C-Index (Vanted 2.8.3 API)

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C

CachedWebDownload - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg
CachedWebDownload() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.CachedWebDownload
calcAlpha() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
calcAlpha() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
calcAverage(Vector<SOMdataEntry>, String) - Method in class qmwi.kseg.som.DataSet
calcBeta() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
calcBeta() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
CalcClassPathJarsMd5 - Class in org.vanted.updater: Calculates all MD5 sums for all the jars found on the classpath of the ClassLoader for VANTED, as provided by the bootstrap.
CalcClassPathJarsMd5() - Constructor for class org.vanted.updater.CalcClassPathJarsMd5
calcCounter - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PatternSpringembedder3d
calcDistances(int) - Method in class org.vanted.plugins.layout.stressminimization.StressMinimizationImplementation: Calculates the distance vector from the node at the specified index to all other nodes.
calcDistances(int, IndexedNodeSet) - Static method in class org.vanted.indexednodes.IndexedGraphOperations
calcDistances(Node, IndexedNodeSet) - Static method in class org.vanted.indexednodes.IndexedGraphOperations: Calculates the distance vector from the specified node to all other nodes in the given org.vanted.indexednodes.IndexedNodeSet.
calcMean() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
calcMean() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
calcNodeDifferenceDistance(Node, Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ApplyGraphLayout
calcPairwiseDistances(IndexedNodeSet) - Method in class org.vanted.plugins.layout.stressminimization.StressMinimizationImplementation: Calculates the distance matrix of the given nodes set.
CalculateAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes
CalculateAttribute() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.CalculateAttribute
calculateBoxAndWhiskerStatistics(List) - Static method in class org.jfree.data.statistics.BoxAndWhiskerCalculator: Calculates the statistics required for a BoxAndWhiskerItem.
calculateConnectedComponentsOfSelection(Set<Node>) - Static method in enum org.vanted.plugins.layout.multilevelframework.MlfHelper: Calculate the subgraph induced by the selection and split it up into its connected components.
calculateCorrelation(MyXML_XYDataset, String, String, boolean, int, double, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.TabStatistics
calculateHighestVisibleTickValue() - Method in class org.jfree.chart.axis.NumberAxis: Calculates the value of the highest visible tick on the axis.
calculateHighestVisibleTickValue(DateTickUnit) - Method in class org.jfree.chart.axis.DateAxis: Calculates the value of the highest visible tick on the axis.
calculateLayout() - Method in class org.vanted.plugins.layout.stressminimization.StressMinimizationImplementation: Calculates an optimized layout for this instances nodes.
calculateLowestVisibleTickValue() - Method in class org.jfree.chart.axis.NumberAxis: Calculates the value of the lowest visible tick on the axis.
calculateLowestVisibleTickValue(DateTickUnit) - Method in class org.jfree.chart.axis.DateAxis: Calculates the value of the lowest visible tick on the axis.
calculateMean(Number[]) - Static method in class org.jfree.data.statistics.Statistics: Returns the mean of an array of numbers.
calculateMean(Collection) - Static method in class org.jfree.data.statistics.Statistics: Returns the mean of a collection of Number objects.
calculateMean(List) - Static method in class org.jfree.data.statistics.BoxAndWhiskerCalculator: Deprecated.
This method has been moved to the Statistics class.
calculateMedian(List) - Static method in class org.jfree.data.statistics.BoxAndWhiskerCalculator: Deprecated.
Moved to the Statistics class.
calculateMedian(List) - Static method in class org.jfree.data.statistics.Statistics: Calculates the median for a list of values (Number objects).
calculateMedian(List, boolean) - Static method in class org.jfree.data.statistics.Statistics: Calculates the median for a list of values (Number objects) that are assumed to be in ascending order.
calculateMedian(List, int, int) - Static method in class org.jfree.data.statistics.BoxAndWhiskerCalculator: Deprecated.
Moved to the Statistics class.
calculateMedian(List, int, int) - Static method in class org.jfree.data.statistics.Statistics: Calculates the median for a sublist within a list of values (Number objects).
calculateMedian(List, int, int, boolean) - Static method in class org.jfree.data.statistics.Statistics: Calculates the median for a sublist within a list of values (Number objects).
calculatePieDatasetTotal(PieDataset) - Static method in class org.jfree.data.DatasetUtilities: Calculates the total of all the values in a PieDataset.
calculateQ1(List) - Static method in class org.jfree.data.statistics.BoxAndWhiskerCalculator: Calculates the first quartile for a list of numbers in ascending order.
calculateQ3(List) - Static method in class org.jfree.data.statistics.BoxAndWhiskerCalculator: Calculates the third quartile for a list of numbers in ascending order.
calculateSegmentNumber(long) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Calculates the segment number for a given millisecond.
calculateValuesFromSampleData() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleAverage
calculateValuesFromSampleData() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleAverageInterface
calculateVisibleTickCount() - Method in class org.jfree.chart.axis.NumberAxis: Calculates the number of visible ticks.
CalculatingAlgorithm - Interface in org.graffiti.plugin.algorithm: After its execution a CalculatingAlgorithm has computed an AlgorithmResult, that can be obtained through the getResult() method.
call(AttributeEvent) - Method in interface org.graffiti.util.DelayThread.DelayedCallback
cAll - Variable in class qmwi.kseg.som.diagram.DiagrammPaneData
callKeggDBGETbfind(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggHelper
callKeggDBGETbget(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggHelper
callKeggDBGETbinfo(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggHelper
callKeggDBGETbtit(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggHelper
cancel() - Method in class org.graffiti.options.OptionsDialog: Handles the "cancel" button.
cancelCellEditing() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractCellEditor
cancelledSaveAction - Variable in class org.graffiti.editor.MainFrame: Set, when external dialog's been cancelled, to restore flow.
CandlestickDemo - Class in org.jfree.chart.demo: A demo showing a candlestick chart.
CandlestickDemo(String) - Constructor for class org.jfree.chart.demo.CandlestickDemo: A demonstration application showing a candlestick chart.
CandlestickRenderer - Class in org.jfree.chart.renderer: A renderer that draws candlesticks on an XYPlot (requires a HighLowDataset).
CandlestickRenderer() - Constructor for class org.jfree.chart.renderer.CandlestickRenderer: Creates a new renderer for candlestick charts.
CandlestickRenderer(double) - Constructor for class org.jfree.chart.renderer.CandlestickRenderer: Creates a new renderer for candlestick charts.
CandlestickRenderer(double, boolean, XYToolTipGenerator) - Constructor for class org.jfree.chart.renderer.CandlestickRenderer: Creates a new renderer for candlestick charts.
canLoadFile(File) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentLoader
canProcess(File) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin
canProcess(File) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.DragAndDropHandler
canProcess(File) - Method in class de.ipk_gatersleben.ag_pbi.datahandling.TemplateLoader
canRedo() - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm
canUndo() - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm
CAPSULE - org.LabelFrameSetting
cascade() - Method in class org.graffiti.util.DesktopMenuManager: Arrange all internal frames in cascading order.
CAT_ALGORITHMS - Static variable in class org.graffiti.options.OptionsDialog
CAT_ATTR_COMP - Static variable in class org.graffiti.options.OptionsDialog
CAT_GENERAL - Static variable in class org.graffiti.options.OptionsDialog
CAT_TABS - Static variable in class org.graffiti.options.OptionsDialog
CAT_TOOLS - Static variable in class org.graffiti.options.OptionsDialog
CAT_VIEWS - Static variable in class org.graffiti.options.OptionsDialog
CATALYZES - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule
Category - Enum in org.graffiti.plugin.algorithm: An enum containing a set of categories for algorithms These fixed categories enable possiblities of grouping and searching algorithms Algorithms can be part of multiple categories
CATEGORY - Static variable in class org.jfree.chart.axis.CategoryLabelWidthType: Percentage of category.
CATEGORY_BACKGROUND_A - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
CATEGORY_BACKGROUND_B - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
CATEGORY_BACKGROUND_C - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
CategoryAnchor - Class in org.jfree.chart.axis: Used to indicate one of three positions within a category: START, MIDDLE and END.
CategoryAnnotation - Interface in org.jfree.chart.annotations: The interface that must be supported by annotations that are to be added to an CategoryPlot.
CategoryAxis - Class in org.jfree.chart.axis: An axis that displays categories.
CategoryAxis() - Constructor for class org.jfree.chart.axis.CategoryAxis: Creates a new category axis with no label.
CategoryAxis(String) - Constructor for class org.jfree.chart.axis.CategoryAxis: Constructs a category axis, using default values where necessary.
CategoryAxis3D - Class in org.jfree.chart.axis: An axis that displays categories and has a 3D effect.
CategoryAxis3D() - Constructor for class org.jfree.chart.axis.CategoryAxis3D: Creates a new axis.
CategoryAxis3D(String) - Constructor for class org.jfree.chart.axis.CategoryAxis3D: Creates a new axis using default attribute values.
CategoryDataset - Interface in org.jfree.data: The interface for a dataset with one or more series, and values associated with categories.
CATEGORYDATASET_TAG - Static variable in interface org.jfree.data.xml.DatasetTags: The 'CategoryDataset' element name.
CategoryDatasetHandler - Class in org.jfree.data.xml: A SAX handler for reading a CategoryDataset from an XML file.
CategoryDatasetHandler() - Constructor for class org.jfree.data.xml.CategoryDatasetHandler: Creates a new handler.
CategoryItemEntity - Class in org.jfree.chart.entity: A chart entity that represents one item within a category plot.
CategoryItemEntity(Shape, String, int, Object, int) - Constructor for class org.jfree.chart.entity.CategoryItemEntity: Deprecated.
Use alternative constructor.
CategoryItemEntity(Shape, String, String, int, Object, int) - Constructor for class org.jfree.chart.entity.CategoryItemEntity: Deprecated.
Use alternative constructor.
CategoryItemEntity(Shape, String, String, CategoryDataset, int, Object, int) - Constructor for class org.jfree.chart.entity.CategoryItemEntity: Creates a new category item entity.
CategoryItemRenderer - Interface in org.jfree.chart.renderer: A plug-in object that is used by the CategoryPlot class to display individual data items from a CategoryDataset.
CategoryItemRendererState - Class in org.jfree.chart.renderer: An object that retains temporary state information for a CategoryItemRenderer.
CategoryItemRendererState(PlotRenderingInfo) - Constructor for class org.jfree.chart.renderer.CategoryItemRendererState: Creates a new object for recording temporary state information for a renderer.
CategoryLabelGenerator - Interface in org.jfree.chart.labels: A category item label generator is an object that can be assigned to a CategoryItemRenderer and that assumes responsibility for creating text items to be used as labels for the items in a CategoryPlot.
CategoryLabelPosition - Class in org.jfree.chart.axis: The attributes that control the position of the labels for the categories on a CategoryAxis.
CategoryLabelPosition() - Constructor for class org.jfree.chart.axis.CategoryLabelPosition: Creates a new position record with default settings.
CategoryLabelPosition(RectangleAnchor, TextBlockAnchor) - Constructor for class org.jfree.chart.axis.CategoryLabelPosition: Creates a new category label position record.
CategoryLabelPosition(RectangleAnchor, TextBlockAnchor, CategoryLabelWidthType, float) - Constructor for class org.jfree.chart.axis.CategoryLabelPosition: Creates a new category label position record.
