
parent - Variable in class idare.imagenode.Interfaces.DataSets.NodeData
parent - Variable in class idare.subnetwork.internal.NetworkNode
parseCobraNotes(SBase) - Static method in class idare.ThirdParty.CobraUtil: Parses the notes of the given SBase element.
parseSerializableString(String) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
plotShape(Shape, Graphics2D) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryPanel: Plot the shape.
POICell - Class in idare.imagenode.internal.DataSetReaders.POIReader
POICell(Cell) - Constructor for class idare.imagenode.internal.DataSetReaders.POIReader.POICell
POIReader - Class in idare.imagenode.internal.DataSetReaders.POIReader
POIReader() - Constructor for class idare.imagenode.internal.DataSetReaders.POIReader.POIReader
POIRow - Class in idare.imagenode.internal.DataSetReaders.POIReader
POIRow(Row) - Constructor for class idare.imagenode.internal.DataSetReaders.POIReader.POIRow
POISheet - Class in idare.imagenode.internal.DataSetReaders.POIReader
POISheet(Sheet) - Constructor for class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
POIToIDARE - Static variable in class idare.imagenode.internal.Services.POI.POIToIDARETypes
POIToIDARE_ACCESS_TYPES - Static variable in class idare.imagenode.internal.Services.POI.POIToIDARETypes
POIToIDARETypes - Class in idare.imagenode.internal.Services.POI
POIToIDARETypes() - Constructor for class idare.imagenode.internal.Services.POI.POIToIDARETypes
POIWorkBook - Class in idare.imagenode.internal.DataSetReaders.POIReader
POIWorkBook(Workbook) - Constructor for class idare.imagenode.internal.DataSetReaders.POIReader.POIWorkBook
popupMenuCanceled(PopupMenuEvent) - Method in class idare.ThirdParty.BoundsPopupMenuListener
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class idare.ThirdParty.BoundsPopupMenuListener
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class idare.ThirdParty.BoundsPopupMenuListener: Alter the bounds of the popup just before it is made visible.
popupWider(BasicComboPopup) - Method in class idare.ThirdParty.BoundsPopupMenuListener
pos - Variable in class idare.imagenode.Properties.Localisation
position - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.ShapePosition
position - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout.LabelAndPosition
position - Variable in class idare.imagenode.internal.Layout.SimpleLink
PREFERRED_OPTION - Static variable in class idare.subnetwork.internal.NetworkViewSwitcher
preferredLayoutSize(Container) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
preferredLayoutSize(Container) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualNodeLayoutManager
preProcessWorkBook(IDAREWorkbook) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
preProcessWorkBook(IDAREWorkbook) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Do preprocessing for the setup Process.
print() - Method in class idare.subnetwork.internal.NetworkNode
PrintFDebugger - Class in idare.imagenode.internal.Debug: Helper class to provide formatted Output for PrintFDebugging, indicating time, and origin of the printf.
PrintFDebugger() - Constructor for class idare.imagenode.internal.Debug.PrintFDebugger
printSheetsContained() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData
printWithChildren(String) - Method in class idare.subnetwork.internal.NetworkNode
PrismScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A DiscreteColorScale providing the colors of a prism.
PrismScale() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.PrismScale
PRODUCT_EDGE - Static variable in class idare.Properties.IDAREProperties.EdgeType
properties - Variable in class idare.imagenode.internal.Layout.DataSetLayoutInfoBundle
properties - Variable in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnPropertiesSelectionTask
propertyOptions - Variable in class idare.imagenode.Interfaces.DataSets.DataSet
PROPERTYOPTIONSAVAILABLE - Static variable in class idare.imagenode.Interfaces.DataSets.DataSet
protectSheet(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
Protein - Class in idare.sbmlannotator.internal.gpr
Protein(HashMap<String, String>) - Constructor for class idare.sbmlannotator.internal.gpr.Protein
Protein(String, String) - Constructor for class idare.sbmlannotator.internal.gpr.Protein
PROTEIN_BASE - Static variable in class idare.sbmlannotator.internal.gpr.GPRManager
proteinAnnotationDataBase - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
ProteinID - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties: IDs for the individual types
proteinTypeSelector - Variable in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser
putAll(Map<String, T>) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
putAll(Map<String, T>) - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
putAll(Map<String, T>) - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction
putMapValue(String, T) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
putMapValue(String, T) - Method in class idare.imagenode.internal.VisualStyle.IDAREDependentMapper
putMapValue(String, T) - Method in class idare.imagenode.internal.VisualStyle.IDAREMappingFunction

