Serialized Form (IDARE [idare] 1.0 API)

Package idare.imagenode.ColorManagement
- Class idare.imagenode.ColorManagement.ColorMap extends Object implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - cs
```
ColorScale cs
```
- Class idare.imagenode.ColorManagement.ColorScalePane extends JPanel implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - cs
```
ColorScale cs
```
- Class idare.imagenode.ColorManagement.DiscreteColorScalePane extends ColorScalePane implements Serializable
  
  serialVersionUID:
  
  1001L
Package idare.imagenode.ColorManagement.ColorMapTypes
- Class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap extends ColorMap implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - maxval
```
double maxval
```
    - minval
```
double minval
```
    - range
```
double range
```
    - oddrange
```
boolean oddrange
```
    - ColorPane
```
JPanel ColorPane
```
    - DescriptionPanes
```
Vector<E> DescriptionPanes
```
    - ColorScaleFractions
```
float[] ColorScaleFractions
```
    - ColorScaleColors
```
Color[] ColorScaleColors
```
- Class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - xpositions
```
Double[] xpositions
```
- Class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap extends ContinousColorMap implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - zerocentered
```
boolean zerocentered
```
    - translate
```
HashMap<K,V> translate
```
- Class idare.imagenode.ColorManagement.ColorMapTypes.DiscreteColorMap extends ColorMap implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - colors
```
HashMap<K,V> colors
```
    - MINIMAL_FONT_SIZE
```
int MINIMAL_FONT_SIZE
```
Package idare.imagenode.Data.BasicDataTypes.ArrayData
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout extends ContainerLayout implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - rows
```
int rows
```
    - cols
```
int cols
```
    - DisplayNodePositions
```
HashMap<K,V> DisplayNodePositions
```
    - LegendNodePositions
```
HashMap<K,V> LegendNodePositions
```
    - LabelForDataSet
```
LegendLabel LabelForDataSet
```
    - legendOffset
```
Point legendOffset
```
    - LegendFrame
```
Rectangle LegendFrame
```
    - upperright
```
Point upperright
```
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.LegendShapePosition extends AbstractArrayContainerLayout.ShapePosition implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - FontPosition
```
Point2D FontPosition
```
    - ItemID
```
String ItemID
```
    - labelFont
```
Font labelFont
```
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.ShapePosition extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - shape
```
Shape shape
```
    - position
```
Rectangle2D position
```
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayDataSetProperties extends DataSetLayoutProperties implements Serializable
  
  serialVersionUID:
  
  1L
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription extends JPanel implements Serializable
  - Serialized Fields
    - Itemdescriptions
```
Vector<E> Itemdescriptions
```
    - separators
```
Insets separators
```
    - oldsize
```
Dimension oldsize
```
    - maxitemwidth
```
int maxitemwidth
```
    - ComponentLayout
```
GridLayout ComponentLayout
```
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionPane extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ID
```
JLabel ID
```
    - Description
```
JLabel Description
```
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet extends DataSet implements Serializable
  - Serialized Fields
    - NodeLabels
```
HashMap<K,V> NodeLabels
```
    - Data
```
HashMap<K,V> Data
```
    - defaultEntry
```
ArrayNodeData defaultEntry
```
    - colormaps
```
Vector<E> colormaps
```
    - columncount
```
int columncount
```
    - emptycolumns
```
boolean[] emptycolumns
```
    - columnLabels
```
Vector<E> columnLabels
```
      A Vector indicating the labels of each column
- Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData extends NodeData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - values
```
Vector<E> values
```
Package idare.imagenode.Data.BasicDataTypes.MultiArrayData
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainerLayout extends ContainerLayout implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataProperties extends DataSetLayoutProperties implements Serializable
  
  serialVersionUID:
  
  1L
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet extends DataSet implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - Data
```
HashMap<K,V> Data
```
    - Headerlines
```
HashMap<K,V> Headerlines
```
    - SheetNames
```
Vector<E> SheetNames
```
    - stringheaders
```
boolean stringheaders
```
      Indicator whether String headers are used