CategoryLabelPosition(RectangleAnchor, TextBlockAnchor, TextAnchor, double) - Constructor for class org.jfree.chart.axis.CategoryLabelPosition: Deprecated.
Use alternative constructor.
CategoryLabelPosition(RectangleAnchor, TextBlockAnchor, TextAnchor, double, CategoryLabelWidthType, float) - Constructor for class org.jfree.chart.axis.CategoryLabelPosition: Creates a new position record.
CategoryLabelPositions - Class in org.jfree.chart.axis: Records the label positions for a category axis.
CategoryLabelPositions() - Constructor for class org.jfree.chart.axis.CategoryLabelPositions: Default constructor.
CategoryLabelPositions(CategoryLabelPosition, CategoryLabelPosition, CategoryLabelPosition, CategoryLabelPosition) - Constructor for class org.jfree.chart.axis.CategoryLabelPositions: Creates a new position specification.
CategoryLabelWidthType - Class in org.jfree.chart.axis: Represents the width types for a category label.
CategoryPlot - Class in org.jfree.chart.plot: A general plotting class that uses data from a CategoryDataset and renders each data item using a CategoryItemRenderer.
CategoryPlot() - Constructor for class org.jfree.chart.plot.CategoryPlot: Default constructor.
CategoryPlot(CategoryDataset, CategoryAxis, ValueAxis, CategoryItemRenderer) - Constructor for class org.jfree.chart.plot.CategoryPlot: Creates a new plot.
CategorySeriesHandler - Class in org.jfree.data.xml: A handler for reading a series for a category dataset.
CategorySeriesHandler(RootHandler) - Constructor for class org.jfree.data.xml.CategorySeriesHandler: Creates a new item handler.
CategoryStepChartDemo - Class in org.jfree.chart.demo: A simple demonstration application showing how to create an area chart using data from a CategoryDataset.
CategoryStepChartDemo(String) - Constructor for class org.jfree.chart.demo.CategoryStepChartDemo: Creates a new demo application.
CategoryStepRenderer - Class in org.jfree.chart.renderer: A "step" renderer similar to XYStepRenderer but that can be used with the CategoryPlot class.
CategoryStepRenderer() - Constructor for class org.jfree.chart.renderer.CategoryStepRenderer: Creates a new renderer (stagger defaults to false).
CategoryStepRenderer(boolean) - Constructor for class org.jfree.chart.renderer.CategoryStepRenderer: Creates a new renderer.
CategoryTableXYDataset - Class in org.jfree.data: An implementation variant of the TableXYDataset where every series shares the same x-values (required for generating stacked area charts).
CategoryTableXYDataset() - Constructor for class org.jfree.data.CategoryTableXYDataset: Creates a new empty CategoryTableXYDataset.
CategoryTextAnnotation - Class in org.jfree.chart.annotations: A text annotation that can be placed on a CategoryPlot.
CategoryTextAnnotation(String, Comparable, double) - Constructor for class org.jfree.chart.annotations.CategoryTextAnnotation: Creates a new annotation to be displayed at the given location.
CategoryTick - Class in org.jfree.chart.axis: A tick for a CategoryAxis.
CategoryTick(Comparable, TextBlock, TextBlockAnchor, TextAnchor, double) - Constructor for class org.jfree.chart.axis.CategoryTick: Creates a new tick.
CategoryToolTipGenerator - Interface in org.jfree.chart.labels: A category tool tip generator is an object that can be assigned to a CategoryItemRenderer and that assumes responsibility for creating text items to be used as tooltips for the items in a CategoryPlot.
CategoryToPieDataset - Class in org.jfree.data: A PieDataset implementation that obtains its data from one row or column of a CategoryDataset.
CategoryToPieDataset(CategoryDataset, int, int) - Constructor for class org.jfree.data.CategoryToPieDataset: Deprecated.
Use the other constructor.
CategoryToPieDataset(CategoryDataset, TableOrder, int) - Constructor for class org.jfree.data.CategoryToPieDataset: An adaptor class that converts any CategoryDataset into a PieDataset, by taking the values from a single row or column.
CategoryURLGenerator - Interface in org.jfree.chart.urls: A URL generator for items in a CategoryDataset.
CategoryURLGeneratorTable - Class in org.jfree.chart.renderer: Deprecated.
This class is no longer being used in JFreeChart and will be removed before version 1.0.0 is released.
CategoryURLGeneratorTable() - Constructor for class org.jfree.chart.renderer.CategoryURLGeneratorTable: Deprecated.

Creates a new URL generator table.
CBRACE - Static variable in class org.graffiti.plugins.ios.importers.gml.sym
center - Static variable in class org.vanted.scaling.ScalingSlider
CENTER - Static variable in class info.clearthought.layout.SingleFiledLayout: Center components
CENTER - Static variable in interface info.clearthought.layout.TableLayoutConstants: Indicates that the component is centered in its cell
CENTER - Static variable in class org.jfree.chart.labels.ItemLabelAnchor: Center.
CENTER - Static variable in class org.jfree.chart.title.Title: Useful constant for the title alignment (horizontal or vertical).
CENTER_ELEMENT_LITERAL - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLConstants
CENTERED - org.AlignmentSetting
CENTERED - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Constant used to specify the position of a label according to a node.
CENTERED_FIT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Constant used to specify the position of a label according to a node.
CenterLayouterAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover: DOCTODO: Include class header
CenterLayouterAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover.CenterLayouterAlgorithm
CenterLayouterPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover
CenterLayouterPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover.CenterLayouterPlugin
centerRange(double) - Method in class org.jfree.chart.axis.CyclicNumberAxis: Centers the range about the given value.
centerRange(double) - Method in class org.jfree.chart.axis.ValueAxis: Centers the axis range about the specified value and sends an AxisChangeEvent to all registered listeners.
changeActiveMode(Mode) - Method in class org.graffiti.session.Session: Changes the active mode of this session.
ChangeAttributesEdit - Class in org.graffiti.undo: ChangeAttributesEdit
ChangeAttributesEdit(Graph, Map, Map) - Constructor for class org.graffiti.undo.ChangeAttributesEdit: Creates a new AttributeChangeEdit object.
ChangeAttributesEdit(Graph, Attribute, Map) - Constructor for class org.graffiti.undo.ChangeAttributesEdit: Creates a new AttributeChangeEdit object.
ChangeAttributeValueAction - Class in org.graffiti.editor.actions: DOCUMENT ME!
ChangeAttributeValueAction(MainFrame) - Constructor for class org.graffiti.editor.actions.ChangeAttributeValueAction: Creates a new ChangeAttributeValueAction object.
changeBoolean(String, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeBoolean(String, boolean) - Method in class org.graffiti.attributes.AbstractAttributable: Changes the Attribute at the given path to the given value.
changeBoolean(String, boolean) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
changeByte(String, byte) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeByte(String, byte) - Method in class org.graffiti.attributes.AbstractAttributable: Changes the Attribute at the given path to the given value.
changeByte(String, byte) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
changeDouble(String, double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeDouble(String, double) - Method in class org.graffiti.attributes.AbstractAttributable: Changes the Attribute at the given path to the given value.
changeDouble(String, double) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
ChangeEdgeStyle - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
ChangeEdgeStyle() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ChangeEdgeStyle
ChangeElementStyle - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
ChangeElementStyle() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ChangeElementStyle
changeFloat(String, float) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeFloat(String, float) - Method in class org.graffiti.attributes.AbstractAttributable: Sets the Attribute at the given path to the given value.
changeFloat(String, float) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
changeInteger(String, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeInteger(String, int) - Method in class org.graffiti.attributes.AbstractAttributable: Changes the Attribute at the given path to the given value.
changeInteger(String, int) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
ChangeLabelsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing: Deprecated.
ChangeLabelsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing.ChangeLabelsAlgorithm: Deprecated.
changeLong(String, long) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeLong(String, long) - Method in class org.graffiti.attributes.AbstractAttributable: Changes the Attribute at the given path to the given value.
changeLong(String, long) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
ChangeNodeStyle - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
ChangeNodeStyle() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ChangeNodeStyle
changeShort(String, short) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeShort(String, short) - Method in class org.graffiti.attributes.AbstractAttributable: Changes the Attribute at the given path to the given value.
changeShort(String, short) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
changeString(String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
changeString(String, String) - Method in class org.graffiti.attributes.AbstractAttributable: Changes the Attribute at the given path to the given value.
changeString(String, String) - Method in interface org.graffiti.attributes.Attributable: Changes the Attribute at the given path to the given value.
changeTickFontSize(int) - Method in class org.jfree.chart.plot.JThermometer: Increases or decreases the tick font size.
characters(char[], int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathXMLparser
characters(char[], int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xlsx.SheetHandler
characters(char[], int, int) - Method in class org.graffiti.plugins.ios.importers.graphml.parser.GraphMLFilter: Filter a character data event.
characters(char[], int, int) - Method in class org.jfree.data.xml.KeyHandler: Receives some (or all) of the text in the current element.
characters(char[], int, int) - Method in class org.jfree.data.xml.RootHandler: Receives some (or all) of the text in the current element.
characters(char[], int, int) - Method in class org.jfree.data.xml.ValueHandler: Receives some (or all) of the text in the current element.
CHARGE - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
CHART - org.graffiti.plugin.algorithm.Category
CHART_COMMANDS - Static variable in class org.jfree.chart.demo.JFreeChartDemoBase: CHART_COMMANDS holds information on charts that can be created Format is Name, Creation Method, Resource file prefix Steps To add a chart 1) Create a createChart method which returns a JFreeChart 2) Append details to CHART_COMMANDS 3) Append details to DemoResources
ChartAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartAttribute() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttribute
ChartAttribute(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttribute
ChartAttribute(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttribute
ChartAttributeComponent - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartAttributeComponent() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttributeComponent
ChartAttributeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartAttributeEditor(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttributeEditor
ChartAttributePlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors
ChartAttributePlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartAttributePlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartAttributePlugin
ChartAttributePlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttributePlugin
CHARTBACKGROUNDCOLOR - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
chartChanged(ChartChangeEvent) - Method in class org.jfree.chart.ChartPanel: Receives notification of changes to the chart, and redraws the chart.
chartChanged(ChartChangeEvent) - Method in class org.jfree.chart.demo.PanScrollZoomDemo: Handles a ChartChangeEvent.
chartChanged(ChartChangeEvent) - Method in interface org.jfree.chart.event.ChartChangeListener: Receives notification of a chart change event.
ChartChangeEvent - Class in org.jfree.chart.event: A change event that encapsulates information about a change to a chart.
ChartChangeEvent(Object) - Constructor for class org.jfree.chart.event.ChartChangeEvent: Creates a new chart change event.
ChartChangeEvent(Object, JFreeChart) - Constructor for class org.jfree.chart.event.ChartChangeEvent: Creates a new chart change event.
ChartChangeEvent(Object, JFreeChart, int) - Constructor for class org.jfree.chart.event.ChartChangeEvent: Creates a new chart change event.
ChartChangeListener - Interface in org.jfree.chart.event: The interface that must be supported by classes that wish to receive notification of chart events.
ChartColor - Class in org.jfree.chart: Class to extend the number of Colors available to the charts.
ChartColor(int, int, int) - Constructor for class org.jfree.chart.ChartColor: Creates a Color with an opaque sRGB with red, green and blue values in range 0-255.
ChartColorAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors: All StringAttributes with the name id "chart_colors" will be converted into a ChartColorAttribute (see ChartAttributePlugin, where the mapping information from id to class type is initialized.
ChartColorAttribute() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartColorAttribute
ChartColorAttribute(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartColorAttribute
ChartColorAttribute(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartColorAttribute
ChartColorAttributeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors
ChartColorAttributeEditor(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartColorAttributeEditor
ChartComponent - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartComponentManager - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartEntity - Class in org.jfree.chart.entity: A class that captures information about some component of a chart (a bar, line etc).
ChartEntity(Shape) - Constructor for class org.jfree.chart.entity.ChartEntity: Creates a new chart entity.
ChartEntity(Shape, String) - Constructor for class org.jfree.chart.entity.ChartEntity: Creates a new chart entity.
ChartEntity(Shape, String, String) - Constructor for class org.jfree.chart.entity.ChartEntity: Creates a new entity.
ChartFactory - Class in org.jfree.chart: A collection of utility methods for creating some standard charts with JFreeChart.
ChartFactory() - Constructor for class org.jfree.chart.ChartFactory
ChartFrame - Class in org.jfree.chart: A frame for displaying a chart.
ChartFrame(String, JFreeChart) - Constructor for class org.jfree.chart.ChartFrame: Constructs a frame for a chart.
ChartFrame(String, JFreeChart, boolean) - Constructor for class org.jfree.chart.ChartFrame: Constructs a frame for a chart.
chartMouseClicked(ChartMouseEvent) - Method in interface org.jfree.chart.ChartMouseListener: Callback method for receiving notification of a mouse click on a chart.
chartMouseClicked(ChartMouseEvent) - Method in class org.jfree.chart.demo.ScatterPlotDemo3: Callback method for receiving notification of a mouse click on a chart.
ChartMouseEvent - Class in org.jfree.chart: A mouse event for a chart that is displayed in a ChartPanel.
ChartMouseEvent(JFreeChart, MouseEvent, ChartEntity) - Constructor for class org.jfree.chart.ChartMouseEvent: Constructs a new event.
ChartMouseListener - Interface in org.jfree.chart: The interface that must be implemented by classes that wish to receive ChartMouseEvent notifications.
chartMouseMoved(ChartMouseEvent) - Method in interface org.jfree.chart.ChartMouseListener: Callback method for receiving notification of a mouse movement on a chart.
chartMouseMoved(ChartMouseEvent) - Method in class org.jfree.chart.demo.ScatterPlotDemo3: Callback method for receiving notification of a mouse movement on a chart.
ChartOptions - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent
ChartOptions() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
ChartOptions(GraphElement, Graph, BioStatisticalCategoryDataset, String, PlotOrientation, boolean, String, String, boolean, boolean, float, int, double, double, boolean, boolean, double, double, Color, Color, int, boolean, double, boolean, float, float, boolean, boolean, boolean, boolean, boolean, int, boolean, int, int, Color, Color, Color, boolean, double, boolean) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
ChartPanel - Class in org.jfree.chart: A Swing GUI component for displaying a JFreeChart object.
ChartPanel(JFreeChart) - Constructor for class org.jfree.chart.ChartPanel: Constructs a JFreeChart panel.
ChartPanel(JFreeChart, boolean) - Constructor for class org.jfree.chart.ChartPanel: Constructs a panel containing a chart.
ChartPanel(JFreeChart, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.jfree.chart.ChartPanel: Constructs a JFreeChart panel.
ChartPanel(JFreeChart, int, int, int, int, int, int, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.jfree.chart.ChartPanel: Constructs a JFreeChart panel.
ChartPanelConstants - Interface in org.jfree.chart: Useful constants for the ChartPanel class.
ChartPanelSerializationTest - Class in org.jfree.chart.demo: This demo tests the ability to serialize/deserialize a ChartPanel.
ChartPanelSerializationTest(String) - Constructor for class org.jfree.chart.demo.ChartPanelSerializationTest: A demonstration application showing how to create a simple time series chart.
CHARTPOSITION - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttribute
chartProgress(ChartProgressEvent) - Method in class org.jfree.chart.ChartPanel: Receives notification of a chart progress event.
chartProgress(ChartProgressEvent) - Method in interface org.jfree.chart.event.ChartProgressListener: Receives notification of a chart progress event.
ChartProgressEvent - Class in org.jfree.chart.event: An event that contains information about the drawing progress of a chart.
ChartProgressEvent(Object, JFreeChart, int, int) - Constructor for class org.jfree.chart.event.ChartProgressEvent: Creates a new chart change event.
ChartProgressListener - Interface in org.jfree.chart.event: The interface that must be supported by classes that wish to receive notification of chart progress events.
ChartPropertyEditPanel - Class in org.jfree.chart.ui: A panel for editing chart properties (includes subpanels for the title, legend and plot).
ChartPropertyEditPanel(JFreeChart) - Constructor for class org.jfree.chart.ui.ChartPropertyEditPanel: Standard constructor - the property panel is made up of a number of sub-panels that are displayed in the tabbed pane.
ChartRenderingInfo - Class in org.jfree.chart: A structure for storing rendering information from one call to the JFreeChart.draw() method.
ChartRenderingInfo() - Constructor for class org.jfree.chart.ChartRenderingInfo: Constructs a new ChartRenderingInfo structure that can be used to collect information about the dimensions of a rendered chart.
ChartRenderingInfo(EntityCollection) - Constructor for class org.jfree.chart.ChartRenderingInfo: Constructs a new ChartRenderingInfo structure.
ChartsColumnAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartsColumnAttribute(int) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartsColumnAttribute
ChartsColumnAttribute(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartsColumnAttribute
ChartsColumnAttribute(String, int) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartsColumnAttribute
ChartsColumnAttribute(String, Integer) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartsColumnAttribute
ChartsColumnAttributeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
ChartsColumnAttributeEditor(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartsColumnAttributeEditor
ChartTiming1 - Class in org.jfree.chart.demo: Draws a pie chart over and over for 10 seconds.
ChartTiming1() - Constructor for class org.jfree.chart.demo.ChartTiming1: Creates a new application.
ChartTiming2 - Class in org.jfree.chart.demo: Draws a scatter plot over and over for 10 seconds.
ChartTiming2() - Constructor for class org.jfree.chart.demo.ChartTiming2: Creates a new application.
ChartTiming3 - Class in org.jfree.chart.demo: Draws a scatter plot over and over for 10 seconds.
ChartTiming3() - Constructor for class org.jfree.chart.demo.ChartTiming3: Creates a new application.
ChartTiming4 - Class in org.jfree.chart.demo: Draws a scatter plot over and over for 10 seconds.
ChartTiming4() - Constructor for class org.jfree.chart.demo.ChartTiming4: Creates a new application.
chartTitle - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
ChartUtilities - Class in org.jfree.chart: A collection of utility methods for JFreeChart.
ChartUtilities() - Constructor for class org.jfree.chart.ChartUtilities
CHEBI - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter.QueryType
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.circle_search.CircleSearchAndLayoutAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.ColorizeAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.DavidTestAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.GrubbsTestAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation.BarabasiAlbertGraphGenerator
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation.ErdosRenyiGraphGenerator
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation.WattsStrogatzGraphGenerator
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance.HammingDistanceAlgorithm: Checks the preconditions of the algorithm.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.lines_as_substances.LinesToSubstancesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.NaivePatternFinderAlgorithm: Checks the preconditions of the algorithm.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.ExchangeNodePositionsAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.RatioViewAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.SubstanceRatioCalculationAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.ShortestPathSelectionAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.WeightedShortestPathSelectionAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.MultiDataView
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOMclusterAnalysis
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOMclusterAnalysisDoCluster
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.AddDiagramLegendAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.ColorScaleLegendAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.ExtractMappingDataAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.RemoveMappingDataAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.CombineMappingData
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram.ClusterHistogramFisherTest
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go.CreateGOtreeAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction.CreateKeggReactionNetworkAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.ReplaceDiagramTitleFromAlternativeSubstanceNames
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectCompoundsAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectEdgesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectEnzymesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectGenesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectMapNodesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectMapTitleNodesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectNodesWithExperimentalDataAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands.SelectReactionsAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.CloseAllWindows
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.EvaluateKGML
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.RecreateView
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.ColorizeSuperGraphAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.CreateOrgSpecificSuperGraphsAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.SelectWindowsAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate.RotateAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.set_background_color.WindowSettings: DOCTODO: Include method header
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.startlayout.StartLayoutAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ApplyGraphLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterAlgorithm: Checks, if a graph was given and that the radius is positive.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterWithMinimumCrossingsAlgorithm: Checks, if a graph was given and that the radius is positive.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.DotLayoutAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components.ConnectedComponentLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout.CopyPatternLayoutAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_no_overlapp.NoOverlappLayoutAlgorithm: Checks, if a graph was given and that the radius is positive.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_reduce_space.ExpandReduceLayouterAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fd_edge_routing.ForceDirectedEdgeLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye.FishEyeLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover.CenterLayouterAlgorithm: DOCTODO: Include method header
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover.NoOverlappOfClustersAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement.GridPlacementAlgorithm: Checks, if a graph was given.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid.GridLayouterAlgorithm: Checks parameters
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.no_overlapp_as_tim.NoOverlappLayoutAlgorithmAS: Checks, if a graph was given and that the radius is positive.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache.PatternSpringembedder: Error Checking
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.BringToFrontOrBackAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.BundleParallelEdges
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterGraphLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterIndividualLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.DuplicateEdge
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.IntroduceBendsAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.IntroduceParallelEdgeBends
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.IntroduceSelfEdgeBends
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.PajekClusterColor
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.RemoveBendsAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.RemoveParallelEdges
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ResetEdgeSourceOrTarget
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ResizeNodesDepDegreeAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.SelectClusterAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.SetClusterInfoAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.SetClusterInfoFromLabelAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.SetClusterInfoFromSubgraphAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ShowClusterGraphAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PatternSpringembedder: Error Checking
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PatternSpringembedder3d: Error Checking
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree.RadialTreeLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random.RandomLayouterAlgorithm: Checks, if a graph was given.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.ArrayLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.GridLayoutAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.ResizeFromMappingCountLayoutAlgorithm: Checks parameters
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree.RTTreeLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.springembedder_1.SpringEmbedderAlgorithm: Error Checking
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple.GraphTreeLayout
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup.NumberNodesAndEdgesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy.HideOrShowChildNodes
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.RemoveSelectedNodesPreserveEdgesAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SetToolTipAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SetURLAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayReferenceAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayReferenceAutoCreationAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer.PrintAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids.ReplaceLabelFromAlternativeSubstanceNames
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.scripting.BeanShellDesktopAlgorithm: No special checks implemented.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PDFAlgorithm: Unused for this plugin.