R

range - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
REACTANT_EDGE - Static variable in class idare.Properties.IDAREProperties.EdgeType
Reaction - Class in idare.imagenode.internal.Services.JSBML
Reaction(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Reaction
REACTION_REVERSIBLE - Static variable in class idare.Properties.IDAREProperties.EdgeType
ReactionID - Variable in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnProperties
reactionTypeSelector - Variable in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser
reactionTypeSelector - Variable in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser
readData(File) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: Read an input File and create an IDARE compatible Workbook structure.
readData(File) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVReader
readData(File) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.TSVReader
readData(File) - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIReader
readLayout(DataSetManager, ObjectInputStream, Object) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
readLayout(DataSetManager, ObjectInputStream, Object) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Read a layout object from an ObjectInputStream given the last object read (which is the first object of the layout)
readLayout(ObjectInputStream, Object, DataSetManager) - Method in class idare.imagenode.internal.Layout.io.LayoutIOManager: Read a Layout from a stream
readLayout(DataSetManager, ObjectInputStream, Object) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
readLayout(DataSetManager, ObjectInputStream, Object) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
readNodeLayouts(File, IDAREImageNodeApp) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Read Layout data saved in a given File to restore old nodemanager data.
readSBML(CyNetwork) - Method in class idare.imagenode.internal.Services.JSBML.SBMLManagerHolder
readURIString(String, Set<String>, boolean) - Method in class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
readWorkBookData(IDAREWorkbook) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
readWorkBookData(IDAREWorkbook) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
readWorkBookData(IDAREWorkbook) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Read the Data for this workbook into the dataset.
ReadWorkBookTask - Class in idare.imagenode.internal.GUI.DataSetAddition.Tasks
ReadWorkBookTask(IDAREDatasetReader, DataSetReadingInfo) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.Tasks.ReadWorkBookTask
RectangleContainer - Class in idare.imagenode.internal.Data.Array.RectangleData: Class to provide a Container for Rectangle related data
RectangleContainer(DataSet, ArrayNodeData) - Constructor for class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainer
RectangleContainerLayout - Class in idare.imagenode.internal.Data.Array.RectangleData: Class to provide a ContainerLayout for Rectangle related data
RectangleContainerLayout() - Constructor for class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout
RectangleContainerLayout.RectangleLegendShapePosition - Class in idare.imagenode.internal.Data.Array.RectangleData: A Class that provides A Legend represenatation of a RectangleContainerLayout.RectangleShapePosition for a Rectangle This is necessary, as we need a slightly different draw method (black borders around everything and not contrasting colors for Rectangles in comparison to circles.
RectangleContainerLayout.RectangleShapePosition - Class in idare.imagenode.internal.Data.Array.RectangleData: A Class that provides A ShapePosition for a Rectangle This is necessary, as we need a slightly different draw method (black borders around everything and not contrasting colors for Rectangles in comparison to circles.
RectangleDataSetProperties - Class in idare.imagenode.internal.Data.Array.RectangleData: Properties for a Dataset with representation as rectangles It will be termed as HeatMap.
RectangleDataSetProperties() - Constructor for class idare.imagenode.internal.Data.Array.RectangleData.RectangleDataSetProperties
RectangleLegendShapePosition(Shape, Rectangle2D, String, Point2D, Font) - Constructor for class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout.RectangleLegendShapePosition: Default Constructor
RectangleShapePosition(Shape, Rectangle2D) - Constructor for class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout.RectangleShapePosition
redo() - Method in class idare.NodeDuplicator.Internal.NodeDuplicatorImpl
redo() - Method in class idare.NodeDuplicator.Internal.NodeMergerImpl
redraw() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription: Redraw this panel.
RedWhiteBlueScale - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale ranging from red via white to blue
RedWhiteBlueScale() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.RedWhiteBlueScale
reg - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFactory
registerDataSetProperties(Class<? extends DataSet>, DataSetLayoutProperties) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Register DataSetProperties for a DataSet of the given Type.
registerDataSetProperties(Class<? extends DataSet>, Collection<DataSetLayoutProperties>) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Register DataSetProperties for a DataSet of the given Type.
registerDataSetReader(IDAREDatasetReader) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Register a IDAREDatasetReader to be available for file reading.
registerDataSetReader(IDAREDatasetReader) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Register an IDAREDatasetReader to be available in the app.
registerDataSetType(String, Class<? extends DataSet>) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Register a DataSetType that can be accessed by the TypeName.
registerDataSetType(DataSet) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Register a the type of a dataset provided to the set of avilable DataSet classes
registerLayout(ImageNodeLayout) - Method in class idare.imagenode.internal.Layout.io.LayoutIOManager: Register a specific type of Layout.
registerPlugin(IDAREPlugin) - Method in class idare.imagenode.IDAREImageNodeAppService: Register a plugin to the IDARE App;
registerPlugin(IDAREPlugin) - Method in class idare.imagenode.internal.IDAREImageNodeApp: Register a plugin.
registerPropertiesForDataSet(Class<? extends DataSet>, DataSetLayoutProperties) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Add DataSetProperties for a specific dataset
registerPropertiesForDataSet(Class<? extends DataSet>, Collection<DataSetLayoutProperties>) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Register a set of properties for a datasetclass.
removeArrayFormula(Cell) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
removeCell(Cell) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
removeCellComment() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
removeChild(NetworkNode) - Method in class idare.subnetwork.internal.NetworkNode
removeChild(CyNetwork) - Method in class idare.subnetwork.internal.NetworkNode