    - numericheaders
```
boolean numericheaders
```
      Indicator whether numeric headers are used
    - mixedheaders
```
boolean mixedheaders
```
      Mixed headers can appear due to e.g. numeric strings
    - defaultData
```
MultiArrayNodeData defaultData
```
    - colormaps
```
Collection<E> colormaps
```
    - allHeaders
```
Vector<E> allHeaders
```
    - headerpos
```
SortedSet<E> headerpos
```
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataValue extends NodeValue implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - yvalues
```
Vector<E> yvalues
```
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDescription extends JPanel implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - Itemdescriptions
```
Vector<E> Itemdescriptions
```
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryDescriptionPane extends JPanel implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - entry
```
JPanel entry
```
    - description
```
JTextPane description
```
    - minimalDescriptionWidth
```
int minimalDescriptionWidth
```
    - minimalEntryWidth
```
int minimalEntryWidth
```
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayEntryPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - ShapeColor
```
Color ShapeColor
```
- Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayNodeData extends NodeData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - Data
```
HashMap<K,V> Data
```
Package idare.imagenode.exceptions.io
- Class idare.imagenode.exceptions.io.DuplicateIDException extends Exception implements Serializable
  - Serialized Fields
    - duplicateID
```
String duplicateID
```
- Class idare.imagenode.exceptions.io.WrongFormat extends Exception implements Serializable
Package idare.imagenode.exceptions.layout
- Class idare.imagenode.exceptions.layout.ContainerUnplaceableExcpetion extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class idare.imagenode.exceptions.layout.DimensionMismatchException extends Exception implements Serializable
- Class idare.imagenode.exceptions.layout.TooManyItemsException extends Exception implements Serializable
- Class idare.imagenode.exceptions.layout.WrongDatasetTypeException extends Exception implements Serializable
Package idare.imagenode.Interfaces.DataSets
- Class idare.imagenode.Interfaces.DataSets.DataSet extends Object implements Serializable
  - Serialized Fields
    - isnumeric
```
boolean isnumeric
```
      An Indicator whether the dataset uses numeric representation
    - isstring
```
boolean isstring
```
      An Indicator whether the dataset uses numeric representation
    - numericstrings
```
boolean numericstrings
```
      an indicator whether the dataset uses numeric data represented by strings
    - isdiscreet
```
boolean isdiscreet
```
      An Indicator whether this is a discreet data set (i.e. no more than 5 different values)
    - useTwoColHeaders
```
boolean useTwoColHeaders
```
      An Indicator whether this dataset uses one or two columns to provide label/ID
    - Description
```
String Description
```
      The Description of this Dataset.
    - datasetProperties
```
DataSetLayoutProperties datasetProperties
```
      The properties to be used for this dataset, need to be set during reading of data.
    - propertyOptions
```
Vector<E> propertyOptions
```
    - Valueset
```
Vector<E> Valueset
```
    - dataSetID
```
int dataSetID
```
    - MinValue
```
Double MinValue
```
    - MaxValue
```
Double MaxValue
```
- Class idare.imagenode.Interfaces.DataSets.NodeData extends Object implements Serializable
  - Serialized Fields
    - label
```
String label
```
    - id
```
String id
```
    - parent
```
DataSet parent
```
- Class idare.imagenode.Interfaces.DataSets.NodeValue extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Comparable<T> value
```
    - type
```
NodeValueType type
```
Package idare.imagenode.Interfaces.Layout
- Class idare.imagenode.Interfaces.Layout.ContainerLayout extends Object implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - layoutarea
```
Rectangle layoutarea
```
- Class idare.imagenode.Interfaces.Layout.DataSetLayoutProperties extends Object implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.ColorManagement.ColorScales
- Class idare.imagenode.internal.ColorManagement.ColorScales.BlackYellowRed extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.BlueWhiteRedScale extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.BlueYellowRed extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.DiscreteColorScale extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - availablecolors
```
Color[] availablecolors
```
      A general field from which additional colors are generated.
