Index (IDARE 2.0 API)

A B C D E F G H I J L M N O P R S T U V W
All Classes All Packages

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
addData(MultiArrayDataValue, String) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData: Add a new MultiArrayDataValue to this NodeData, for a specific SetID
addIDs(Collection<Long>) - Method in class idare.Properties.IDARESettingsManager: Add all IDs of the collection to this manager.
addLayoutComponent(String, Component) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
addPropertyOption(DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Add Property options to this Dataset, and indicate whether the addition was successful.
allHeaders - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
applyAll(CyNetworkView, Iterable<DelayedVizProp>) - Static method in class idare.ThirdParty.DelayedVizProp: Assign the visual properties stored in delayedProps to the given CyNetworkView.
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(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
ArrayDataSet(String) - Constructor for class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Basic constructor using a specific DataSetName
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

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
BLANK - idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell.CellType
BLUEWHITERED - Static variable in class idare.imagenode.ColorManagement.ColorScaleFactory
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(boolean, boolean, int, boolean) - Constructor for class idare.ThirdParty.BoundsPopupMenuListener: General purpose constructor to set all popup properties at once.
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
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.

C

cancel() - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREReaderSetupTask
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.
CENTER - idare.imagenode.Properties.IMAGENODEPROPERTIES.LayoutStyle
CENTER - idare.imagenode.Properties.Localisation.Position
changeItemCount(int) - Method in class idare.imagenode.Utilities.ColorScalePopupAdjuster: Change the number of items that are being adjusted by this adjuster
clearTemporaryFolder() - Static method in class idare.imagenode.Utilities.IOUtils: Clear the Temporary folder.
CobraUtil - Class in idare.ThirdParty: Contains some useful methods to manipulate 'COBRA SBML'
CobraUtil() - Constructor for class idare.ThirdParty.CobraUtil
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
colormaps - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
colormaps - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet
ColorPane - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
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.
ColorUtils - Class in idare.imagenode.ColorManagement: Color Utils provide some static convenience functions for Colors
ColorUtils() - Constructor for class idare.imagenode.ColorManagement.ColorUtils
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
compareTo(NodeValue) - Method in class idare.imagenode.Interfaces.DataSets.NodeValue
ComponentLayout - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
componentResized(ComponentEvent) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionResizeListener
componentResized(ComponentEvent) - Method in class idare.imagenode.GUI.Legend.Utilities.TextPaneResizer
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
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.
createCell() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Create a Blank Cell at the end of this row.
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) - 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(IDARECell.CellType, int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Create a Cell of the specified type at the specified position.
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.
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.
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
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.
createSVGDoc() - Static method in class idare.imagenode.Utilities.LayoutUtils: Create an SVG Document using a default DOM implementation.
createTemporaryFolder() - Static method in class idare.imagenode.Utilities.IOUtils: Create the Temporary folder (if it does not exist).
cs - Variable in class idare.imagenode.ColorManagement.ColorMap
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
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.MultiArrayData.MultiArrayContainer: The NodeData this container is associated with
Data - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
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_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
DATASETCOLLECTION_FILE_NAME - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
DATASETCOLORSCALE - Static variable in class idare.imagenode.Interfaces.DataSets.DataSet
DATASETDESCRIPTION - Static variable in class idare.imagenode.Interfaces.DataSets.DataSet
dataSetID - Variable in class idare.imagenode.Interfaces.DataSets.DataSet
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
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.
DataSetType - Static variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
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
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.
deRegisterPlugin(IDAREPlugin) - Method in class idare.imagenode.IDAREImageNodeAppService: Deregister a plugin from the IDARE App;
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
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.
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.
draw(SVGGraphics2D) - Method in class idare.imagenode.Utilities.LegendLabel: Draw the Label in the given SVGGraphics2D context
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, String) - Method in class idare.imagenode.Utilities.LegendLabel: Draw the Label in the given SVGGraphics2D context
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

E

EDGE - idare.imagenode.Properties.IMAGENODEPROPERTIES.LayoutStyle
EDGE - idare.imagenode.Properties.Localisation.Position
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.
execute(TaskMonitor) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREReaderSetupTask: Execute the Task.