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm
check() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.SVGAlgorithm: Unused for this plugin.
check() - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm
check() - Method in interface org.graffiti.plugin.algorithm.Algorithm: Checks whether all preconditions of the current graph are satisfied.
check() - Method in class org.vanted.plugins.layout.adaptagrams.edgerouting.EdgeRoutingAlgorithm: Check preconditions: (1) a graph with edges, (2) native layout library can be loaded.
check() - Method in class org.vanted.plugins.layout.multilevelframework.ForceDirectedLayoutWrapper
check() - Method in class org.vanted.plugins.layout.multilevelframework.MultilevelFrameworkLayout: Checks, if a graph was given and that the radius is positive.
check() - Method in class org.vanted.plugins.layout.stressminimization.BackgroundExecutionAlgorithm
check() - Method in class org.vanted.plugins.layout.stressminimization.StressMinimizationLayout: Checks whether all preconditions of the current graph are satisfied.
checkAddAndSetClassesPreferences(PreferencesInterface) - Method in class org.graffiti.managers.PreferenceManager: This method will do several things, that are repeatedly done to get possibly existing Preferences and add the class to the list of Preferencing Classes and also call the implementing object for first-time setup during startup of the program
checkAndAddAGNWContainer(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the top level container attribute "AGNW" to the given edge, if it is not already there.
checkAndAddAGNWContainer(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the top level container attribute "AGNW" to the given graph, if it is not already there.
checkAndAddAGNWContainer(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the top level container attribute "AGNW" to the given node, if it is not already there.
checkAndAddPattern(Edge, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container for the pattern position to the given edge, if it is not already there.
checkAndAddPattern(Node, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container for the pattern position to the given node, if it is not already there.
checkAndAddPatternContainer(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container attribute "AGNW.PATTERN" to the given edge, if it is not already there.
checkAndAddPatternContainer(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container attribute "AGNW.PATTERN" to the given graph, if it is not already there.
checkAndAddPatternContainer(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container attribute "AGNW.PATTERN" to the given node, if it is not already there.
checkAndChangePath(String, Attribute) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImageAttributeComponent
checkAndUpdateLink(Preferences, String, String, String) - Static method in class org.vanted.updater.PreferencesUpdater: Update any deeply stored preferences values.
checkAndUpdateMonashLink(Preferences, String, String) - Static method in class org.vanted.updater.PreferencesUpdater: Deprecated.
checkColor() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.label_alignment.PositionButton
checkComponent(Component) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ReColorBars
checkConstraints() - Method in class org.graffiti.session.GraphConstraintChecker: Checks whether all constraints are satisfied on the specified graph.
checkDistanceAndMemorizePossibleSourceElement(GraphElement, double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.WeightedDistanceInfo
checkEnableOK(ListSelectionEvent) - Method in class org.graffiti.editor.ViewTypeChooser: Updates the ok button.
checkEnableOK(ListSelectionEvent) - Method in class org.graffiti.managers.pluginmgr.PluginSelector: Updates the ok button.
checkEventDispatchThread() - Static method in class org.graffiti.editor.GravistoService: Prints a log message in case this method is not called on the Event Dispatch Thread.
checkExistenceAGNWContainer(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the top level container attribute "AGNW" exists at the given edge.
checkExistenceAGNWContainer(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the top level container attribute "AGNW" exists at the given graph.
checkExistenceAGNWContainer(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the top level container attribute "AGNW" exists at the given node.
checkExistenceOfAnyPattern(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks if a pattern exists at the given edge.
checkExistenceOfAnyPattern(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks if a pattern exists at the given node.
checkExistencePattern(Edge, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the pattern container for the pattern position exists at the given edge.
checkExistencePattern(Node, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the pattern container for the pattern position exists at the given node.
checkExistencePatternContainer(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the pattern container attribute "AGNW.PATTERN" exists at the given edge.
checkExistencePatternContainer(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the pattern container attribute "AGNW.PATTERN" exists at the given graph.
checkExistencePatternContainer(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Checks, if the pattern container attribute "AGNW.PATTERN" exists at the given node.
checkExistingPreferences(Class<?>, List<? extends Parameter>) - Method in class org.graffiti.managers.PreferenceManager: if no preferences found, create a new preferences object from default parameters.
checkFailed(String) - Method in interface org.graffiti.session.ConstraintCheckerListener: Handles the message received by the constraint checker indicating an unsatisfied constraint.
checkFailed(String) - Method in class org.graffiti.session.Session: Handles the failed constraint check.
checkMaxGraphElementId(long) - Method in class org.graffiti.graph.AdjListGraph: Deprecated.
checkMaxGraphElementId(long) - Method in interface org.graffiti.graph.Graph
checkRSSfile() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.RSSFeedManager
checkStatusForAllToolButtons() - Static method in class org.graffiti.plugin.gui.ToolButton
CheckTreeCellRenderer - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui
CheckTreeCellRenderer(TreeCellRenderer, CheckTreeSelectionModel) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui.CheckTreeCellRenderer
CheckTreeManager - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui
CheckTreeManager(JTree) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui.CheckTreeManager
CheckTreeSelectionModel - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui: You can ask the the above selection model whether B is selected as below: checkSelectionModel.isPathSelected(getPath(B), true); // the second argument tells that selection is to be digged.
CheckTreeSelectionModel(TreeModel) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui.CheckTreeSelectionModel
CheckUpdateDate - Class in org.vanted.updater
CheckUpdateDate() - Constructor for class org.vanted.updater.CheckUpdateDate
checkVisibility(int) - Method in class org.graffiti.plugin.attributecomponent.AbstractAttributeComponent: Attribute components can use this method to check if they are or should be visible in the view.
checkZoom() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm
checkZoom() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.SVGAlgorithm
chooseClassToPutAttributesToModell(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UtilityClassSelectorFromGraph
chooseClassToPutAttributesToNodes(GraphElement, Object) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UtilityClassSelectorToGraph
chooseClassToPutAttributesToNodes(GraphElement, Object) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UtilityClassSelectorToGraph
CHORD - Static variable in class org.jfree.chart.plot.DialShape: Chord.
circle - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.kgmlGraphicsType
CIRCLE - org.LabelFrameSetting
CIRCLE - Static variable in class org.jfree.chart.plot.DialShape: Circle.
CIRCLE_CLASSNAME - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: circle node shape class name
CIRCLE_FILLED - org.LabelFrameSetting
CIRCLE_HALF_FILLED - org.LabelFrameSetting
circleArrow - Static variable in class org.graffiti.plugins.editcomponents.defaults.EdgeArrowShapeEditComponent
CircleArrowShape - Class in org.graffiti.plugins.views.defaults
CircleArrowShape() - Constructor for class org.graffiti.plugins.views.defaults.CircleArrowShape
CircleArrowShape(float) - Constructor for class org.graffiti.plugins.views.defaults.CircleArrowShape
circleConnectArrow - Static variable in class org.graffiti.plugins.editcomponents.defaults.EdgeArrowShapeEditComponent
CircleConnectArrowShape - Class in org.graffiti.plugins.views.defaults
CircleConnectArrowShape() - Constructor for class org.graffiti.plugins.views.defaults.CircleConnectArrowShape
CircleConnectArrowShape(float) - Constructor for class org.graffiti.plugins.views.defaults.CircleConnectArrowShape
CircleDrawer - Class in org.jfree.chart.demo: An implementation of the Drawable interface, to illustrate the use of the XYDrawableAnnotation class.
CircleDrawer(Paint, Stroke, Paint) - Constructor for class org.jfree.chart.demo.CircleDrawer: Creates a new instance.
CircleLayouterAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle: Places all nodes on a circle with a user specified radius.
CircleLayouterAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterAlgorithm: Creates a new CircleLayouterAlgorithm object.
CircleLayouterAlgorithm(double) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterAlgorithm: Creates a new CircleLayouterAlgorithm object.
CircleLayouterPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle: Plugin container for the CircleLayoutAlgorithm.
CircleLayouterPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterPlugin: Creates a new CircleLayouterPlugin object.
CircleLayouterWithMinimumCrossingsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle: Places all nodes on a circle with a user specified radius.
CircleLayouterWithMinimumCrossingsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterWithMinimumCrossingsAlgorithm: Creates a new CircleLayouterAlgorithm object.
CircleLayouterWithMinimumCrossingsAlgorithm(double) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterWithMinimumCrossingsAlgorithm: Creates a new CircleLayouterAlgorithm object.
CircleNodeShape - Class in org.graffiti.plugins.views.defaults: Class representing a circle.
CircleNodeShape() - Constructor for class org.graffiti.plugins.views.defaults.CircleNodeShape: The constructor creates a circle using default values.
CircleSearchAndLayoutAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.circle_search: Searches for circular sub-graphs and optionally applies a CircleLayouter.
CircleSearchAndLayoutAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.circle_search.CircleSearchAndLayoutAlgorithm
CircularNodeShape - Class in org.graffiti.plugins.views.defaults: Concrete class representing an ellipse.
CircularNodeShape() - Constructor for class org.graffiti.plugins.views.defaults.CircularNodeShape: The constructor creates an ellipse using default values.
claimNodePositions() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.AreaManager
clamp(int) - Static method in class org.graffiti.editor.GaussFilter
CLASS - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule
ClassesAll - Class in qmwi.kseg.som.diagram: Insert the type's description here.
ClassesAll() - Constructor for class qmwi.kseg.som.diagram.ClassesAll: AllClasses constructor comment.
ClassesClass - Class in qmwi.kseg.som.diagram: Insert the type's description here.
ClassesClass() - Constructor for class qmwi.kseg.som.diagram.ClassesClass: SomClass constructor comment.
ClassesClass(int) - Constructor for class qmwi.kseg.som.diagram.ClassesClass: SomClass constructor comment.
ClassesNeuron - Class in qmwi.kseg.som.diagram: Insert the type's description here.
ClassesNeuron() - Constructor for class qmwi.kseg.som.diagram.ClassesNeuron: Insert the method's description here.
ClassesNeuron(int) - Constructor for class qmwi.kseg.som.diagram.ClassesNeuron: Insert the method's description here.
ClassesObject - Class in qmwi.kseg.som.diagram: Insert the type's description here.
ClassesObject(int) - Constructor for class qmwi.kseg.som.diagram.ClassesObject: Insert the method's description here.
ClassesObjectInputVector - Class in qmwi.kseg.som.diagram: Insert the type's description here.
ClassesObjectInputVector() - Constructor for class qmwi.kseg.som.diagram.ClassesObjectInputVector: Insert the method's description here.
ClassesObjectInputVector(int, int, double[]) - Constructor for class qmwi.kseg.som.diagram.ClassesObjectInputVector: Insert the method's description here.
ClassPathAttributeCollector - Class in org.graffiti.plugins.inspectors.defaults: Searches for attributes in the current CLASSPATH.
ClassPathAttributeCollector() - Constructor for class org.graffiti.plugins.inspectors.defaults.ClassPathAttributeCollector
ClassPathPluginDescriptionCollector - Class in org.graffiti.managers.pluginmgr: Searches for plugin description files in the current CLASSPATH.