removeColumnBreak(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
removeData(DataSet) - Method in class idare.imagenode.internal.DataManagement.ImageNodeModel: Remove a DataSet from this node
removeDataSet(DataSet) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Remove a DataSet from this Manager
removeDataSet(DataSet) - Method in class idare.imagenode.internal.Layout.Automatic.ImageNodeContainer: Remove a DataSet from this layout container.
removeDataSet(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout: Remove a dataset represented by the given bundle.
removeDataSetAboutToBeChangedListener(DataSetAboutToBeChangedListener) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Remove a DataSetAboutToBeChangedListener listening to changes in DataSets
removeDataSetChangeListener(DataSetChangeListener) - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Remove a Listener that needs to be informed, if a dataset state was changed
removeFBCNodes - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
removeFBCNodes - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFBC
removeLayoutComponent(Component) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
removeLayoutComponent(Component) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualNodeLayoutManager
removeMergedRegion(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
removeName(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
removeName(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
removeNodeChangeListener(NodeChangedListener) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Remove a listener that had listened to changes in nodes in this manager.
removeNodes(TaskMonitor) - Method in class idare.imagenode.internal.VisualStyle.StyleManager: Remove the IDARE Ndoes from the current Visualstyle (if they were added) and restore default values.
removeNodes() - Method in class idare.imagenode.internal.VisualStyle.Tasks.RemoveNodesFromStyleTaskFactory: Add Nodes to the current style
RemoveNodesFromStyleTaskFactory - Class in idare.imagenode.internal.VisualStyle.Tasks: A TaskFactory that adds nodes to Styles.
RemoveNodesFromStyleTaskFactory(StyleManager, DialogTaskManager) - Constructor for class idare.imagenode.internal.VisualStyle.Tasks.RemoveNodesFromStyleTaskFactory
removePrintArea(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
removePropertyOption(DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Remove the given PropertyOptions from this dataset.
removeRow(Row) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
removeRowBreak(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
removeSheetAt(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
removeStyleUsingNodes(String) - Method in class idare.imagenode.internal.ImageManagement.ActiveNodeManager
reset() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
reset() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
reset() - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: Resets the reader.
reset() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: reset this Dataset to a stage as if it would have been just initialized.
reset(int) - Method in class idare.imagenode.internal.DataManagement.DataSetIDProvider: Reset the IDs, with the provided id being the highest ID already used.
reset() - Method in class idare.imagenode.internal.DataManagement.DataSetManager: Reset this DataSetManager clearing all datastructures.
reset() - Method in class idare.imagenode.internal.DataManagement.NodeManager: Reset this NodeManager clearing fields
reset() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend: reset the legend Panel when loading a new session
reset() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Reset the images available in this mapping
reset() - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle: Reset the Visual Style to use its default properties
reset() - Method in class idare.subnetwork.internal.NetworkViewSwitcher: Reset the Switcher (e.g.
resetColorData() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Clear all color related data i.e.
resetNetworks(Collection<CyNetwork>) - Static method in class idare.Properties.IDARESettingsManager
resetReader() - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: Reset the reader, clearing any temporary fields.
resetReader() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVReader
resetReader() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POIReader
resetSubNetworkTypes() - Method in class idare.Properties.IDARESettingsManager: Reset the SubNetworkTypes.
RETURN_BLANK_AS_NULL - Static variable in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow
RETURN_NULL_AND_BLANK - Static variable in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARERow
roundToCommonOrder(Double, Double) - Static method in class idare.imagenode.Interfaces.Layout.ContainerLayout: Round the number to the numbers Order.
roundToOrder(Double, boolean) - Static method in class idare.imagenode.Interfaces.Layout.ContainerLayout: Round the number to the numbers Order.
rowIterator() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet
rowIterator() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARESheet: Get an Iterator over all rows in this Sheet.
rowIterator() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
rowIterator() - Method in class idare.imagenode.internal.DataSetReaders.POIReader.POISheet
run(TaskMonitor) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREReaderSetupTask: Runs the Task specified by the execute method and catches any exception, converting the exception into a status message.
run(TaskMonitor) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.AddDataSetToManagerTask
run(TaskMonitor) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTask
run(TaskMonitor) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.FailureTask
run(TaskMonitor) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.IDAREReaderTask
run(TaskMonitor) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.ReadWorkBookTask
run(Set<DataSet>, ImageNodeLayout) - Method in class idare.imagenode.internal.GUI.DataSetController.CreateNodesTaskFactory: Run the task factory.
run(TaskMonitor) - Method in class idare.imagenode.internal.GUI.Legend.Tasks.CreateNodeImageTask
run(TaskMonitor) - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTask
run(TaskMonitor) - Method in class idare.imagenode.internal.Layout.Manual.GUI.Tasks.AddDataSetToManuaLayoutTask
run(TaskMonitor) - Method in class idare.NodeDuplicator.Internal.NodeDuplicatorImpl
run(TaskMonitor) - Method in class idare.NodeDuplicator.Internal.NodeMergerImpl
run(TaskMonitor) - Method in class idare.sbmlannotator.internal.SBMLAnnotaterTask
run(TaskMonitor) - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
run(TaskMonitor) - Method in class idare.sbmlannotator.internal.Tasks.SBMLDocumentSelectionTask
run(TaskMonitor) - Method in class idare.subnetwork.internal.NetworkViewSwitchTask
run(TaskMonitor) - Method in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnPropertiesSelectionTask
run(TaskMonitor) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask

S

SBase - Class in idare.imagenode.internal.Services.JSBML
SBase(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.SBase
SBML_EDGE_TYPE - Static variable in class idare.Properties.IDAREProperties
SBML_GENE_STRING - Static variable in class idare.Properties.IDAREProperties: Some specifications for SBML data fields
SBML_ID_STRING - Static variable in class idare.Properties.IDAREProperties
SBML_NAME_STRING - Static variable in class idare.Properties.IDAREProperties
SBML_REACTION_STRING - Static variable in class idare.Properties.IDAREProperties
SBML_SPECIES_STRING - Static variable in class idare.Properties.IDAREProperties
SBML_TYPE_STRING - Static variable in class idare.Properties.IDAREProperties
SBMLAnnotaterTask - Class in idare.sbmlannotator.internal
SBMLAnnotaterTask(CyApplicationManager, SBMLDocument, boolean, CyEventHelper, String, String, Map<String, Set<CVTerm>>, String, String, String, String, IDAREImageNodeApp) - Constructor for class idare.sbmlannotator.internal.SBMLAnnotaterTask: A Task reading in an SBML File and parsing its Notes fields adding the information to the Nodes of the current network.
SBMLAnnotationTaskFactory - Class in idare.sbmlannotator.internal
SBMLAnnotationTaskFactory(CyApplicationManager, CyEventHelper, FileUtil, CySwingApplication, SBMLManagerHolder, IDAREImageNodeApp) - Constructor for class idare.sbmlannotator.internal.SBMLAnnotationTaskFactory
SBMLAnnotatorTask - Class in idare.sbmlannotator.internal.Tasks: A Task that annotates an network with data from an SBML file that is gene and protein specific.
SBMLAnnotatorTask(SBMLManagerHolder, CyNetwork, CyNetworkView, IDARESettingsManager, CyServiceRegistrar, SBMLDocument) - Constructor for class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
SBMLAnnotatorTaskFactory - Class in idare.sbmlannotator.internal.Tasks
SBMLAnnotatorTaskFactory(CyServiceRegistrar, SBMLManagerHolder, IDAREImageNodeApp) - Constructor for class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFactory
SBMLAnnotatorTaskFBC - Class in idare.sbmlannotator.internal.Tasks
SBMLAnnotatorTaskFBC(SBMLManagerHolder, CyNetwork, CyNetworkView, IDARESettingsManager, CyServiceRegistrar, SBMLDocument) - Constructor for class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTaskFBC
SBMLDocument - Class in idare.imagenode.internal.Services.JSBML
SBMLDocument(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.SBMLDocument
SBMLDocumentSelectionTask - Class in idare.sbmlannotator.internal.Tasks
sbmlidcolsel - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
SBMLManagerHolder - Class in idare.imagenode.internal.Services.JSBML
SBMLManagerHolder(FileUtil, CySwingApplication, BundleContext) - Constructor for class idare.imagenode.internal.Services.JSBML.SBMLManagerHolder
SBMLToIDARE - Static variable in class idare.Properties.IDAREProperties
sbmltypecolsel - Variable in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
scaleFont(Dimension, Font, Graphics, String) - Static method in class idare.imagenode.Utilities.LayoutUtils: Scale a Font so that a given label fits into a specific dimension.
scaleSVGFont(Dimension, Font, String) - Static method in class idare.imagenode.Utilities.LayoutUtils: Scale a Font so that a given label fits into a specific dimension in an SVG context.
ScatterContainer - Class in idare.imagenode.internal.Data.MultiArray.ScatterData: Container Class for GraphData
ScatterContainer(DataSet, NodeData, int) - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainer
ScatterContainerLayout - Class in idare.imagenode.internal.Data.MultiArray.ScatterData: ContainerLayout Class for Graph Data, storing common information like the location fo axes, labels and frames.
ScatterContainerLayout(int) - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout: Default Constructor
ScatterContainerLayout.LabelAndPosition - Class in idare.imagenode.internal.Data.MultiArray.ScatterData: A Class that provides Label and position of the label
ScatterDataSetProperties - Class in idare.imagenode.internal.Data.MultiArray.ScatterData
ScatterDataSetProperties() - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
selectedLayoutAlgorithmName - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties: IDs for the individual types
separators - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
serialVersionUID - Static variable in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties
setActiveSheet(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setAddNodesTaskFactory(AddNodesToStyleTaskFactory) - Method in class idare.imagenode.internal.VisualStyle.StyleManager: set the AddNodesTaskFactory
setArrayFormula(String, CellRangeAddress) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setAsActiveCell() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setAutobreaks(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setAutoFilter(CellRangeAddress) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setBounds(int, int, int, int) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
setBounds(int, int, int, int) - Method in class idare.imagenode.Utilities.GUI.JSVGGlassCanvas
setBufferedImage(BufferedImage) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomImageLayer: Set the BufferedImage used
setCanUpdatePreferredSize(boolean) - Method in class idare.imagenode.internal.GUI.Legend.NodeSVGCanvas: define whether a preferresizeupdate is accepted
setCellComment(Comment) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellErrorValue(byte) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellFormula(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellStyle(CellStyle) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellType(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellValue(double) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellValue(Date) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellValue(Calendar) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellValue(RichTextString) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellValue(String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCellValue(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setCodingGenes(Set<Gene>, GPRManager) - Method in class idare.sbmlannotator.internal.gpr.Protein
setColorCount(int) - Method in interface idare.imagenode.ColorManagement.ColorScale: Set the number of colors used by this scale.
setColorCount(int) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale
setColorCount(int) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
setColorScale(ColorScale) - Method in class idare.imagenode.ColorManagement.ColorMap: Set a specific ColorScale to be used by this ColorMap.
setColorScale(ColorScale) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap
setColorScale(ColorScale) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.DiscreteColorMap
setColorScaleProperties(ColorScaleProperties) - Method in interface idare.imagenode.ColorManagement.ColorScale: Set the ColorScaleProperties used by this ColorScale This can e.g.
setColorScaleProperties(ColorScaleProperties) - Method in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
setColumnBreak(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setColumnGroupCollapsed(int, boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setColumnHidden(int, boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setColumnWidth(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setData(Vector<NodeValue>) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData: Set the Data of this ArrayNodeData.
setDataSetAdded() - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
setDatasetAdderFactory(DataSetAdderTaskFactory) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel: Set the DataSetAdderTaskFactory used by this Panel.
setDataSetManager(DataSetManager) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Set the DatasetManager used by this NodeManager.
setDataSetProperties() - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Set the properties of the DataSets according to the selected values.
setDefaultColumnStyle(int, CellStyle) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDefaultColumnWidth(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDefaultRowHeight(short) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDefaultRowHeightInPoints(float) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDefaultSize(double) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
SetDescription - Variable in class idare.imagenode.internal.GUI.DataSetAddition.DataSetGenerationParameters
setDisplayFormulas(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDisplayGridlines(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDisplayGuts(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDisplayName(String) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
setDisplayRowColHeadings(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setDisplaySize(Rectangle) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout: Set the size of the display.
setDisplayZeros(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setEntryData(Vector<Double>) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataValue: Set the Line Data for this NodeValue.
setFirstVisibleTab(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setFitRatio(float) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
setFitToPage(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setForceFormulaRecalculation(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setForceFormulaRecalculation(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setHeight(short) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
setHeight(int) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