- Class idare.imagenode.internal.ColorManagement.ColorScales.FlagScale extends DiscreteColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.GreenBlackRed extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.GreenYellow extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.HSVScale extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.JetScale extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.LineScale extends DiscreteColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.MultiColorScale extends Object implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - ColorSteps
```
Color[] ColorSteps
```
    - fractions
```
float[] fractions
```
    - usedColors
```
Color[] usedColors
```
- Class idare.imagenode.internal.ColorManagement.ColorScales.PrismScale extends DiscreteColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.RedWhiteBlueScale extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.WhiteBlack extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.WhiteBlue extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.WhiteRed extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.YellowGreen extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.ColorManagement.ColorScales.YellowRed extends MultiColorScale implements Serializable
  
  serialVersionUID:
  
  1001L
Package idare.imagenode.internal.Data.Array.CircleData
- Class idare.imagenode.internal.Data.Array.CircleData.CircleContainerLayout extends AbstractArrayContainerLayout implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.Data.Array.CircleData.CircleDataSetProperties extends AbstractArrayDataSetProperties implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.Data.Array.CircleGridData
- Class idare.imagenode.internal.Data.Array.CircleGridData.CircleGridProperties extends CircleDataSetProperties implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.Data.Array.RectangleData
- Class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout extends AbstractArrayContainerLayout implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout.RectangleLegendShapePosition extends RectangleContainerLayout.RectangleShapePosition implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - FontPosition
```
Point2D FontPosition
```
    - ItemID
```
String ItemID
```
    - labelFont
```
Font labelFont
```
- Class idare.imagenode.internal.Data.Array.RectangleData.RectangleContainerLayout.RectangleShapePosition extends AbstractArrayContainerLayout.ShapePosition implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.Data.Array.RectangleData.RectangleDataSetProperties extends AbstractArrayDataSetProperties implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.Data.Array.TimeSeriesData
- Class idare.imagenode.internal.Data.Array.TimeSeriesData.TimeSeriesDataSetProperties extends AbstractArrayDataSetProperties implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.Data.MultiArray.GraphData
- Class idare.imagenode.internal.Data.MultiArray.GraphData.GraphContainerLayout extends MultiArrayContainerLayout implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - LegendAxes
```
Path2D LegendAxes
```
    - NodeAxes
```
Path2D NodeAxes
```
    - ZeroLine
```
Line2D ZeroLine
```
    - LegendZeroLine
```
Line2D LegendZeroLine
```
    - LegendFrame
```
Rectangle2D LegendFrame
```
    - LabelForDataSet
```
LegendLabel LabelForDataSet
```
    - YMinval
```
LegendLabel YMinval
```
    - YMaxval
```
LegendLabel YMaxval
```
    - YZeroval
```
LegendLabel YZeroval
```
    - XMinval
```
LegendLabel XMinval
```
    - XMaxval
```
LegendLabel XMaxval
```
    - yminval
```
Double yminval
```
    - ymaxval
```
Double ymaxval
```
    - yrange
```
Double yrange
```
    - xminval
```
Double xminval
```
    - xmaxval
```
Double xmaxval
```
    - xrange
```
Double xrange
```
    - LineArea
```
Rectangle2D LineArea
```
    - LegendLineArea
```
Rectangle2D LegendLineArea
```
    - LineHeaders