F

fileTypeAccepted(File) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: Test, whether the file can potentially be read by this reader.
Flexible - Variable in class idare.imagenode.Properties.Localisation
FORMULA - idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell.CellType
FREE - idare.imagenode.Properties.Localisation.Position

G

getBufferedImage() - Method in class idare.ThirdParty.BufferedImageTranscoder
getCell(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 class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
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.
getCellIndex(BasicIDARECell) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow: Get the position/index of a given Cell
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
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
getColor(double) - Method in interface idare.imagenode.ColorManagement.ColorScale: get a color
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
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
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
getColorScaleProperties() - Method in interface idare.imagenode.ColorManagement.ColorScale: Get the Properties of this ColorScale.
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.
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.
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.
getData() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainer
getData() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainer
getData() - Method in interface idare.imagenode.Interfaces.DataSets.DataContainer: Get the NodeData associated with this Container
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(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.
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.
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.Data.BasicDataTypes.ArrayData.AbstractArrayDataSetProperties
getDataSetDescriptionPane(JScrollPane, String, ColorMap, DataSet) - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Plot the Legend for this Dataset.
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
getDefaultColor() - Method in class idare.imagenode.ColorManagement.ColorMap
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
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
getDiscreetColorScales(int) - Static method in class idare.imagenode.ColorManagement.ColorScaleFactory: Get a set of discreet ColorScales.
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
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).
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.
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.
getImage(int, int) - Method in class idare.imagenode.ColorManagement.ColorScalePane: Get an image that represents this ColorScalePane, with the given width and height
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.
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.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.
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.!
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
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
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.
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.
getMaximumWidth() - Method in class idare.ThirdParty.BoundsPopupMenuListener: Return the maximum width of the popup.
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.
getNetworkIDAREIDs(CyNetwork, String) - Static method in class idare.Properties.IDARESettingsManager: Get the set of nodeIDs present in the provided network
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.
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.
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.
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.
getNonWhiteDiscreteColorScales(int) - Static method in class idare.imagenode.ColorManagement.ColorScaleFactory
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
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.
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.
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
getPropertyOptions() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the selection of different properties available for this dataset
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
getRowIndex(BasicIDARERow) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet: Get the index of a given Row
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;
getRowsAndCols(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription: Get the rows and columns for this panel based on the available width.
getScrollBarWidth(BasicComboPopup, JScrollPane) - Method in class idare.ThirdParty.BoundsPopupMenuListener
getScrollPane(BasicComboPopup) - Method in class idare.ThirdParty.BoundsPopupMenuListener
getServices() - Method in interface idare.imagenode.Interfaces.Plugin.IDAREPlugin: Provide all instances of IDAREInterfaces this plugin shall provide to the app.
getSetNames() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Get the names of the Sheets represented in this DataSet
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.
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.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout: Get the Shape to be used for individual items in the specified area.
getShapePosition(Shape, Rectangle2D) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout: Generate a AbstractArrayContainerLayout.ShapePosition from a Rectangle and a given Shape.
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
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-
getSheetIndex(IDARESheet) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
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.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
getSheetName() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet
getSheetName() - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARESheet: Get the Name of this Sheet.
getSheetName(int) - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDAREWorkbook
getSheetName(int) - Method in interface idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDAREWorkbook: Get the name of the sheet at the provided position
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.
getSubNetworkType(String) - Method in class idare.Properties.IDARESettingsManager: Get the IDAREType associated with a specific Target Type for the subnetwork generation.
getSVGFontMetrics(Font) - Static method in class idare.imagenode.Utilities.LayoutUtils
getTemporaryFile(String, String) - Static method in class idare.imagenode.Utilities.IOUtils: Get a Temporary file with a given Filename and a given Extension.
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.
getTypeName() - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Get the type of DataSet (this can be used for display purposes
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.
getViewFactory() - Method in class idare.ThirdParty.TextPaneEditorKit
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.
getYAxisLimits() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Get the limits (minimum and maximum value) if this is a numeric dataset.
GUIUtils - Class in idare.imagenode.Utilities: Class proviing static utilitits for multiple GUI classes.
GUIUtils() - Constructor for class idare.imagenode.Utilities.GUIUtils