setHeight(int) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Set the height of the graphics created by this factory
setHeightInPoints(float) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
setHidden(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setHorizontallyCenter(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setHyperlink(Hyperlink) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
setID(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
setID(int) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
setID(int) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Set the ID of this DataSet
setID(String) - Method in class idare.imagenode.Interfaces.DataSets.NodeData: Set the ID of this NodeData
setID(String) - Method in class idare.imagenode.internal.Layout.Manual.GUI.IDPanel
setIDARENames(CyNetwork, Collection<String>, String) - Static method in class idare.Properties.IDARESettingsManager: Set the matching IDARENames to the values set in the Selected Column(except that Strings will be used in the IDARE_NAME column
setIDCol(String) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationGUIHandlerFactory
setIdentifier(Long) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
setImageApp(IDAREImageNodeApp) - Method in class idare.internal.IDAREApp: Set the IDAREImageNodeApp object used in this app.
setLabel(String) - Method in class idare.imagenode.Interfaces.DataSets.NodeData: Set the Label of this NodeData
setLegendData(ImageNodeLayout, ImageNodeModel) - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend: Set the Legend Data using the given imagenode for data and the given layout for the node layout.
setLegendNode(String) - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend: Set the current Node (by its ID) to display a legend for
setLinkNodeVisualProperties(Collection<DelayedVizProp>, CyNode) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask
setLocation(int, int) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
setMargin(short, double) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setMaximumWidth(int) - Method in class idare.ThirdParty.BoundsPopupMenuListener: Set the maximum width for the popup.
setMissingCellPolicy(Row.MissingCellPolicy) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setName(String, String) - Method in class idare.sbmlannotator.internal.gpr.Gene
setName(String, String) - Method in class idare.sbmlannotator.internal.gpr.Protein
setNetwork(CyNetwork, IDARESettingsManager) - Method in class idare.subnetwork.internal.NetworkNode
SetNetworkData(CyNetwork, IDARESettingsManager, String, String, boolean, NodeManager) - Static method in class idare.Properties.IDARESettingsManager: Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types
setNodeFactory(CreateNodesTaskFactory) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel: Set the CreateNodesTaskFactory used by this Panel.
setNodeManager(NodeManager) - Method in class idare.imagenode.internal.ImageManagement.ActiveNodeManager
setNodeManager(NodeManager) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Set the NodeManager linked to this ImageStorage
setObject(Object) - Method in class idare.imagenode.internal.Services.JSBML.SBMLManagerHolder
setPopupAbove(boolean) - Method in class idare.ThirdParty.BoundsPopupMenuListener: Change the location of the popup relative to the combo box.
setPopupWider(boolean) - Method in class idare.ThirdParty.BoundsPopupMenuListener: Change the width of the popup to be the greater of the width of the combo box or the preferred width of the popup.
setPreferredSize(Dimension) - Method in class idare.imagenode.internal.GUI.Legend.NodeSVGCanvas
setPrintArea(int, String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setPrintArea(int, int, int, int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setPrintGridlines(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setProperties(Properties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet
setProperties(DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Set the DataSetLayoutProperties currently used for this dataset
setPropertyOptionsUnchecked(Collection<DataSetLayoutProperties>) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Sets the Options potentially available to this Dataset.
setRepeatingRowsAndColumns(int, int, int, int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setRightToLeft(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setRowBreak(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setRowGroupCollapsed(int, boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setRowNum(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
setRowStyle(CellStyle) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
setRowSumsBelow(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setRowSumsRight(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setScrollBarRequired(boolean) - Method in class idare.ThirdParty.BoundsPopupMenuListener: For some reason the default implementation of the popup removes the horizontal scrollBar from the popup scroll pane which can result in the truncation of the rendered items in the popop.
setSelected(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setSelectedTab(int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setSheetHidden(int, boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setSheetHidden(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setSheetName(int, String) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setSheetOrder(String, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
setSize(int, int) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
setStatusMessage(String) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: This function allows setting the Status Message if an exception is thrown during reading.
setSubNetworkType(String, String) - Method in class idare.Properties.IDARESettingsManager: Set the IDAREType associated with a specific Target Type for subnetwork generation.
setSubsysManager(SubnetworkSessionManager) - Method in class idare.internal.IDAREApp: Set the SubnetworkSessionManager used in this app.
setTargetNetworkView(CyNetworkView) - Method in class idare.subnetwork.internal.NodeViewLink: Set the target CyNetworkView for the node of this Link.
setTargetNodeView(View<CyNode>) - Method in class idare.subnetwork.internal.NodeViewLink: Set the target View for the node of this Link.
setTwoColumnHeaders(boolean) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
setTwoColumnHeaders(boolean) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Define what type of headers are being used.
setType(String, String) - Method in class idare.Properties.IDAREProperties
setType(String, String) - Method in class idare.Properties.IDARESettingsManager: Set the IDAREType associated with a specific Target Type.
setUIHelper(TunableUIHelper) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTask
setUIHelper(TunableUIHelper) - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupTask
setUIHelper(TunableUIHelper) - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
setUIHelper(TunableUIHelper) - Method in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnPropertiesSelectionTask
setUIHelper(TunableUIHelper) - Method in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask
setup() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Setup this Color Map.
setup() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap
setupItemDescription(NodeData, String, JScrollPane) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription: Set up the Itemdescription for a specific set of data and a given DatasetLabel.
setupItemDescription(DataSet, ColorMap) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDescription: Set up the data description using a specific ColorMap to obtain the line colors and the respective DataSet to obtain the Line names.
setupItemDescription(NodeData, String, JScrollPane) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.HeaderDescription: Set up the Description for a specific set of data and a given DataSetLabel.
setupLayout(NodeData, Rectangle, String, DataSetLayoutProperties) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout
setupLayout(NodeData, Rectangle, String, DataSetLayoutProperties) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainerLayout
setupLayout(NodeData, Rectangle, String, DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.Layout.ContainerLayout: Setup the layout specific positions and data.
setupLayout(NodeData, Rectangle, String, DataSetLayoutProperties) - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
setupLayout(NodeData, Rectangle, String, DataSetLayoutProperties) - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
setupLayout(NodeData, Rectangle, String, DataSetLayoutProperties) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
setupLayout(List<DataSetLayoutInfoBundle>, List<LayoutComparator>) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout: The assumption is, that the order in the given Vector is the expected order!
setupNetwork() - Method in class idare.imagenode.internal.GUI.NetworkSetup.NetworkSetupTunableGUI: Setup the Network (using the default methodology from the Visualstyle
SetupNetwork(CyNetwork, IDARESettingsManager, String, String) - Static method in class idare.Properties.IDARESettingsManager: Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types
setupNetworkForSubNetworkCreation(CyNetwork, IDARESettingsManager, String) - Static method in class idare.subnetwork.internal.SubNetworkUtils: Set up the Network for SubNetwork Generation, i.e.
setupNetworkReferences(CyNetworkManager) - Method in class idare.subnetwork.internal.NetworkNode