```
HashMap<K,V> LineHeaders
```
- Class idare.imagenode.internal.Data.MultiArray.GraphData.GraphDataSetProperties extends MultiArrayDataProperties implements Serializable
- Class idare.imagenode.internal.Data.MultiArray.GraphData.LineDescription extends MultiArrayDescription implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.Data.MultiArray.IndividualGraph
- Class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphContainerLayout extends MultiArrayContainerLayout implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - LegendAxes
```
Path2D LegendAxes
```
    - NodeAxes
```
Path2D NodeAxes
```
    - ZeroLine
```
Line2D ZeroLine
```
    - LegendZeroLine
```
Line2D LegendZeroLine
```
    - LegendFrame
```
Rectangle2D LegendFrame
```
    - LabelForDataSet
```
LegendLabel LabelForDataSet
```
    - YMinval
```
LegendLabel YMinval
```
    - YMaxval
```
LegendLabel YMaxval
```
    - YZeroval
```
LegendLabel YZeroval
```
    - XMinval
```
LegendLabel XMinval
```
    - XMaxval
```
LegendLabel XMaxval
```
    - yminval
```
Double yminval
```
    - ymaxval
```
Double ymaxval
```
    - yrange
```
Double yrange
```
    - xminval
```
Double xminval
```
    - xmaxval
```
Double xmaxval
```
    - xrange
```
Double xrange
```
    - LineArea
```
Rectangle2D LineArea
```
    - LegendLineArea
```
Rectangle2D LegendLineArea
```
    - LineHeaders
```
HashMap<K,V> LineHeaders
```
- Class idare.imagenode.internal.Data.MultiArray.IndividualGraph.IndividualGraphDataSetProperties extends MultiArrayDataProperties implements Serializable
- Class idare.imagenode.internal.Data.MultiArray.IndividualGraph.LineDescription extends MultiArrayDescription implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.Data.MultiArray.ScatterData
- Class idare.imagenode.internal.Data.MultiArray.ScatterData.HeaderDescription extends ArrayDataDescription implements Serializable
  
  serialVersionUID:
  
  1L
- Class idare.imagenode.internal.Data.MultiArray.ScatterData.LargeScatterProperties extends ScatterDataSetProperties implements Serializable
  
  serialVersionUID:
  
  1L
- Class idare.imagenode.internal.Data.MultiArray.ScatterData.MarkerDataDescription extends MultiArrayDescription implements Serializable
  
  serialVersionUID:
  
  1001L
- Class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout extends MultiArrayContainerLayout implements Serializable
  
  serialVersionUID:
  
  1001L
  - Serialized Fields
    - LegendAxes
```
Path2D LegendAxes
```
    - NodeAxes
```
Path2D NodeAxes
```
    - ZeroLine
```
Line2D ZeroLine
```
    - LegendZeroLine
```
Line2D LegendZeroLine
```
    - LegendFrame
```
Rectangle2D LegendFrame
```
    - LabelForDataSet
```
LegendLabel LabelForDataSet
```
    - YMinval
```
LegendLabel YMinval
```
    - YMaxval
```
LegendLabel YMaxval
```
    - YZeroval
```
LegendLabel YZeroval
```
    - XLabels
```
Vector<E> XLabels
```
    - yminval
```
Double yminval
```
    - ymaxval
```
Double ymaxval
```
    - yrange
```
Double yrange
```
    - xminval
```
Double xminval
```
    - xmaxval
```
Double xmaxval
```
    - xrange
```
Double xrange
```
    - LineArea
```
Rectangle2D LineArea
```
    - LegendLineArea
```
Rectangle2D LegendLineArea
```
    - itemxPositions
```
HashMap<K,V> itemxPositions
```
    - labelSize
```
int labelSize
```
    - numericHeaders
```
boolean numericHeaders
```
    - LineHeaders
```
HashMap<K,V> LineHeaders
```
- Class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterContainerLayout.LabelAndPosition extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - label
```
String label
```
    - position
```
Double position
```
- Class idare.imagenode.internal.Data.MultiArray.ScatterData.ScatterDataSetProperties extends MultiArrayDataProperties implements Serializable
  
  serialVersionUID:
  
  1L
- Class idare.imagenode.internal.Data.MultiArray.ScatterData.SmallScatterProperties extends ScatterDataSetProperties implements Serializable
  