ClassPathPluginDescriptionCollector() - Constructor for class org.graffiti.managers.pluginmgr.ClassPathPluginDescriptionCollector: Constructs a new class path plugin description collector.
clear() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
clear() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
clear() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
clear() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
clear() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
clear() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
clear() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
clear() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
clear() - Method in class org.graffiti.editor.StatusBar: Clears the current text of the status bar.
clear() - Method in class org.graffiti.graph.AbstractGraph: Deletes the current graph by resetting all its attributes.
clear() - Method in interface org.graffiti.graph.Graph: Deletes the current Graph by resetting all its attributes.
clear() - Method in class org.graffiti.options.GravistoPreferences
clear() - Method in class org.graffiti.selection.Selection: Remove all elements from this selection.
clear() - Method in class org.graffiti.util.Queue
clear() - Method in class org.jfree.chart.ChartRenderingInfo: Clears the information recorded by this object.
clear() - Method in interface org.jfree.chart.entity.EntityCollection: Clears all entities.
clear() - Method in class org.jfree.chart.entity.StandardEntityCollection: Clears the entities.
clear() - Method in class org.jfree.data.DefaultCategoryDataset: Clears all data from the dataset and sends a DatasetChangeEvent to all registered listeners.
clear() - Method in class org.jfree.data.DefaultKeyedValues2D: Clears all the data and associated keys.
clear() - Method in class org.jfree.data.time.TimeSeries: Removes all data items from the series and sends a SeriesChangeEvent to all registered listeners.
clear() - Method in class org.jfree.data.XYSeries: Removes all data items from the series.
clear() - Method in class placement.RectangleDrawerPanel
clearAnnotations() - Method in class org.jfree.chart.plot.ContourPlot: Clears all the annotations.
clearAnnotations() - Method in class org.jfree.chart.plot.XYPlot: Clears all the annotations and sends a PlotChangeEvent to all registered listeners.
clearAttributeComponentList() - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface: Removes all entries in the attributeComponent list.
clearAttributeComponentList() - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Removes all entries in the attributeComponent list.
clearCategoryLabelToolTips() - Method in class org.jfree.chart.axis.CategoryAxis: Clears the category label tooltips and sends an AxisChangeEvent to all registered listeners.
clearComponents() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView
clearCornerTextItem() - Method in class org.jfree.chart.plot.PolarPlot: Clear the list of corner text items.
clearDataset() - Method in class org.jfree.data.statistics.HistogramDataset
clearDependentComponentList() - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface: Removes a GraphElementComponent from the list of dependent GraphElementComponents.
clearDependentComponentList() - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Removes a GraphElementComponent from the list of dependent GraphElementComponents.
clearDomainAxes() - Method in class org.jfree.chart.plot.CategoryPlot: Clears the domain axes from the plot and sends a PlotChangeEvent to all registered listeners.
clearDomainAxes() - Method in class org.jfree.chart.plot.XYPlot: Clears the domain axes from the plot and sends a PlotChangeEvent to all registered listeners.
clearDomainMarkers() - Method in class org.jfree.chart.plot.ContourPlot: Clears all the domain markers.
clearDomainMarkers() - Method in class org.jfree.chart.plot.XYPlot: Clears all the (foreground and background) domain markers and sends a PlotChangeEvent to all registered listeners.
clearEntries() - Method in class qmwi.kseg.som.DataSet: Clears the dataset, use addEntry to fill it again.
clearErrorMessages() - Static method in class org.ErrorMsg: Removes the current error messages.
clearGraphElementComponentMap() - Method in class org.graffiti.plugin.view.AbstractView
clearGuiComponentList() - Method in class org.FolderPanel: Removes all current known GUI component rows from the internal list.
clearItems() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.MyDynamicObjectListModel
clearModifiedPool() - Method in class org.vanted.scaling.ComponentRegulator: Reset the supporting data structure for reuse.
clearRangeAxes() - Method in class org.jfree.chart.plot.CategoryPlot: Clears the range axes from the plot and sends a PlotChangeEvent to all registered listeners.
clearRangeAxes() - Method in class org.jfree.chart.plot.XYPlot: Clears the range axes from the plot and sends a PlotChangeEvent to all registered listeners.
clearRangeMarkers() - Method in class org.jfree.chart.plot.CategoryPlot: Clears all the range markers for the plot and sends a PlotChangeEvent to all registered listeners.
clearRangeMarkers() - Method in class org.jfree.chart.plot.ContourPlot: Clears all the range markers.
clearRangeMarkers() - Method in class org.jfree.chart.plot.XYPlot: Clears all the range markers and sends a PlotChangeEvent to all registered listeners.
clearRangeMarkers(int) - Method in class org.jfree.chart.plot.CategoryPlot: Clears all the range markers for the specified renderer.
clearRangeMarkers(int) - Method in class org.jfree.chart.plot.XYPlot: Clears the (foreground and background) range markers for a particular renderer.
clearScalersMap() - Method in class org.vanted.scaling.ComponentRegulator: Reset the supporting data structure for reuse.
clearSelection() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
ClearSelection - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
ClearSelection() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ClearSelection
clearSynonyms() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
clearSynonyms() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
CLICK_TOLERANCE - Static variable in interface org.graffiti.plugin.view.EdgeShape: The allowed distance of a mouse click from an edge where the edge is still selected.
ClickableHTMLtableCellRenderer - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.addons
ClickableHTMLtableCellRenderer() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.ClickableHTMLtableCellRenderer
ClickableInspectorLabel - Class in org.graffiti.plugins.inspectors.defaults
ClickableInspectorLabel(String, Runnable) - Constructor for class org.graffiti.plugins.inspectors.defaults.ClickableInspectorLabel
ClickableInspectorLabel(String, ClickableInspectorLabel) - Constructor for class org.graffiti.plugins.inspectors.defaults.ClickableInspectorLabel
ClipboardService - Class in org.graffiti.editor.actions
ClipboardService() - Constructor for class org.graffiti.editor.actions.ClipboardService
ClipPath - Class in org.jfree.chart: This class would typically be used with a ContourPlot.
ClipPath() - Constructor for class org.jfree.chart.ClipPath: Constructor for ClipPath.
ClipPath(double[], double[]) - Constructor for class org.jfree.chart.ClipPath: Constructor for ClipPath.
ClipPath(double[], double[], boolean, boolean, boolean) - Constructor for class org.jfree.chart.ClipPath: Constructor for ClipPath.
ClipPath(double[], double[], boolean, boolean, Paint, Paint, Stroke, Composite) - Constructor for class org.jfree.chart.ClipPath: Constructor for ClipPath.
clone() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.UllmannSubraphIsomAdjMatrixState
clone() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
clone() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentHeader
clone() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentHeaderInterface
clone() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
clone() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
clone() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
clone() - Method in class org.graffiti.selection.Selection
clone() - Method in class org.jfree.chart.annotations.CategoryTextAnnotation: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.annotations.XYDrawableAnnotation: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.annotations.XYImageAnnotation: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.annotations.XYLineAnnotation: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.annotations.XYPointerAnnotation: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.annotations.XYTextAnnotation: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.axis.Axis: Returns a clone of the axis.
clone() - Method in class org.jfree.chart.axis.AxisSpace: Returns a clone of the object.
clone() - Method in class org.jfree.chart.axis.CategoryAxis: Creates a clone of the axis.
clone() - Method in class org.jfree.chart.axis.CategoryAxis3D: Returns a clone of the axis.
clone() - Method in class org.jfree.chart.axis.ColorBar: Returns a clone of the object.
clone() - Method in class org.jfree.chart.axis.DateAxis: Returns a clone of the object.
clone() - Method in class org.jfree.chart.axis.NumberAxis: Returns a clone of the axis.
clone() - Method in class org.jfree.chart.axis.SegmentedTimeline: Returns a clone of the timeline.
clone() - Method in class org.jfree.chart.axis.Tick: Returns a clone of the tick.
clone() - Method in class org.jfree.chart.axis.TickUnits: Returns a clone of the collection.
clone() - Method in class org.jfree.chart.axis.ValueAxis: Returns a clone of the object.
clone() - Method in class org.jfree.chart.ChartRenderingInfo: Returns a clone of this object.
clone() - Method in class org.jfree.chart.ClipPath: Returns a clone of the object (a deeper clone than default to avoid bugs when setting values in cloned object).
clone() - Method in class org.jfree.chart.demo.SampleXYSymbolicDataset: Clone the SampleXYSymbolicDataset object
clone() - Method in class org.jfree.chart.demo.SampleYSymbolicDataset: Clone the SampleYSymbolicDataset object
clone() - Method in class org.jfree.chart.entity.ChartEntity: Returns a clone of the entity.
clone() - Method in class org.jfree.chart.entity.ContourEntity: Returns a clone of the entity.
clone() - Method in class org.jfree.chart.entity.LegendItemEntity: Returns a clone of the entity.
clone() - Method in class org.jfree.chart.entity.StandardEntityCollection: Returns a clone.
clone() - Method in class org.jfree.chart.JFreeChart: Clones the object, and takes care of listeners.
clone() - Method in class org.jfree.chart.labels.AbstractCategoryItemLabelGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.labels.AbstractXYItemLabelGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.labels.CustomXYToolTipGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.labels.HighLowItemLabelGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.labels.StandardPieItemLabelGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.labels.StandardXYLabelGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.labels.StandardXYToolTipGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.labels.SymbolicXYItemLabelGenerator: Returns an independent copy of the generator.
clone() - Method in class org.jfree.chart.plot.CategoryPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.CombinedDomainCategoryPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.CombinedDomainXYPlot: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.plot.CombinedRangeCategoryPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.CombinedRangeXYPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.CompassPlot: Returns a clone of the annotation.
clone() - Method in class org.jfree.chart.plot.ContourPlot: Extends plot cloning to this plot type
clone() - Method in class org.jfree.chart.plot.DefaultDrawingSupplier: Returns a clone.
clone() - Method in class org.jfree.chart.plot.FastScatterPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.IntervalMarker: Returns a clone of the marker.
clone() - Method in class org.jfree.chart.plot.MeterPlot: Correct cloning support, management of deeper copies and listeners
clone() - Method in class org.jfree.chart.plot.PiePlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.Plot: Creates a clone of the plot.
clone() - Method in class org.jfree.chart.plot.PlotRenderingInfo: Returns a clone of this object.
clone() - Method in class org.jfree.chart.plot.PolarPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.ThermometerPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.plot.XYPlot: Returns a clone of the plot.
clone() - Method in class org.jfree.chart.renderer.AbstractCategoryItemRenderer: Returns an independent copy of the renderer.
clone() - Method in class org.jfree.chart.renderer.AreaRenderer: Returns an independent copy of the renderer.
clone() - Method in class org.jfree.chart.renderer.AreaXYRenderer: Deprecated.

Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.CandlestickRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.ClusteredXYBarRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.HighLowRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.LineAndShapeRenderer: Returns an independent copy of the renderer.
clone() - Method in class org.jfree.chart.renderer.SignalRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.StackedXYAreaRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.StackedXYAreaRenderer2: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.StandardXYItemRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.WindItemRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYAreaRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYAreaRenderer2: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYBarRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYBoxAndWhiskerRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYBubbleRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYDifferenceRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYDotRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYLineAndShapeRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYStepAreaRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.XYStepRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.renderer.YIntervalRenderer: Returns a clone of the renderer.
clone() - Method in class org.jfree.chart.title.TextTitle: Returns a clone of this object.
clone() - Method in class org.jfree.chart.title.Title: Returns a clone of the title.
clone() - Method in class org.jfree.chart.ui.ColorPalette: Returns a clone of the palette.
clone() - Method in interface org.jfree.chart.urls.CategoryURLGenerator: Returns an independent copy of the URL generator.
clone() - Method in class org.jfree.chart.urls.CustomPieURLGenerator: Returns a clone of the generator.
clone() - Method in class org.jfree.chart.urls.StandardCategoryURLGenerator: Returns an independent copy of the URL generator.
clone() - Method in class org.jfree.data.AbstractDataset: Returns a clone of the dataset.
clone() - Method in class org.jfree.data.DatasetGroup: Clones the group.
clone() - Method in class org.jfree.data.DefaultKeyedValue: Returns a clone.
clone() - Method in class org.jfree.data.DefaultKeyedValueDataset: Creates a clone of the dataset.
clone() - Method in class org.jfree.data.DefaultKeyedValues: Returns a clone.
clone() - Method in class org.jfree.data.DefaultKeyedValues2D: Returns a clone.
clone() - Method in class org.jfree.data.DefaultPieDataset: Returns a clone.
clone() - Method in class org.jfree.data.KeyedObject: Returns a clone of this object.
clone() - Method in class org.jfree.data.KeyedObjects: Returns a clone of this object.
clone() - Method in class org.jfree.data.KeyedObjects2D: Returns a clone.
clone() - Method in class org.jfree.data.KeyToGroupMap: Returns a clone of the map.
clone() - Method in class org.jfree.data.Series: Returns a clone of the series.
clone() - Method in class org.jfree.data.statistics.HistogramBin: Returns a clone of the bin.
clone() - Method in class org.jfree.data.statistics.HistogramDataset: Returns a clone of the dataset.
clone() - Method in class org.jfree.data.time.TimePeriodValue: Clones the data pair.
clone() - Method in class org.jfree.data.time.TimePeriodValues: Returns a clone of the collection.
clone() - Method in class org.jfree.data.time.TimeSeries: Returns a clone of the time series.
clone() - Method in class org.jfree.data.time.TimeSeriesDataItem: Clones the data item.
clone() - Method in class org.jfree.data.XYDataItem: Returns a clone of this object.
clone() - Method in class org.jfree.data.XYSeries: Returns a clone of the series.
clone(ConditionInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
clone(ConditionInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
clone(SampleInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NumericMeasurement
clone(SampleInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NumericMeasurementInterface
clone(SubstanceInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
clone(SubstanceInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
cloneOldStyle() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
CloneViewAction - Class in org.graffiti.editor.actions: Represents an action, which can clone the current view.
CloneViewAction() - Constructor for class org.graffiti.editor.actions.CloneViewAction: Constructs a new clone view action.
close() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.ManageAddonDialog
close() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView
close() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.IPKGraffitiView
close() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView
close() - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.MyOutputStream
close() - Method in class org.graffiti.managers.pluginmgr.PluginManagerDialog: Called, iff the user presses the "close" button.
close() - Method in class org.graffiti.plugin.view.AbstractView: Closes the current view.
close() - Method in interface org.graffiti.plugin.view.View: Closes the current view.
close() - Method in class org.graffiti.plugins.ios.exporters.graphml.Base64.OutputStream: Flushes and closes (I think, in the superclass) the stream.
close() - Method in class org.graffiti.plugins.ios.importers.graphml.parser.Base64.OutputStream: Flushes and closes (I think, in the superclass) the stream.
close() - Method in class org.graffiti.plugins.views.defaults.GraffitiView: Closes the current view.
close() - Method in class org.graffiti.plugins.views.matrix.MatrixView
close() - Method in class org.graffiti.session.Session: Closes this session.
close() - Method in class org.jfree.data.JDBCPieDataset: Close the database connection
close() - Method in class org.jfree.data.JDBCXYDataset: Close the database connection
CLOSE - Static variable in class org.jfree.chart.renderer.HighLow: Useful constant for open/close value types.
CloseAllWindows - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools
CloseAllWindows() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.CloseAllWindows
closeAndCancel() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.FontChooser
closeAndSave() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.FontChooser
closeDialogBeforeExecution(Algorithm) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOManalysis
closeDialogBeforeExecution(Algorithm) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui.LaunchGui
closeDialogBeforeExecution(Algorithm) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterOverviewNetworkLaunchGui
closeDialogBeforeExecution(Algorithm) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.SetClusterLaunchGui
closeDialogBeforeExecution(Algorithm) - Method in interface org.graffiti.plugin.algorithm.ProvidesAccessToOtherAlgorithms
closeDialogBeforeExecution(Algorithm) - Method in class vanted_feature.SelectAlgorithm: Deprecated.
closeGravisto() - Method in class org.graffiti.editor.MainFrame
closeParentDialog(Component) - Static method in class org.FolderPanel
closeSession(Session) - Method in class org.graffiti.editor.MainFrame: Closes all views of the given session and removes the session from the list of sessions.
closeSession(Session) - Method in interface org.graffiti.session.SessionManager: Removes the given session from the list of sessions.
CloseViewAction - Class in org.graffiti.editor.actions: Represents a clone view action.
CloseViewAction() - Constructor for class org.graffiti.editor.actions.CloseViewAction: Constructs a new close view action.
closeWriter() - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
closing(AWTEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView
closing(AWTEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView
closing(AWTEvent) - Method in class org.graffiti.plugin.view.AbstractView
closing(AWTEvent) - Method in interface org.graffiti.plugin.view.View
CLUSTER - org.graffiti.plugin.algorithm.Category
CLUSTER_ANALYSIS_NAME - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.helper.DBEgravistoHelper
CLUSTER_ANALYSIS_VERSION - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.helper.DBEgravistoHelper
cluster2color - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.ClusterBackgroundDraw
ClusterAnalysisMain - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart: Contains the graffiti editor.
ClusterAnalysisMain() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.ClusterAnalysisMain: Constructs a new instance of the editor.
ClusterBackgroundDraw - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview
ClusterBackgroundDraw() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.ClusterBackgroundDraw
ClusterColorAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors: All StringAttributes with the name id "chart_colors" will be converted into a ChartColorAttribute (see ChartAttributePlugin, where the mapping information from id to class type is initialized.
ClusterColorAttribute() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttribute
ClusterColorAttribute(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttribute
ClusterColorAttribute(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttribute
ClusterColorAttributeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors
ClusterColorAttributeEditor(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttributeEditor
ClusterColorAttributePlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors
ClusterColorAttributePlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttributePlugin
ClusterColorParameter - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors
ClusterColorParameter(Object, String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorParameter
ClusteredXYBarRenderer - Class in org.jfree.chart.renderer: An extension of XYBarRenderer that displays bars for different series values at the same x next to each other.
ClusteredXYBarRenderer() - Constructor for class org.jfree.chart.renderer.ClusteredXYBarRenderer: Default constructor.
ClusteredXYBarRenderer(double, boolean) - Constructor for class org.jfree.chart.renderer.ClusteredXYBarRenderer: Constructs a new XY clustered bar renderer.
ClusterGraphLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
ClusterGraphLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterGraphLayout
ClusterHelperToolbarComponent - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar: DOCUMENT ME!
ClusterHelperToolbarComponent(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.ClusterHelperToolbarComponent
ClusterHistogramFisherTest - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram
ClusterHistogramFisherTest() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram.ClusterHistogramFisherTest
ClusterIndividualLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
ClusterIndividualLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterIndividualLayout
ClusterOverviewNetworkLaunchGui - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
ClusterOverviewNetworkLaunchGui() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterOverviewNetworkLaunchGui
ClusterSplashScreen - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart
ClusterSplashScreen(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.ClusterSplashScreen
cm - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.SizeSettingDPIunit
CoarsenedGraph - Interface in org.vanted.plugins.layout.multilevelframework: Adds a method to get the MergedNodes of a coarsening level to the Graph interface.
col1 - Variable in class info.clearthought.layout.TableLayoutConstraints: Cell in which the upper left corner of the component lays
col2 - Variable in class info.clearthought.layout.TableLayoutConstraints: Cell in which the lower right corner of the component lays
COLLAPSE_PATHWAY - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.KeggNavigationToolbarCommand.Command
collapsePathway(Graph, String, Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.pathway_kegg_operation.PathwayKeggLoading
collectAttributes() - Method in class org.graffiti.plugins.inspectors.defaults.ClassPathAttributeCollector: Collects all attributes from the given class path.
CollectionAttribute - Interface in org.graffiti.attributes: Contains a Collection of Attributes.
collectPluginDescriptions() - Method in class org.graffiti.managers.pluginmgr.ClassPathPluginDescriptionCollector: Collects all plugin description files from the given class path.
collectPluginDescriptions() - Method in interface org.graffiti.managers.pluginmgr.PluginDescriptionCollector: Returns an enumeration of PluginEntrys.
COLOR - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
Color_CIE_Lab - Class in org.color
Color_CIE_Lab(double, double, double) - Constructor for class org.color.Color_CIE_Lab
ColorAnimation - Class in org.vanted.animation.animations: Animates the color of an Attributable object.
ColorAnimation(Attributable, List<ColorTimePoint>, double) - Constructor for class org.vanted.animation.animations.ColorAnimation: Uses RGB interpolation
ColorAnimation(Attributable, List<ColorTimePoint>, double, double) - Constructor for class org.vanted.animation.animations.ColorAnimation: Uses RGB interpolation
ColorAnimation(Attributable, List<ColorTimePoint>, double, double, int) - Constructor for class org.vanted.animation.animations.ColorAnimation: Uses RGB interpolation
ColorAnimation(Attributable, List<ColorTimePoint>, double, double, int, Looper) - Constructor for class org.vanted.animation.animations.ColorAnimation: Uses RGB interpolation
ColorAnimation(Attributable, List<ColorTimePoint>, double, double, int, Looper, Interpolator) - Constructor for class org.vanted.animation.animations.ColorAnimation: Uses RGB interpolation
ColorAnimation(Attributable, List<ColorTimePoint>, double, double, int, Looper, Interpolator, ColorMode) - Constructor for class org.vanted.animation.animations.ColorAnimation
ColorAttribute - Class in org.graffiti.graphics: Contains the color graphic attribute.
ColorAttribute(String) - Constructor for class org.graffiti.graphics.ColorAttribute: Constructs a new ColorAttribute.
ColorAttribute(String, int, int, int, int) - Constructor for class org.graffiti.graphics.ColorAttribute: Constructs a new ColorAttribute and initialises with the given values.
ColorAttribute(String, Color) - Constructor for class org.graffiti.graphics.ColorAttribute: Constructs a new ColorAttribute.
ColorAttribute(String, ColorAttribute) - Constructor for class org.graffiti.graphics.ColorAttribute: Constructs a new ColorAttribute.
ColorBar - Class in org.jfree.chart.axis: A color bar.
ColorBar(String) - Constructor for class org.jfree.chart.axis.ColorBar: Constructs a horizontal colorbar axis, using default values where necessary.
ColorBarPropertyEditPanel - Class in org.jfree.chart.ui: A ColorBarPropertyEditPanel.
ColorBarPropertyEditPanel(ColorBar) - Constructor for class org.jfree.chart.ui.ColorBarPropertyEditPanel: Creates a new edit panel for a color bar.
ColorChooserEditComponent - Class in org.graffiti.plugins.editcomponents.defaults: This class provides an edit component for editing color attributes by offering a JColorChooser.
ColorChooserEditComponent(Displayable) - Constructor for class org.graffiti.plugins.editcomponents.defaults.ColorChooserEditComponent: Constructs a new ColorChooserEditComponent.
