All Classes

Class	Description
AbstractArrayContainer	A Basis class for container using ArrayNodeData.
AbstractArrayContainerLayout	The AbstractArrayContainerLayout provides basic features for any AbstractArrayContainerLayout, such as shape placements etc.
AbstractArrayDataSetProperties	Basic properties for a ArrayDataSet.
ArrayDataDescription	ItemDataDescription is a Panel, that manages the description of ArrayNodeData using the labels for these items.
ArrayDataSet	An Abstract basis class for item based datasets.
ArrayNodeData	NodeData that can be used for any ArrayDataSet
BasicIDARECell	Basic implementation of a Simple Cell for a BasicIDAREWorkbook.
BasicIDARERow	A simple implementation of an IDARERow
BasicIDARESheet	This is a basic implementation of a IDARESheet for convenience.
BasicIDAREWorkbook	A simple implementation of an IDAREWorkbook
BoundsPopupMenuListener	This class will change the bounds of the JComboBox popup menu to support different functionality.
BufferedImageTranscoder	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
CobraUtil	Contains some useful methods to manipulate 'COBRA SBML'
ColorMap	A ColorMap provides an interface to a DataSet to obtain colors for specific values present in the DataSet.
ColorScale	A ColorScale provides Colors based on its properties for values between 0 and 1.
ColorScaleFactory	The ColorScaleFactory can either generate individual ColorScales or sets of ColorScales which possess specific properties.
ColorScalePane	A Colorscale pane is a graphical representation of a ColorScale, that can be added to Swing Components.
ColorScalePopupAdjuster	A PopupAdjuster for ColorScales, that updates the size of the colorscale being displayed, when selecting colors.
ColorUtils	Color Utils provide some static convenience functions for Colors
ContainerLayout	Classes implementing this interface need to be able to generate a layout when provided with an area to generate the layout
ContainerUnplaceableExcpetion	Exception indicating, that there was at least one unplaceable container in a given layout.
ContinousColorMap	An Abstract class representing general continuous color maps and providing some functionality for such maps.
ContinousZeroBalancedMap
CytoscapeUtils
DataContainer	A DataContainer is a class that is able to provide a specific ContainerLayout for a node.
DataSet	A DataSet is a storage for data.
DataSetLayoutProperties	DataSetLayoutProperties allow the use of a specific class of DataSets for multiple different layouts.
DelayedVizProp	DelayedVizProp, as suggested in the Cytoscape cookbook.
DimensionMismatchException	Exception indicating, that a Container was too larger and could not be placed.
DiscreteColorMap	A Colormap that can provide colors for a discrete number of values (i.e.
DiscreteColorScalePane	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.
DuplicateIDException	Exception indicating that there was a duplicate ID.
EOOMarker	Helper Class for Serializable Input/OUTPUT Streams to mark the end of objects.
GUIUtils	Class proviing static utilitits for multiple GUI classes.
IDARECell	A general class of cells in a Workbook used for IDARE.
IDARECell.CellType	Different Types of Cells that can be available.
IDARECellIterator	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.
IDAREDatasetReader	A IDAREDatasetReader must be able to read a Datafile into a
IDAREImageNodeAppService	The IDAREImageNodeAppService is the interaction point for plugins that want to provide additional features for the IDARE image generation tool.
IDARENodeManager
IDAREPlugin
IDAREProperties	Class containing all static Fields for the IDARE Columns.
IDAREProperties.EdgeType
IDAREProperties.NodeType
IDAREReaderSetupTask	An Abstract Basis Class that defines a Task that is necessary to set up a reader for dataset parsing.
IDARERow	An IDARERow is a row in a data sheet.
IDARERowIterator	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.
IDARESettingsManager	Class to keep track of IDARE IDs and complain (throw exceptions) if duplicate IDs are found.
IDARESheet	An IDARESheet is a sheet containing multiple rows (i.e.
IDAREWorkbook	An IDAREWorkbook contains one or multiple sets of data in individual IDARESheets
IMAGENODEPROPERTIES	Class that stores the Static properties used by imagenodeS.
IMAGENODEPROPERTIES.LayoutStyle
IOUtils	A few useful IO Functions
JSVGGlassCanvas
LabelGenerator	A Class to produce continuous labels in an alphanumeric fashion.
LayoutUtils	Class that provides several utility function to handle SVG Objects (like DOM initialization etc pp
LegendLabel	Class that represents a LegendLabel, which can be drawn in a specific graphics context.
LegendSizeListener
Localisation	A Class encapsulating the Localisation information (i.e.
Localisation.Position
MouseDraggingListener<T extends JComponent>
MouseResizerListener<T extends JComponent>
MultiArrayContainer	A Container for a MultiArrayDataSet
MultiArrayContainerLayout	Abstract class providing some functionalities for Layouts of Value Sets
MultiArrayDataProperties	A basic class for all MultiArrayDataProperties
MultiArrayDataSet	Class to provide a basic setting for MultiArray Datasets.
MultiArrayDataValue	A NodeValue for MultiArrayDataSet The Value of a NodeValue is always the String representing the Sheet it is contained in.
MultiArrayDescription	Abstract class that provides an entry to building basic Descriptions in a Legend for given shapes.
MultiArrayEntryDescriptionPane	Abstract description of an Entry (i.e.
MultiArrayEntryPanel	A SetEntryPanel is a simple abstract representation of a marker or shape along with the color of a specific entry.
MultiArrayNodeData	NodeData for MultiArrayDataSets
NodeData	A Data Entry will always only have numbers stored in it as it is used for data representation on color scales or in graphs.
NodeValue	A NodeValue represents the Value at a specific node.
NodeValueType	Enumerator for different types of NodeValues.
SizeAdaptableComponent	This interface defines classes which allow to adjust their height when a given width is set.
StringUtils
TextPaneEditorKit	Source obtained from http://java-sl.com/tip_center_vertically.html
TextPaneResizer	A Listener that adapts a JTextPane according to the Scrollpane enclosing the pane.
TooManyItemsException	Exception indicating that a container was too large and could not be placed.
WrongDatasetTypeException
WrongFormat	Exception indicating that there was an error in the format of the file used.