setupPropertyOptions() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Set up the property options for this DataSet.
setupSBMLObjectIDs() - Method in class idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask
setupVisualStyle() - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle: Setup the visual Style
setupWorkBook(IDAREWorkbook) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Set up the data properties from the provided workbook and read the data into this dataset.
setValue(String) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARECell: Set the value (this is unchecked wrt the type defined).
setVerticallyCenter(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
setVisibleWidth(int) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDescription
setVisibleWidth(int) - Method in interface idare.imagenode.GUI.Legend.Utilities.SizeAdaptableComponent: Adapt the width of the component to the provided visible width.
setVisualStyle(IDAREVisualStyle) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: set the IDAREVisualStyle linked to this ImageStorage
setWidth(int) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
setWidth(int) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Set the width of the graphics created by this factory
setWorkbook(IDAREWorkbook) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetReadingInfo
setZeroHeight(boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
setZoom(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
shape - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.ShapePosition
ShapePosition(Shape, Rectangle2D) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.ShapePosition: A Basic constructor using a shape and a Rectangle as position.
SheetNames - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
shiftRows(int, int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
shiftRows(int, int, int, boolean, boolean) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
showInPane(short, short) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
shutdown() - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle: Remove the Visualstyle from Cytoscape.
shutDown() - Method in class idare.imagenode.internal.VisualStyle.StyleManager: Restore the stored values to all styles.
shutDown() - Method in class idare.internal.CyActivator
SimpleLink - Class in idare.imagenode.internal.Layout: A Simple Holder class for a Dataset.
SimpleLink(DataSet, int) - Constructor for class idare.imagenode.internal.Layout.SimpleLink
SizeAdaptableComponent - Interface in idare.imagenode.GUI.Legend.Utilities: This interface defines classes which allow to adjust their height when a given width is set.
skipLabels(Iterator<IDARECell>) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Skip the Cells containing the labels from a cell iterator
SmallScatterProperties - Class in idare.imagenode.internal.Data.MultiArray.ScatterData
SmallScatterProperties() - Constructor for class idare.imagenode.internal.Data.MultiArray.ScatterData.SmallScatterProperties
Species - Class in idare.imagenode.internal.Services.JSBML
Species(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.Species
start(BundleContext) - Method in class idare.internal.CyActivator
stringheaders - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Indicator whether String headers are used
StringUtils - Class in idare.imagenode.Utilities
StringUtils() - Constructor for class idare.imagenode.Utilities.StringUtils
STYLE_MAPPINGS_SAVE_FILE - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES: IDs for style management during save and load
STYLE_MAPPINGS_SAVE_NAME - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
StyleManager - Class in idare.imagenode.internal.VisualStyle: The StyleManager handles the availability of Images in a given Style.
StyleManager(ImageStorage, VisualMappingManager, CyNetworkViewManager, CyEventHelper, NodeManager, CyApplicationManager, ActiveNodeManager) - Constructor for class idare.imagenode.internal.VisualStyle.StyleManager: Default Constructor.
styleUsed(String) - Method in class idare.imagenode.internal.VisualStyle.StyleManager: Test whether a given Style uses IDARE Image Nodes.
SubnetworkColumnProperties - Class in idare.subnetwork.internal.Tasks.propertySelection
SubnetworkColumnProperties() - Constructor for class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnProperties
SubnetworkColumnPropertiesSelectionTask - Class in idare.subnetwork.internal.Tasks.propertySelection: A Task that sets up the network according to user selected columns and identifiers and calls the subnetworkpropertyselection after successful completion
SubnetworkColumnPropertiesSelectionTask(CyServiceRegistrar, NetworkViewSwitcher, IDARESettingsManager, SubnetworkCreationGUIHandlerFactory) - Constructor for class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnPropertiesSelectionTask
SubnetworkCreationGUIHandler - Class in idare.subnetwork.internal.Tasks.SubsystemGeneration
SubnetworkCreationGUIHandler(Method, Method, Object, Tunable, NetworkViewSwitcher, CyNetwork, CyNetworkView, HashMap<String, CyLayoutAlgorithm>, String) - Constructor for class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationGUIHandler
SubnetworkCreationGUIHandler(Field, Object, Tunable, NetworkViewSwitcher, CyNetwork, CyNetworkView, HashMap<String, CyLayoutAlgorithm>, String) - Constructor for class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationGUIHandler
SubnetworkCreationGUIHandlerFactory - Class in idare.subnetwork.internal.Tasks.SubsystemGeneration
SubnetworkCreationGUIHandlerFactory(NetworkViewSwitcher, CyApplicationManager, CyLayoutAlgorithmManager) - Constructor for class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationGUIHandlerFactory
SubnetworkCreationTask - Class in idare.subnetwork.internal.Tasks.SubsystemGeneration: A Task creating Subnetworks for a Network.
SubnetworkCreationTask(CyServiceRegistrar, NetworkViewSwitcher, IDARESettingsManager) - Constructor for class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask: Default constructor
SubnetworkCreatorTaskFactory - Class in idare.subnetwork.internal.Tasks.SubsystemGeneration: Task Factory for Subnetwork Creation
SubnetworkCreatorTaskFactory(CyServiceRegistrar, NetworkViewSwitcher, IDARESettingsManager, SubnetworkCreationGUIHandlerFactory) - Constructor for class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreatorTaskFactory
SubnetworkInteractionAndCompoundChooser - Class in idare.subnetwork.internal.GUI
SubnetworkInteractionAndCompoundChooser(CyNetwork, Vector<String>) - Constructor for class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Default Constructor using the available columnNames
subnetworkNameSeparator - Static variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubnetworkCreationTask
SubNetworkProperties - Class in idare.subnetwork.internal.Tasks.SubsystemGeneration
SubNetworkProperties() - Constructor for class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
SubnetworkPropertiesSelectionGUI - Class in idare.subnetwork.internal.GUI: A GUI for the selection of the properties for SubNetwork Generation.
SubnetworkPropertiesSelectionGUI(Collection<String>, Vector<String>, CyNetwork, NetworkViewSwitcher, String) - Constructor for class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI: Generate the GUI for selection of Subnetwork generation properties
SubnetworkPropertyColumnChooser - Class in idare.subnetwork.internal.GUI
SubnetworkPropertyColumnChooser(Vector<String>, CyNetwork) - Constructor for class idare.subnetwork.internal.GUI.SubnetworkPropertyColumnChooser: A Constructor requiring the column names to select the columns for the different properties from, In addition, the current network is needed, along with the cySwingApp (for hierarchy reference), the IDARESettingsManager for idare specific settings, and a nodemanager to be informed of the updated nodes.
SubnetworkPropertyColumnGUIHandler - Class in idare.subnetwork.internal.Tasks.propertySelection
SubnetworkPropertyColumnGUIHandler(Method, Method, Object, Tunable, CyNetwork) - Constructor for class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkPropertyColumnGUIHandler
SubnetworkPropertyColumnGUIHandler(Field, Object, Tunable, CyNetwork) - Constructor for class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkPropertyColumnGUIHandler
SubnetworkPropertyColumnGUIHandlerFactory - Class in idare.subnetwork.internal.Tasks.propertySelection
SubnetworkPropertyColumnGUIHandlerFactory(CyApplicationManager) - Constructor for class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkPropertyColumnGUIHandlerFactory
SubnetworkSessionManager - Class in idare.subnetwork.internal: A SessionListener that restores the SubNetwork Interaction Links from a former Session.
SubnetworkSessionManager(NetworkViewSwitcher, IDARESettingsManager) - Constructor for class idare.subnetwork.internal.SubnetworkSessionManager
SubNetworkUtils - Class in idare.subnetwork.internal
SubNetworkUtils() - Constructor for class idare.subnetwork.internal.SubNetworkUtils
subSystems - Variable in class idare.subnetwork.internal.Tasks.SubsystemGeneration.SubNetworkProperties
SUBSYSTEMS_SAVE_FILE - Static variable in class idare.Properties.IDAREProperties: IDARE SubSystems Save File
SUBSYSTEMS_SAVE_ID - Static variable in class idare.Properties.IDAREProperties
SubSystemsToGenerate() - Method in class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI: Get the selected SubSystems from the SubSystemSelector
supportsMime(String) - Method in class idare.imagenode.internal.ImageManagement.ImageStorage
swingApp - Variable in class idare.imagenode.internal.Services.JSBML.SBMLManagerHolder