  serialVersionUID:
  
  1L
Package idare.imagenode.internal.exceptions.debug
- Class idare.imagenode.internal.exceptions.debug.DebugException extends Exception implements Serializable
  - Serialized Fields
    - source
```
Object source
```
Package idare.imagenode.internal.GUI.DataSetAddition
- Class idare.imagenode.internal.GUI.DataSetAddition.TunableDataSetAdderGUI extends JPanel implements Serializable
  - Serialized Fields
    - util
```
org.cytoscape.util.swing.FileUtil util
```
    - dsm
```
DataSetManager dsm
```
    - DataSetFileLocation
```
JTextField DataSetFileLocation
```
    - DataSetDescriptionField
```
JTextField DataSetDescriptionField
```
    - useTwoColCheckBox
```
JCheckBox useTwoColCheckBox
```
    - DataSetTypeSelector
```
JComboBox<E> DataSetTypeSelector
```
    - descriptionModified
```
boolean descriptionModified
```
    - fileNameUpdate
```
boolean fileNameUpdate
```
    - cySwingApp
```
org.cytoscape.application.swing.CySwingApplication cySwingApp
```
Package idare.imagenode.internal.GUI.DataSetController
- Class idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - DataSetTable
```
DataSetSelectionTable DataSetTable
```
    - commons
```
idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel.IDValueLabel commons
```
    - totals
```
idare.imagenode.internal.GUI.DataSetController.DataSetControlPanel.IDValueLabel totals
```
    - PreviewFrame
```
JDialog PreviewFrame
```
    - PreviewLegendFrame
```
JDialog PreviewLegendFrame
```
    - dssm
```
DataSetSelectionModel dssm
```
    - app
```
IDAREImageNodeApp app
```
    - nodeFactory
```
CreateNodesTaskFactory nodeFactory
```
    - dsatf
```
DataSetAdderTaskFactory dsatf
```
- Class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionModel extends DefaultTableModel implements Serializable
  - Serialized Fields
    - renderers
```
HashMap<K,V> renderers
```
    - colorscalerenderer
```
HashMap<K,V> colorscalerenderer
```
    - colorscaleBoxes
```
HashMap<K,V> colorscaleBoxes
```
    - colorscalesperdataset
```
HashMap<K,V> colorscalesperdataset
```
    - colorscaleselection
```
HashMap<K,V> colorscaleselection
```
- Class idare.imagenode.internal.GUI.DataSetController.DataSetSelectionTable extends JTable implements Serializable
  - Serialized Fields
    - tablemodel
```
DataSetSelectionModel tablemodel
```
Package idare.imagenode.internal.GUI.Legend
- Class idare.imagenode.internal.GUI.Legend.IDARELegend extends JScrollPane implements Serializable
  - Serialized Fields
    - Node
```
NodeSVGCanvas Node
```
    - Content
```
JPanel Content
```
    - resizer
```
NodeResizer resizer
```
    - currentNode
```
String currentNode
```
    - manager
```
NodeManager manager
```
    - active
```
boolean active
```
- Class idare.imagenode.internal.GUI.Legend.NodeSVGCanvas extends org.apache.batik.swing.JSVGCanvas implements Serializable
  - Serialized Fields
    - canupdatepreferredsize
```
boolean canupdatepreferredsize
```
Package idare.imagenode.internal.GUI.NetworkSetup
- Class idare.imagenode.internal.GUI.NetworkSetup.ColumnTypeChooser extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - network
```
org.cytoscape.model.CyNetwork network
```
    - bgcolor
```
Color bgcolor
```
    - ColumnNames
```
Vector<E> ColumnNames
```
    - acceptbydefault
```
boolean acceptbydefault
```
    - SelectedColName
```
String SelectedColName
```
    - selectedObjects
```
HashMap<K,V> selectedObjects
```
    - compoundTypeSelector
```
JComboBox<E> compoundTypeSelector
```
    - reactionTypeSelector
```
JComboBox<E> reactionTypeSelector
```
    - geneTypeSelector
```
JComboBox<E> geneTypeSelector
```
    - proteinTypeSelector
```
JComboBox<E> proteinTypeSelector
```
    - compoundDesc
```
JTextPane compoundDesc
```
    - reactionDesc
```
JTextPane reactionDesc
```
    - geneDesc
```
JTextPane geneDesc
```
    - proteinDesc
```
JTextPane proteinDesc
```