H

handleSessionLoadedEvent(SessionLoadedEvent) - Method in class idare.Properties.IDARESettingsManager: Handle the loading of a session
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.
hasNext() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARECellIterator
hasNext() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARERowIterator
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

I

id - Variable in class idare.imagenode.Interfaces.DataSets.NodeData
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_SUBNETWORK_TYPE - Static variable in class idare.Properties.IDAREProperties
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.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.Properties - package idare.Properties: This package contains Properties and Static Variables used in multiple parts of the IDARE App.
idare.ThirdParty - package idare.ThirdParty: This package contains Classes and Code obtained from third party sites.
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
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
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.
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.
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.
IDAREWorkbook - Interface in idare.imagenode.Interfaces.DataSetReaders.WorkBook: An IDAREWorkbook contains one or multiple sets of data in individual IDARESheets
IDFont - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
IMAGEHEIGHT - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
IMAGENODE_TEMP_FOLDER - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
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
IMAGEWIDTH - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
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
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
isColumnSet(int) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet: Check whether a specific column is set or empty.
isdiscreet - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: An Indicator whether this is a discreet data set (i.e.
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.
isFlexibility() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Return the flexibility of this dataset for layout purposes.
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.
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
isScrollBarRequired() - Method in class idare.ThirdParty.BoundsPopupMenuListener: Determine if the horizontal scroll bar might be required for the popup
isSetupNetwork(CyNetwork) - Static method in class idare.Properties.IDARESettingsManager: Test whether a Network has the table Columns required for usage in IDARE
isstring - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: An Indicator whether the dataset uses numeric representation
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.Utilities.GUI.JSVGGlassCanvas
iterator() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARERow
iterator() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.BasicIDARESheet

J

JSVGGlassCanvas - Class in idare.imagenode.Utilities.GUI
JSVGGlassCanvas(Container) - Constructor for class idare.imagenode.Utilities.GUI.JSVGGlassCanvas

L

label - Variable in class idare.imagenode.Interfaces.DataSets.NodeData
Label - Variable in class idare.imagenode.Utilities.LegendLabel
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
LAYOUT_FILE_NAME - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
LAYOUT_FILES - Static variable in class idare.imagenode.Properties.IMAGENODEPROPERTIES
layoutarea - Variable in class idare.imagenode.Interfaces.Layout.ContainerLayout
layoutContainer(Container) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
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
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
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.
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
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

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
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
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.
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
movePointOnScale(float, float) - Method in interface idare.imagenode.ColorManagement.ColorScale: Move a point in the 0-1 scale to the target value.
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

N

newContainerInstance(DataSet, NodeData) - Method in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties: Create a new Container for a specific DataSet and a given NodeData.
next() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARECellIterator
next() - Method in class idare.imagenode.Interfaces.DataSetReaders.WorkBook.BasicImplementation.IDARERowIterator
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.
NodeLabels - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet
NodeType() - Constructor for class idare.Properties.IDAREProperties.NodeType
NodeValue - Class in idare.imagenode.Interfaces.DataSets: A NodeValue represents the Value at a specific node.
NodeValue(boolean) - Constructor for class idare.imagenode.Interfaces.DataSets.NodeValue: Create a NodeValue indicating whether it is a numeric or non numeric value.
NodeValue(Double) - Constructor for class idare.imagenode.Interfaces.DataSets.NodeValue: Create a NodeValue using a Double 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.
numeric - idare.imagenode.Properties.NodeValueType
NUMERIC - idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell.CellType
numericheaders - Variable in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet: Indicator whether numeric headers are used
numericstrings - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: an indicator whether the dataset uses numeric data represented by strings

O

oddrange - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
oldsize - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
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