T

taskFinished(ObservableTask) - Method in class idare.imagenode.internal.GUI.DataSetAddition.Tasks.DataSetAdderTask
testAll(CyNetworkView, Iterable<DelayedVizProp>) - Static method in class idare.ThirdParty.DelayedVizProp: Test whether the DelayedVizProps got properly applied.
testValidity(DataSet) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayDataSetProperties
testValidity(DataSet) - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Test, whether the provided DataSet is valid to be used with these properties.
testValidity(DataSet) - Method in class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties
testValidity(DataSet) - Method in class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties
testValidity(DataSet) - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
testValidity(DataSet) - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
testValidity(DataSet) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
TextPaneEditorKit - Class in idare.ThirdParty: Source obtained from http://java-sl.com/tip_center_vertically.html
TextPaneEditorKit() - Constructor for class idare.ThirdParty.TextPaneEditorKit
TextPaneResizer - Class in idare.imagenode.GUI.Legend.Utilities: A Listener that adapts a JTextPane according to the Scrollpane enclosing the pane.
TextPaneResizer(JTextPane, int, int) - Constructor for class idare.imagenode.GUI.Legend.Utilities.TextPaneResizer: Default constructor with a provided minimal width, an offset to adjust the width coming in and the Pane to resize.
TextPaneResizer(JTextPane) - Constructor for class idare.imagenode.GUI.Legend.Utilities.TextPaneResizer: Default parameters will be used for the given pane (300 width, 2 offset)
TimeSeriesDataSetProperties - Class in idare.imagenode.internal.Data.Array.TimeSeriesData: Properties for a Time Series DataSet
TimeSeriesDataSetProperties() - Constructor for class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties
Title - Static variable in class idare.subnetwork.internal.NetworkViewSwitcher
TooManyItemsException - Exception in idare.imagenode.exceptions.layout: Exception indicating that a container was too large and could not be placed.
TooManyItemsException(String) - Constructor for exception idare.imagenode.exceptions.layout.TooManyItemsException
toSerializableString() - Method in class idare.imagenode.internal.ImageManagement.IDARECustomGraphics
toString() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: The String representation of a DataSet is its description.
toString() - Method in class idare.imagenode.Interfaces.DataSets.NodeValue
toString() - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Override the ToString Method
toString() - Method in class idare.imagenode.internal.Data.Array.CircleData.CircleDataSetProperties
toString() - Method in class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties
toString() - Method in class idare.imagenode.internal.Data.Array.RectangleData.RectangleDataSetProperties
toString() - Method in class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties
toString() - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties
toString() - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties
toString() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.LargeScatterProperties
toString() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties
toString() - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.SmallScatterProperties
toString() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVCell
toString() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVRow
toString() - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
toString() - Method in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties
toString() - Method in class idare.sbmlannotator.internal.gpr.Gene
toString() - Method in class idare.sbmlannotator.internal.gpr.GPRAssociation
toString() - Method in class idare.sbmlannotator.internal.gpr.Protein
Trace(Object) - Static method in class idare.imagenode.internal.Debug.PrintFDebugger
TransferGraphicsToDocument(SVGDocument, Dimension, SVGGraphics2D) - Static method in class idare.imagenode.Utilities.LayoutUtils: Transfer data that was writen to an SVGGraphics2D context to a document using a specified canvasdimension.
transform(AffineTransform) - Method in class idare.imagenode.internal.ImageManagement.IDARECustomImageLayer
TSVReader - Class in idare.imagenode.internal.DataSetReaders.CSVReader: A Tab separated File reader is the same as a comma separated file reader, except that it also accepts tsv files and uses Tab instead of commas as separator
TSVReader() - Constructor for class idare.imagenode.internal.DataSetReaders.CSVReader.TSVReader
TunableDataSetAdderGUI - Class in idare.imagenode.internal.GUI.DataSetAddition: A GUI Component which allows the Addition of Datasets.
TunableDataSetAdderGUI(DataSetManager, FileUtil, CySwingApplication) - Constructor for class idare.imagenode.internal.GUI.DataSetAddition.TunableDataSetAdderGUI
type - Variable in class idare.imagenode.Interfaces.DataSets.NodeValue
TypeCol - Variable in class idare.imagenode.internal.GUI.NetworkSetup.NetworkSetupTunableGUI
TypeCol - Variable in class idare.subnetwork.internal.GUI.SubnetworkPropertyColumnChooser
TypeCol - Variable in class idare.subnetwork.internal.Tasks.propertySelection.SubnetworkColumnProperties: The column name of the column containing the Type
TypeColID - Variable in class idare.imagenode.internal.GUI.NetworkSetup.Tasks.NetworkSetupProperties: IDs of the columns to use for names and types

U

undo() - Method in class idare.NodeDuplicator.Internal.NodeDuplicatorImpl
undo() - Method in class idare.NodeDuplicator.Internal.NodeMergerImpl
ungroupColumn(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
ungroupRow(int, int) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVSheet
unregisterAll() - Method in class idare.imagenode.internal.IDAREImageNodeApp: Unregister all Types of DataSet, that were before registered.
update(DataSet, boolean) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Update the Manager/Nodes with the new DataSet, either adding it or removing it form the nodes.
updateActiveNodes(Collection<String>) - Method in class idare.imagenode.internal.DataManagement.NodeManager
updateChoosers(int) - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Update the Choose ComboBoxes according to a selected Column.
updateChoosers(int) - Method in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Update the Choose ComboBoxes according to a selected Column.
updateChoosersWithFourOptions() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Update the Panel with four choosers.
updateChoosersWithThreeOptions() - Method in class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser: Update the Panel with four choosers.
updateChoosersWithTwoOptions() - Method in class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser: Update the Panel with two choosers.
updateColors(ColorMap) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
updateColorScalePane(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ColorToolBarEntry
updateDataSetLabel(String) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
updateDataSetOptions(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetLayoutToolBar
updateDataSetProperties(DataSet) - Method in class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel: Update the dataset Properties
updateGenedbs(Gene, HashMap<String, String>) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
updateID(String) - Method in class idare.imagenode.internal.Layout.Manual.LayoutGUI
updateLabel(String) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout
updateLabel(String) - Method in class idare.imagenode.Interfaces.Layout.ContainerLayout: Update the Label used in this Layout.
updateLabel(String) - Method in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
updateLabel(String) - Method in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
updateLabel(String) - Method in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
updateLayoutToCurrentPosition() - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
updateLegend(String) - Method in class idare.imagenode.internal.GUI.Legend.LegendUpdater
updateLegendData() - Method in class idare.imagenode.internal.GUI.Legend.IDARELegend: Update the legend Data.
updateNetworkNodes() - Method in interface idare.imagenode.IDARENodeManager: Update the set of NetworkNode IDs.
updateNetworkNodes() - Method in class idare.imagenode.internal.DataManagement.NodeManager
updateNode(String) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
updateNode(String) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
updatePosition() - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
updatePosition(DataSetLayoutInfoBundle, Rectangle) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout: Update the position of a Dataset in the layoutbundle.
updatePreferredSize(int) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryDescriptionPane: Update the preferredsize of this Line according to a provided width.
updateProperties(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater: Inform the layout that properties have changed.
updateProperties(DataSetLayoutProperties) - Method in class idare.imagenode.internal.Layout.Manual.GUI.ManualLayoutUpdater
updateProperties(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout: Update the properties of the bundle
updatePropertyPane(DataSetLayoutInfoBundle) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetPropertyToolBarEntry
updateProteindbs(Protein, HashMap<String, String>) - Method in class idare.sbmlannotator.internal.gpr.GPRManager
updateRelevantViews() - Method in class idare.imagenode.internal.VisualStyle.IDAREVisualStyle: Update all views, that are associated with the IDARE visualstyle
updateServices(IDAREPlugin, Vector<IDAREService>, boolean, TaskMonitor) - Method in class idare.imagenode.internal.IDAREImageNodeApp
updateStyle() - Method in class idare.imagenode.internal.ImageManagement.ImageStorage: Update all views using the visualstyle set for this Storage
updateVisualCounts() - Method in class idare.imagenode.internal.ImageManagement.ActiveNodeManager: This function will update ALL visual counts, completely dropping the current visualCounts.
updateVisualisationColors(ColorMap) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
updateVisualisationType(DataSetLayoutProperties) - Method in class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame
usedColors - Variable in class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale
useTwoColHeaders - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: An Indicator whether this dataset uses one or two columns to provide label/ID
useTwoColumns - Variable in class idare.imagenode.internal.GUI.DataSetAddition.DataSetGenerationParameters