- Class idare.imagenode.internal.GUI.NetworkSetup.NetworkSetupTunableGUI extends JPanel implements Serializable
  - Serialized Fields
    - background
```
Color background
```
    - typeColSelector
```
JComboBox<E> typeColSelector
```
    - IDColSelector
```
JComboBox<E> IDColSelector
```
    - overwrite
```
JCheckBox overwrite
```
    - ctc
```
ColumnTypeChooser ctc
```
    - IDCol
```
String IDCol
```
    - TypeCol
```
String TypeCol
```
Package idare.imagenode.internal.Layout.Automatic
- Class idare.imagenode.internal.Layout.Automatic.ImageBag extends Container implements Serializable
  - Serialized Fields
    - parent
```
ImageNodeContainer parent
```
    - FixedContainers
```
HashMap<K,V> FixedContainers
```
    - FlexContainers
```
HashMap<K,V> FlexContainers
```
    - Layout
```
HashMap<K,V> Layout
```
    - itemcount
```
int itemcount
```
    - maxitemcount
```
int maxitemcount
```
    - maxwidth
```
int maxwidth
```
    - maxheight
```
int maxheight
```
    - currentwidth
```
int currentwidth
```
    - position
```
ImageBag.BAGPOSITON position
```
- Class idare.imagenode.internal.Layout.Automatic.ImageNodeContainer extends JLabel implements Serializable
  - Serialized Fields
    - leftBag
```
ImageBag leftBag
```
    - rightBag
```
ImageBag rightBag
```
    - centerBag
```
ImageBag centerBag
```
    - bundles
```
HashMap<K,V> bundles
```
    - flexibleContainers
```
HashMap<K,V> flexibleContainers
```
    - fixedContainers
```
HashMap<K,V> fixedContainers
```
    - freecontainers
```
HashMap<K,V> freecontainers
```
    - containers
```
HashMap<K,V> containers
```
    - addedDataSets
```
Set<E> addedDataSets
```
    - maxcenteritems
```
int maxcenteritems
```
    - maxedgeitems
```
int maxedgeitems
```
    - currentcenteritems
```
int currentcenteritems
```
    - currentedgeitems
```
int currentedgeitems
```
    - currentflexitem
```
int currentflexitem
```

Package idare.imagenode.internal.Layout.Manual

Class idare.imagenode.internal.Layout.Manual.LayoutGUI extends JFrame implements Serializable

Serialized Fields

desktop
```
JDesktopPane desktop
```
dsm
```
DataSetManager dsm
```
app
```
IDAREImageNodeApp app
```
layout
```
ManualLayout layout
```

resizer

idare.imagenode.internal.Layout.Manual.LayoutGUI.FrameResizer resizer

toolbar
```
DataSetLayoutToolBar toolbar
```
IdentifierPanel
```
IDPanel IdentifierPanel
```
updater
```
ManualLayoutUpdater updater
```

draglistener

MouseDraggingListener<T extends JComponent> draglistener

nodeFactory
```
CreateNodesTaskFactory nodeFactory
```

Package idare.imagenode.internal.Layout.Manual.GUI
- Class idare.imagenode.internal.Layout.Manual.GUI.ColorMenuItem extends JMenuItem implements Serializable
  - Serialized Fields
    - pane
```
ColorScalePane pane
```
- Class idare.imagenode.internal.Layout.Manual.GUI.ColorPopup extends JPopupMenu implements Serializable
- Class idare.imagenode.internal.Layout.Manual.GUI.ColorToolBarEntry extends JPanel implements Serializable
  - Serialized Fields
    - colorselector
```
JComboBox<E> colorselector
```
    - colormapping
```
HashMap<K,V> colormapping
```
    - colorLabel
```
JLabel colorLabel
```
    - cpa
```
ColorScalePopupAdjuster cpa
```
- Class idare.imagenode.internal.Layout.Manual.GUI.DataSetFrame extends JInternalFrame implements Serializable
  - Serialized Fields
    - bundle
```
DataSetLayoutInfoBundle bundle
```
    - layout
```
ContainerLayout layout
```
    - origboundingbox
```
Rectangle origboundingbox
```
    - origdesktopsize
```
Rectangle origdesktopsize
```
    - cont
```
DataContainer cont
```
    - parent
```
JComponent parent
```
    - LayoutID
```
String LayoutID
```
    - autoresize
```
boolean autoresize
```
- Class idare.imagenode.internal.Layout.Manual.GUI.DataSetLayoutToolBar extends JToolBar implements Serializable
  - Serialized Fields
    - updater
```
ManualLayoutUpdater updater
```
    - colors
```
ColorToolBarEntry colors
```
    - properties
```
DataSetPropertyToolBarEntry properties