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.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.
parent - Variable in class idare.imagenode.Interfaces.DataSets.NodeData
parseCobraNotes(SBase) - Static method in class idare.ThirdParty.CobraUtil: Parses the notes of the given SBase element.
plotShape(Shape, Graphics2D) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryPanel: Plot the shape.
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
preferredLayoutSize(Container) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
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.
printSheetsContained() - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData
PRODUCT_EDGE - Static variable in class idare.Properties.IDAREProperties.EdgeType
propertyOptions - Variable in class idare.imagenode.Interfaces.DataSets.DataSet
PROPERTYOPTIONSAVAILABLE - Static variable in class idare.imagenode.Interfaces.DataSets.DataSet

R

range - Variable in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap
REACTANT_EDGE - Static variable in class idare.Properties.IDAREProperties.EdgeType
REACTION_REVERSIBLE - Static variable in class idare.Properties.IDAREProperties.EdgeType
readData(File) - Method in class idare.imagenode.Interfaces.DataSetReaders.IDAREDatasetReader: Read an input File and create an IDARE compatible Workbook structure.
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.
redraw() - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription: Redraw this panel.
registerPlugin(IDAREPlugin) - Method in class idare.imagenode.IDAREImageNodeAppService: Register a plugin to the IDARE App;
removeLayoutComponent(Component) - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout
removePropertyOption(DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Remove the given PropertyOptions from this dataset.
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.
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.
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.
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.

S

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
SBMLToIDARE - Static variable in class idare.Properties.IDAREProperties
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.
separators - Variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription
serialVersionUID - Static variable in class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties
setBounds(int, int, int, int) - Method in class idare.imagenode.Utilities.GUI.JSVGGlassCanvas
setColorCount(int) - Method in interface idare.imagenode.ColorManagement.ColorScale: Set the number of colors used by this scale.
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.
setData(Vector<NodeValue>) - Method in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData: Set the Data of this ArrayNodeData.
setEntryData(Vector<Double>) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataValue: Set the Line Data for this NodeValue.
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
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
setLabel(String) - Method in class idare.imagenode.Interfaces.DataSets.NodeData: Set the Label of this NodeData
setMaximumWidth(int) - Method in class idare.ThirdParty.BoundsPopupMenuListener: Set the maximum width for the popup.
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
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.
setProperties(DataSetLayoutProperties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Set the DataSetLayoutProperties currently used for this dataset
setProperties(Properties) - Method in class idare.imagenode.Interfaces.DataSets.DataSet
setPropertyOptionsUnchecked(Collection<DataSetLayoutProperties>) - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Sets the Options potentially available to this Dataset.
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.
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.
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.
setup() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap: Setup this Color Map.
setup() - Method in class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap
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.Data.BasicDataTypes.ArrayData.ArrayDataDescription: Set up the Itemdescription 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.
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
setupPropertyOptions() - Method in class idare.imagenode.Interfaces.DataSets.DataSet: Set up the property options for this DataSet.
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).
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.
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
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
string - idare.imagenode.Properties.NodeValueType
STRING - idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell.CellType
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
SUBSYSTEMS_SAVE_FILE - Static variable in class idare.Properties.IDAREProperties: IDARE SubSystems Save File
SUBSYSTEMS_SAVE_ID - Static variable in class idare.Properties.IDAREProperties

T

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.
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) - Constructor for class idare.imagenode.GUI.Legend.Utilities.TextPaneResizer: Default parameters will be used for the given pane (300 width, 2 offset)
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.
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
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
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.
type - Variable in class idare.imagenode.Interfaces.DataSets.NodeValue

U

UNKNOWN - idare.imagenode.Interfaces.DataSetReaders.WorkBook.IDARECell.CellType
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.
updateNetworkNodes() - Method in interface idare.imagenode.IDARENodeManager: Update the set of NetworkNode IDs.
updatePreferredSize(int) - Method in class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryDescriptionPane: Update the preferredsize of this Line according to a provided width.
useTwoColHeaders - Variable in class idare.imagenode.Interfaces.DataSets.DataSet: An Indicator whether this dataset uses one or two columns to provide label/ID

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.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.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
vector - idare.imagenode.Properties.NodeValueType
VGAP - Static variable in class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription

W

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
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

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