V

value - Variable in class idare.imagenode.Interfaces.DataSets.NodeValue
valueOf(String) - Static method in enum idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell.CellType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum idare.imagenode.internal.Layout.Automatic.ImageBag.BAGPOSITON: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum idare.imagenode.internal.Services.JSBML.CVTerm.Qualifier: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum idare.imagenode.Properties.IMAGENODEPROPERTIES.LayoutStyle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum idare.imagenode.Properties.Localisation.Position: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum idare.imagenode.Properties.NodeValueType: Returns the enum constant of this type with the specified name.
values() - Static method in enum idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell.CellType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum idare.imagenode.internal.Layout.Automatic.ImageBag.BAGPOSITON: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum idare.imagenode.internal.Services.JSBML.CVTerm.Qualifier: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum idare.imagenode.Properties.IMAGENODEPROPERTIES.LayoutStyle: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum idare.imagenode.Properties.Localisation.Position: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum idare.imagenode.Properties.NodeValueType: Returns an array containing the constants of this enum type, in the order they are declared.
Valueset - Variable in class idare.imagenode.Interfaces.DataSets.DataSet
VGAP - Static variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
viewUsesStyleWithNodes(CyNetworkView) - Method in class idare.imagenode.internal.VisualStyle.StyleManager: Test whether a given NetworkView uses a Style containing ImageNodes.

W

wasAdded() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetChangedEvent: Obtain information whether the set is being added.
wasAdded() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetsChangedEvent: Obtain information whether the set is being added.
wasChanged() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetChangedEvent: Obtain information whether the set was changed
wasChanged() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetsChangedEvent: Obtain information whether the set is being changed.
wasRemoved() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetChangedEvent: Obtain information whether the provided set was removed
wasRemoved() - Method in class idare.imagenode.internal.DataManagement.Events.DataSetsChangedEvent: Obtain information whether the set is being removed.
WhiteBlack - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale ranging White to black
WhiteBlack() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.WhiteBlack
WhiteBlue - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale ranging white to blue
WhiteBlue() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.WhiteBlue
WhiteRed - Class in idare.imagenode.internal.ColorManagement.ColorScales
WhiteRed() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.WhiteRed
write(OutputStream) - Method in class idare.imagenode.internal.DataSetReaders.CSVReader.CSVWorkbook
writeDataSet() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Essentially a toString function to write this dataset.
writeImage(BufferedImage, TranscoderOutput) - Method in class idare.ThirdParty.BufferedImageTranscoder
writeLayout(ObjectOutputStream) - Method in class idare.imagenode.internal.Layout.Automatic.AutomaticNodeLayout
writeLayout(ObjectOutputStream) - Method in interface idare.imagenode.internal.Layout.ImageNodeLayout: Write all data that is relevant to restore this nodelayout to a ObjectOutputStream
writeLayout(ImageNodeLayout, ObjectOutputStream) - Method in class idare.imagenode.internal.Layout.io.LayoutIOManager
writeLayout(ObjectOutputStream) - Method in class idare.imagenode.internal.Layout.Manual.ManualLayout
writeLayout(ObjectOutputStream) - Method in class idare.imagenode.internal.Layout.Manual.ManualNodeLayout
writeNodeLayouts(File, IDAREImageNodeApp) - Method in class idare.imagenode.internal.DataManagement.NodeManager: Write a structure that can be read again by a nodemanager to restore the current state of the manager.
WrongDatasetTypeException - Exception in idare.imagenode.exceptions.layout
WrongDatasetTypeException(String) - Constructor for exception idare.imagenode.exceptions.layout.WrongDatasetTypeException
WrongFormat - Exception in idare.imagenode.exceptions.io: Exception indicating that there was an error in the format of the file used.
WrongFormat(String) - Constructor for exception idare.imagenode.exceptions.io.WrongFormat

X

XLabels - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
XMaxval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
xmaxval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
XMaxval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
xmaxval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
xmaxval - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
XMinval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
xminval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
XMinval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
xminval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
xminval - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
XMLNode - Class in idare.imagenode.internal.Services.JSBML
XMLNode(Object) - Constructor for class idare.imagenode.internal.Services.JSBML.XMLNode
xrange - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
xrange - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
xrange - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout

Y

YellowGreen - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale ranging yellow to green
YellowGreen() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.YellowGreen
YellowRed - Class in idare.imagenode.internal.ColorManagement.ColorScales: A MultiColorScale ranging yellow to red
YellowRed() - Constructor for class idare.imagenode.internal.ColorManagement.ColorScales.YellowRed
YMaxval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
ymaxval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
YMaxval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
ymaxval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
YMaxval - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
ymaxval - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
YMinval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
yminval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
YMinval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
yminval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
YMinval - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
yminval - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
yrange - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
yrange - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
yrange - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout
YZeroval - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
YZeroval - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
YZeroval - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout

Z

ZeroLine - Variable in class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout
ZeroLine - Variable in class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout
ZeroLine - Variable in class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout

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