```
    - nodeID
```
NodeIDSelectorToolBarEntry nodeID
```
    - updatingoptions
```
boolean updatingoptions
```
- Class idare.imagenode.internal.Layout.Manual.GUI.DatasetMenu extends JMenu implements Serializable
  - Serialized Fields
    - set
```
DataSet set
```
    - mapping
```
HashMap<K,V> mapping
```
    - gui
```
LayoutGUI gui
```
    - props
```
DataSetLayoutProperties props
```
- Class idare.imagenode.internal.Layout.Manual.GUI.DataSetPropertyToolBarEntry extends JPanel implements Serializable
  - Serialized Fields
    - visualisationTypeSelector
```
JComboBox<E> visualisationTypeSelector
```
    - visualisationTypeLabel
```
JLabel visualisationTypeLabel
```
- Class idare.imagenode.internal.Layout.Manual.GUI.IDPanel extends JPanel implements Serializable
- Class idare.imagenode.internal.Layout.Manual.GUI.NodeIDSelectorToolBarEntry extends JPanel implements Serializable
  - Serialized Fields
    - idOptions
```
JComboBox<E> idOptions
```
    - idLabel
```
JLabel idLabel
```
Package idare.imagenode.internal.Layout.Manual.GUI.Tasks
- Class idare.imagenode.internal.Layout.Manual.GUI.Tasks.LayoutPropertiesGUI extends JPanel implements Serializable
  - Serialized Fields
    - colorselector
```
ColorToolBarEntry colorselector
```
    - propertySelector
```
JComboBox<E> propertySelector
```
    - datasetSelector
```
JComboBox<E> datasetSelector
```
Package idare.imagenode.internal.Layout.Manual.Utilities
- Class idare.imagenode.internal.Layout.Manual.Utilities.LayoutArea extends Rectangle implements Serializable
Package idare.imagenode.Utilities
- Class idare.imagenode.Utilities.EOOMarker extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class idare.imagenode.Utilities.LegendLabel extends Object implements Serializable
  - Serialized Fields
    - Label
```
String Label
```
    - Position
```
Point Position
```
    - LabelFont
```
Font LabelFont
```
Package idare.imagenode.Utilities.GUI
- Class idare.imagenode.Utilities.GUI.JSVGGlassCanvas extends org.apache.batik.swing.JSVGCanvas implements Serializable
Package idare.subnetwork.internal
- Class idare.subnetwork.internal.NetworkNode extends Object implements Serializable
  - Serialization Methods
    - readObject
```
private void readObject(ObjectInputStream in)
```
    - writeObject
```
private void writeObject(ObjectOutputStream out)
```
  - Serialized Fields
    - parent
```
NetworkNode parent
```
    - networkreference
```
org.cytoscape.model.CyNetwork networkreference
```
    - colName
```
String colName
```
    - networkID
```
String networkID
```
    - networkIDAREID
```
Long networkIDAREID
```
    - children
```
Vector<E> children
```
- Class idare.subnetwork.internal.NoNetworksToCreateException extends Exception implements Serializable

Package idare.subnetwork.internal.GUI

Class idare.subnetwork.internal.GUI.SubnetworkInteractionAndCompoundChooser extends JPanel implements Serializable
- Serialized Fields
  - bgcolor
```
Color bgcolor
```
  - ColumnNames
```
Vector<E> ColumnNames
```
  - network
```
org.cytoscape.model.CyNetwork network
```
  - selectedObjects
```
HashMap<K,V> selectedObjects
```
  - SelectedColName
```
String SelectedColName
```
  - compoundTypeSelector
```
JComboBox<E> compoundTypeSelector
```
  - reactionTypeSelector
```
JComboBox<E> reactionTypeSelector
```
  - compoundDesc
```
JTextPane compoundDesc
```
  - reactionDesc
```
JTextPane reactionDesc
```

Class idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI extends JPanel implements Serializable

Serialized Fields

network
```
org.cytoscape.model.CyNetwork network
```
nvs
```
NetworkViewSwitcher nvs
```
layoutSelector
```
JComboBox<E> layoutSelector
```
colSelector
```
JComboBox<E> colSelector
```
metSelTab
```
JTable metSelTab
```
subNetSelTab
```
JTable subNetSelTab
```

metSelMod

idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI.MetaboliteSelectionModel metSelMod

columnNames
```
Vector<E> columnNames
