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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
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.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
 
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
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
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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