ColorHelper - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms
ColorHelper(Graph) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ColorHelper
ColorizeAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest
ColorizeAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.ColorizeAlgorithm
colorizeEnzymesGlycansCompounds(Graph, String, Color, boolean, boolean, boolean, boolean, boolean, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggService
colorizeNodes(List<Node>, Color, Color, double, double, double, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.ColorizeAlgorithm
ColorizeSuperGraphAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar
ColorizeSuperGraphAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.ColorizeSuperGraphAlgorithm
ColorMode - Enum in org.vanted.animation.data
ColorPalette - Class in org.jfree.chart.ui: Defines palette used in Contour Plots.
ColorPalette() - Constructor for class org.jfree.chart.ui.ColorPalette: Default contructor.
ColorParameter - Class in org.graffiti.plugin.parameter
ColorParameter(Color, String, String) - Constructor for class org.graffiti.plugin.parameter.ColorParameter
colorRGB2XYZ(double, double, double) - Static method in class org.color.ColorUtil
Colors - Class in org
Colors() - Constructor for class org.Colors
ColorScaleLegendAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms
ColorScaleLegendAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.ColorScaleLegendAlgorithm
ColorSetAndGetSupport - Interface in org.graffiti.attributes
ColorTimePoint - Class in org.vanted.animation.data
ColorTimePoint(double, Color) - Constructor for class org.vanted.animation.data.ColorTimePoint
ColorUtil - Class in org.color
ColorUtil() - Constructor for class org.color.ColorUtil
ColorXYZ - Class in org.color
ColorXYZ(double, double, double) - Constructor for class org.color.ColorXYZ
ColorXYZ(Color) - Constructor for class org.color.ColorXYZ
colorXYZ2CIELAB(ColorXYZ) - Static method in class org.color.ColorUtil
colour - Variable in class placement.Constraint
colour - Variable in class placement.Variable
column - Variable in class qmwi.kseg.som.diagram.DiagrammData
COLUMN - Static variable in class info.clearthought.layout.SingleFiledLayout: Align components in a column
COLUMN - Static variable in class org.jfree.data.CategoryToPieDataset: Deprecated.
Use the TableOrder class.
columnNames - Variable in class qmwi.kseg.som.diagram.DiagrammPaneData
COMARTMENT_HEADLINE - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
CombinationDataset - Interface in org.jfree.data: Interface that describes the new methods that any combined dataset needs to implement.
combine(Range, Range) - Static method in class org.jfree.data.Range: Creates a new range by combining two existing ranges.
CombinedCategoryPlotDemo1 - Class in org.jfree.chart.demo: A demo for the CombinedDomainCategoryPlot class.
CombinedCategoryPlotDemo1(String) - Constructor for class org.jfree.chart.demo.CombinedCategoryPlotDemo1: Creates a new demo instance.
CombinedCategoryPlotDemo2 - Class in org.jfree.chart.demo: A demo for the CombinedRangeCategoryPlot class.
CombinedCategoryPlotDemo2(String) - Constructor for class org.jfree.chart.demo.CombinedCategoryPlotDemo2: Creates a new demo instance.
CombinedDataset - Class in org.jfree.data: This class can combine instances of XYDataset, HighLowDataset and IntervalXYDataset together exposing the union of all the series under one dataset.
CombinedDataset() - Constructor for class org.jfree.data.CombinedDataset: Default constructor for an empty combination.
CombinedDataset(SeriesDataset[]) - Constructor for class org.jfree.data.CombinedDataset: Creates a CombinedDataset initialized with an array of SeriesDatasets.
CombinedDomainCategoryPlot - Class in org.jfree.chart.plot: A combined category plot where the domain axis is shared.
CombinedDomainCategoryPlot() - Constructor for class org.jfree.chart.plot.CombinedDomainCategoryPlot: Default constructor.
CombinedDomainCategoryPlot(CategoryAxis) - Constructor for class org.jfree.chart.plot.CombinedDomainCategoryPlot: Creates a new plot.
CombinedDomainXYPlot - Class in org.jfree.chart.plot: An extension of XYPlot that contains multiple subplots that share a common domain axis.
CombinedDomainXYPlot() - Constructor for class org.jfree.chart.plot.CombinedDomainXYPlot: Default constructor.
CombinedDomainXYPlot(ValueAxis) - Constructor for class org.jfree.chart.plot.CombinedDomainXYPlot: Creates a new combined plot that shares a domain axis among multiple subplots.
CombinedRangeCategoryPlot - Class in org.jfree.chart.plot: A combined category plot where the range axis is shared.
CombinedRangeCategoryPlot(ValueAxis) - Constructor for class org.jfree.chart.plot.CombinedRangeCategoryPlot: Creates a new plot.
CombinedRangeXYPlot - Class in org.jfree.chart.plot: An extension of XYPlot that contains multiple subplots that share a common range axis.
CombinedRangeXYPlot() - Constructor for class org.jfree.chart.plot.CombinedRangeXYPlot: Default constructor.
CombinedRangeXYPlot(ValueAxis) - Constructor for class org.jfree.chart.plot.CombinedRangeXYPlot: Creates a new plot.
CombinedXYPlotDemo1 - Class in org.jfree.chart.demo: A demonstration application showing how to create a vertical combined chart.
CombinedXYPlotDemo1(String) - Constructor for class org.jfree.chart.demo.CombinedXYPlotDemo1: Constructs a new demonstration application.
CombinedXYPlotDemo2 - Class in org.jfree.chart.demo: A demonstration application showing how to create a combined chart.
CombinedXYPlotDemo2(String) - Constructor for class org.jfree.chart.demo.CombinedXYPlotDemo2: Constructs a new demonstration application.
CombinedXYPlotDemo3 - Class in org.jfree.chart.demo: A demonstration application showing how to create a combined chart using...
CombinedXYPlotDemo3(String) - Constructor for class org.jfree.chart.demo.CombinedXYPlotDemo3: Constructs a new demonstration application.
CombinedXYPlotDemo4 - Class in org.jfree.chart.demo: A demonstration application showing how to create a vertical combined chart.
CombinedXYPlotDemo4(String) - Constructor for class org.jfree.chart.demo.CombinedXYPlotDemo4: Constructs a new demonstration application.
CombinedXYPlotDemo5 - Class in org.jfree.chart.demo: A demonstration application showing how to create a combined chart using...
CombinedXYPlotDemo5(String) - Constructor for class org.jfree.chart.demo.CombinedXYPlotDemo5: Constructs a new demonstration application.
CombineMappingData - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe
CombineMappingData() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.CombineMappingData
combineXSymbolicDataset(XisSymbolic, XisSymbolic) - Static method in class org.jfree.chart.demo.SampleXYSymbolicDataset: This function modify dataset1 and dataset1 in order that they share the same X symbolic value list.
combineYSymbolicDataset(YisSymbolic, YisSymbolic) - Static method in class org.jfree.chart.demo.SampleXYSymbolicDataset: This function modify dataset1 and dataset1 in order that they share the same Y symbolic value list.
combineYSymbolicDataset(YisSymbolic, YisSymbolic) - Static method in class org.jfree.chart.demo.SampleYSymbolicDataset: This function modify dataset1 and dataset1 in order that they share the same symbolic value list.
ComboBoxEditComponent - Class in org.graffiti.plugin.editcomponent: Displays a combo box to let the user choose from several possibilities.
ComboBoxEditComponent(Displayable) - Constructor for class org.graffiti.plugin.editcomponent.ComboBoxEditComponent: Creates a new ComboBoxEditComponent object.
CommandLineStart - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart
CommandLineStart() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.CommandLineStart
COMMENT - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule
COMMENT - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathPathway
COMMENT - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReaction
COMMENT - Static variable in class org.graffiti.plugins.ios.importers.gml.sym
COMMON - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
COMMUNICATION - org.graffiti.plugin.algorithm.Category
compare(DataRowExcelExport, DataRowExcelExport) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.DataRowExcelExport
compare(Object, Object) - Method in class org.jfree.data.KeyedValueComparator: Compares two KeyedValue instances and returns an int that indicates the relative order of the two objects.
compare(String, String) - Static method in enum org.graffiti.event.PathComparisonResult
compareElementsAt(int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.MergeSort
compareTo(KoEntry) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KoEntry
compareTo(ConditionInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
compareTo(ConditionInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
compareTo(DataMappingId) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.DataMappingId
compareTo(ExperimentHeaderInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentHeader
compareTo(SampleInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
compareTo(SampleInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
compareTo(SubstanceInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
compareTo(SubstanceInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
compareTo(DataRowExcelExport) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.DataRowExcelExport
compareTo(PathwayWebLinkItem) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop.PathwayWebLinkItem
compareTo(SessionLinkInfo) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.SessionLinkInfo
compareTo(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.MyComparableDataPoint
compareTo(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.MyComparableNode
compareTo(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggPathwayEntry
compareTo(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.NodeCombination
compareTo(Object) - Method in class org.graffiti.attributes.HashMapAttribute
compareTo(Object) - Method in class org.graffiti.managers.pluginmgr.Version
compareTo(Object) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Will compare this Segment with another Segment (from Comparable interface).
compareTo(Object) - Method in class org.jfree.chart.axis.TickUnit: Compares this tick unit to an arbitrary object.
compareTo(Object) - Method in class org.jfree.chart.plot.PieLabelRecord: Compares this object to an arbitrary object.
compareTo(Object) - Method in class org.jfree.chart.renderer.Outlier: Compares this object with the specified object for order, based on the outlier's point.
compareTo(Object) - Method in class org.jfree.data.OHLCDataItem: Compares this object with the specified object for order.
compareTo(Object) - Method in class org.jfree.data.time.Day: Returns an integer indicating the order of this Day object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.FixedMillisecond: Returns an integer indicating the order of this Millisecond object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.Hour: Returns an integer indicating the order of this Hour object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.Millisecond: Returns an integer indicating the order of this Millisecond object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.Minute: Returns an integer indicating the order of this Minute object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.Month: Returns an integer indicating the order of this Month object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.Quarter: Returns an integer indicating the order of this Quarter object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.Second: Returns an integer indicating the order of this Second object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.TimeSeriesDataItem: Returns an integer indicating the order of this data pair object relative to another object.
compareTo(Object) - Method in class org.jfree.data.time.Week: Returns an integer indicating the order of this Week object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.time.Year: Returns an integer indicating the order of this Year object relative to the specified object: negative == before, zero == same, positive == after.
compareTo(Object) - Method in class org.jfree.data.XYDataItem: Returns an integer indicating the order of this object relative to another object.
compareTo(AbstractGraphElement) - Method in class org.graffiti.graph.AbstractGraphElement
compareTo(GraphElement) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
compareTo(GraphElement) - Method in class org.graffiti.graph.AdjListEdge
compareTo(GraphElement) - Method in class org.graffiti.graph.AdjListNode
compareTo(Constraint) - Method in class placement.Constraint: If the constraint of the argument is more violated than this then it is considered greater (and we return 1).
compareTwoGraphs(Graph, Graph, HashSet<String>, HashSet<String>, WorkSettings) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance.HammingCalculator: Computes the hamming distance between two given graphs
COMPARTMENT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
COMPARTMENT_ID - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
COMPARTMENT_NAME - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
CompassDemo - Class in org.jfree.chart.demo: A demo application showing how to use the CompassPlot class.
CompassDemo() - Constructor for class org.jfree.chart.demo.CompassDemo: Default constructor.