```
IDCol
```
String IDCol
```
colSelected
```
int colSelected
```
algoselected
```
String algoselected
```
accepted
```
boolean accepted
```
bgcolor
```
Color bgcolor
```

Class idare.subnetwork.internal.GUI.SubnetworkPropertyColumnChooser extends JPanel implements Serializable
- Serialized Fields
  - background
```
Color background
```
  - typeColSelector
```
JComboBox<E> typeColSelector
```
  - IDColSelector
```
JComboBox<E> IDColSelector
```
  - ctc
```
SubnetworkInteractionAndCompoundChooser ctc
```
  - IDCol
```
String IDCol
```
  - TypeCol
```
String TypeCol
```

Package idare.subnetwork.internal.Tasks
- Class idare.subnetwork.internal.Tasks.InvalidSelectionException extends Exception implements Serializable
Package idare.ThirdParty
- Class idare.ThirdParty.TextPaneEditorKit extends StyledEditorKit implements Serializable

Serialized Form

Package idare.imagenode.ColorManagement

Class idare.imagenode.ColorManagement.ColorMap extends Object implements Serializable

Serialized Fields

cs

Class idare.imagenode.ColorManagement.ColorScalePane extends JPanel implements Serializable

Serialized Fields

cs

Class idare.imagenode.ColorManagement.DiscreteColorScalePane extends ColorScalePane implements Serializable

Package idare.imagenode.ColorManagement.ColorMapTypes

Class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap extends ColorMap implements Serializable

Serialized Fields

maxval

minval

range

oddrange

ColorPane

DescriptionPanes

ColorScaleFractions

ColorScaleColors

Class idare.imagenode.ColorManagement.ColorMapTypes.ContinousColorMap.ColorScaleLegendLayout extends Object implements Serializable

Serialized Fields

xpositions

Class idare.imagenode.ColorManagement.ColorMapTypes.ContinousZeroBalancedMap extends ContinousColorMap implements Serializable

Serialized Fields

zerocentered

translate

Class idare.imagenode.ColorManagement.ColorMapTypes.DiscreteColorMap extends ColorMap implements Serializable

Serialized Fields

colors

MINIMAL_FONT_SIZE

Package idare.imagenode.Data.BasicDataTypes.ArrayData

Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout extends ContainerLayout implements Serializable

Serialized Fields

rows

cols

DisplayNodePositions

LegendNodePositions

LabelForDataSet

legendOffset

LegendFrame

upperright

Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.LegendShapePosition extends AbstractArrayContainerLayout.ShapePosition implements Serializable

Serialized Fields

FontPosition

ItemID

labelFont

Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayContainerLayout.ShapePosition extends Object implements Serializable

Serialized Fields

shape

position

Class idare.imagenode.Data.BasicDataTypes.ArrayData.AbstractArrayDataSetProperties extends DataSetLayoutProperties implements Serializable

Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription extends JPanel implements Serializable

Serialized Fields

Itemdescriptions

separators

oldsize

maxitemwidth

ComponentLayout

Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataDescription.ItemDescriptionPane extends JPanel implements Serializable

Serialized Fields

ID

Description

Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayDataSet extends DataSet implements Serializable

Serialized Fields

NodeLabels

Data

defaultEntry

colormaps

columncount

emptycolumns

columnLabels

Class idare.imagenode.Data.BasicDataTypes.ArrayData.ArrayNodeData extends NodeData implements Serializable

Serialized Fields

values

Package idare.imagenode.Data.BasicDataTypes.MultiArrayData

Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayContainerLayout extends ContainerLayout implements Serializable

Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataProperties extends DataSetLayoutProperties implements Serializable

Class idare.imagenode.Data.BasicDataTypes.MultiArrayData.MultiArrayDataSet extends DataSet implements Serializable

Serialized Fields