CompassDemo2 - Class in org.jfree.chart.demo: A simple demonstration application showing how to...
CompassDemo2(String) - Constructor for class org.jfree.chart.demo.CompassDemo2: Creates a new demo application.
CompassFormat - Class in org.jfree.chart.axis: A formatter that displays numbers as directions.
CompassFormat() - Constructor for class org.jfree.chart.axis.CompassFormat: Creates a new formatter.
CompassFormatDemo - Class in org.jfree.chart.demo: A demo of the CompassFormat class.
CompassFormatDemo(String) - Constructor for class org.jfree.chart.demo.CompassFormatDemo: Creates a new demo instance.
CompassPlot - Class in org.jfree.chart.plot: A specialised plot that draws a compass to indicate a direction based on the value from a ValueDataset.
CompassPlot() - Constructor for class org.jfree.chart.plot.CompassPlot: Default constructor.
CompassPlot(ValueDataset) - Constructor for class org.jfree.chart.plot.CompassPlot: Constructs a new compass plot.
complement() - Method in class org.vanted.indexednodes.IndexedNodeSet: Performs the complement operation on this set.
COMPLETE - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.LegendType
COMPLETE_WITHOUT_EXPERIMENT - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.LegendType
COMPLETE_WITHOUT_EXPERIMENT_AND_CONDITIONNUMBER - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.LegendType
completeRedraw() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView
completeRedraw() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView
completeRedraw() - Method in interface org.graffiti.plugin.view.View: Instructs the view to do completely refresh its contents.
completeRedraw() - Method in class org.graffiti.plugins.views.defaults.GraffitiView
completeRedraw() - Method in class org.graffiti.plugins.views.matrix.MatrixView
ComplexShape - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes
ComplexShape() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes.ComplexShape
Component - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml
Component() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Component
COMPONENT - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReference
componentAdded(ContainerEvent) - Method in class org.graffiti.util.MaximizeManager
componentHidden(ComponentEvent) - Method in class org.graffiti.plugin.inspector.InspectorTab
componentHidden(ComponentEvent) - Method in class org.graffiti.util.MaximizeManager
componentMoved(ComponentEvent) - Method in class org.graffiti.plugin.inspector.InspectorTab
componentMoved(ComponentEvent) - Method in class org.graffiti.util.MaximizeManager
ComponentRegulator - Class in org.vanted.scaling: Notice: it is advisable to not access it directly, but through the provided ScalingCoordinator, because of factor conversions.
ComponentRegulator(float) - Constructor for class org.vanted.scaling.ComponentRegulator: Constructs a ComponentRegulator instance for upcoming component scaling.
componentRemoved(ContainerEvent) - Method in class org.graffiti.util.MaximizeManager
componentResized(ComponentEvent) - Method in class org.graffiti.plugin.inspector.InspectorTab
componentResized(ComponentEvent) - Method in class org.graffiti.util.MaximizeManager
ComponentScaler - Class in org.vanted.scaling.scalers.component: Applicable to initiated Swing Components.
ComponentScaler(float) - Constructor for class org.vanted.scaling.scalers.component.ComponentScaler
componentShown(ComponentEvent) - Method in class org.graffiti.plugin.inspector.InspectorTab: Override this method to trigger any action to be done, if this tab gains visibility.
componentShown(ComponentEvent) - Method in class org.graffiti.plugin.inspector.SubtabHostTab: This componentShown callback is only called for the upmost tab and not it's children.
componentShown(ComponentEvent) - Method in class org.graffiti.plugins.inspectors.defaults.AbstractTab
componentShown(ComponentEvent) - Method in class org.graffiti.util.MaximizeManager
CompositeAttribute - Class in org.graffiti.attributes: Interfaces a composite attribute.
CompositeAttribute(String) - Constructor for class org.graffiti.attributes.CompositeAttribute: Creates a new CompositeAttribute with the given id.
CompositeIcon - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes: CompositeIcon is an Icon implementation which draws two icons with a specified relative position: LEFT, RIGHT, TOP, BOTTOM specify how icon1 is drawn relative to icon2 CENTER: icon1 is drawn first, icon2 is drawn over it and with horizontal and vertical orientations within the alloted space It's useful with VTextIcon when you want an icon with your text: if icon1 is the graphic icon and icon2 is the VTextIcon, you get a similar effect to a JLabel with a graphic icon and text
CompositeIcon(Icon, Icon) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.CompositeIcon: Create a CompositeIcon from the specified Icons, using the default relative position (icon1 above icon2) and orientations (centered horizontally and vertically)
CompositeIcon(Icon, Icon, int) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.CompositeIcon: Create a CompositeIcon from the specified Icons, using the specified relative position and default orientations (centered horizontally and vertically)
CompositeIcon(Icon, Icon, int, int, int) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.CompositeIcon: Create a CompositeIcon from the specified Icons, using the specified relative position and orientations
COMPOSITION - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReaction
compound - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.EntryType
compound - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.SubtypeName
COMPOUND - de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KeggDatabases
CompoundAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
CompoundAttribute() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundAttribute
CompoundAttribute(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundAttribute
CompoundAttribute(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundAttribute
CompoundImageAttributeComponent - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
CompoundImageAttributeComponent() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImageAttributeComponent
CompoundImageAttributeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
CompoundImageAttributeEditor(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImageAttributeEditor
CompoundImageAttributePlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
CompoundImageAttributePlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImageAttributePlugin
CompoundImagePositionAttributeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
CompoundImagePositionAttributeEditor(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImagePositionAttributeEditor
CompoundListEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui
CompoundListEditor(Reaction, Pathway, boolean, boolean, boolean, HashMap<Entry, Node>) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui.CompoundListEditor
CompoundPositionAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
CompoundPositionAttribute() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundPositionAttribute
CompoundPositionAttribute(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundPositionAttribute
CompoundPositionAttribute(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundPositionAttribute
COMPUTATION - org.graffiti.plugin.algorithm.Category
computeAppropriateDepth(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple.GraphTreeLayout: Initialize the appropriate level of each node
ComputeAttributesAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes
ComputeAttributesAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.ComputeAttributesAlgorithm
computeNextPair(int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.UllmannSubraphIsomAdjMatrixState
CONDENSE_ENTITIES - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.KeggNavigationToolbarCommand.Command
CondenseButtonLayout - Enum in org
Condition - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper
Condition(SubstanceInterface) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
Condition(SubstanceInterface, Map<String, String>) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
Condition.ConditionInfo - Enum in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper
ConditionInterface - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper
configure() - Method in class org.jfree.chart.axis.Axis: Configures the axis to work with the current plot.
configure() - Method in class org.jfree.chart.axis.CategoryAxis: Configures the axis against the current plot.
configure() - Method in class org.jfree.chart.axis.DateAxis: Configures the axis to work with the specified plot.
configure() - Method in class org.jfree.chart.axis.NumberAxis: Configures the axis to work with the specified plot.
configure(Preferences) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_StandardTools: Sets the preferences in all tools this plugin provides.
configure(Preferences) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout.PluginCopyPatternLayout
configure(Preferences) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache.PluginPatternSpringembedderNoCache
configure(Preferences) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PluginPatternSpringembedder
configure(Preferences) - Method in interface org.graffiti.plugin.GenericPlugin: Runs configuration routines for the plugin, e.g.
configure(Preferences) - Method in class org.graffiti.plugin.GenericPluginAdapter: Runs configuration routines for the plugin, e.g.
configure(Preferences) - Method in class org.graffiti.plugins.modes.defaults.StandardTools: Sets the preferences in all tools this plugin provides.
configure(Preferences) - Method in class vanted_feature.PluginFeatureClusterCommands
configure(Preferences) - Method in class vanted_feature.PluginFeatureDataMapping
configure(Preferences) - Method in class vanted_feature.PluginFeatureExtendedFileFormatSupport
configure(Preferences) - Method in class vanted_feature.PluginFeatureHierarchyCommands
configure(Preferences) - Method in class vanted_feature.PluginFeatureMacroRecording
configure(Preferences) - Method in class vanted_feature.PluginFeatureMetaCropAccess
configure(Preferences) - Method in class vanted_feature.PluginFeatureNetworkAnalysisCommands
configure(Preferences) - Method in class vanted_feature.PluginFeatureStatistics
configure(ContourPlot) - Method in class org.jfree.chart.axis.ColorBar: Configures the color bar.
configureDomainAxes() - Method in class org.jfree.chart.plot.CategoryPlot: Configures the domain axes.
configureDomainAxes() - Method in class org.jfree.chart.plot.XYPlot: Configures the domain axes.
configureRangeAxes() - Method in class org.jfree.chart.plot.CategoryPlot: Configures the range axes.
configureRangeAxes() - Method in class org.jfree.chart.plot.XYPlot: Configures the range axes.
ConfigureViewAction - Interface in org.graffiti.editor
CONFIRM - Static variable in class org.UNCFileLocationCheck
ConnectedComponentLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components
ConnectedComponentLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components.ConnectedComponentLayout
ConnectedComponentPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components
ConnectedComponentPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components.ConnectedComponentPlugin
connectedNodes - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.NodeCacheEntry: Contains the connected nodes (NodeCacheEntrys)
connectedNodes - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.NodeCacheEntry3d: Contains the connected nodes (NodeCacheEntrys)
connectFailed(URI, SocketAddress, IOException) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.LoggingProxy
connectGraphToGraphs(Collection<Graph>, String, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayReferenceAutoCreationAlgorithm
connectMoleculeNodes(Graph, Node, Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule
connectNodesWithSameLabel(List<Node>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelperBio
connectPriorItems - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
consEdgeLabels - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance.WorkSettings
consEdges - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance.WorkSettings
consNodes - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance.WorkSettings
CONSTANT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
ConstantsName - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml
ConstantsName() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.ConstantsName
constrain(double) - Method in class org.jfree.data.Range: Returns the value within the range that is closest to the specified value.
Constraint - Class in placement
CONSTRAINT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
ConstraintCheckerListener - Interface in org.graffiti.session: Defines a listener to the GraphConstraintChecker.
contained(long, long) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Returns true if this segment is contained in an interval.
contains(double) - Method in class org.jfree.data.Range: Returns true if the range contains the specified value and false otherwise.
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.AbstractArrowShape: DOCUMENT ME!
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.CircularNodeShape: DOCUMENT ME!
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.LineEdgeShape: Decides whether or not a point lies within this shape.
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.PolygonalNodeShape
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.PolyLineEdgeShape: Returns true if the edge has been hit.
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.QuadCurveEdgeShape: Returns true if the edge has been hit.
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.RectangleNodeShape
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.RectangularNodeShape
contains(double, double) - Method in class org.graffiti.plugins.views.defaults.StraightLineEdgeShape: Decides whether or not a point lies within this shape.
contains(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.AbstractArrowShape: DOCUMENT ME!
contains(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.CircularNodeShape: DOCUMENT ME!
contains(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.LineEdgeShape: Checks whether or not a rectangle lies entirely within this shape.
contains(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.PolygonalNodeShape
contains(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.RectangleNodeShape
contains(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.RectangularNodeShape
contains(int) - Method in class org.vanted.indexednodes.IndexedNodeSet: Adds the node at index to this set.
contains(int, int) - Method in class org.graffiti.plugin.view.GraphElementComponent: Returns whether the given coordinates lie within this component and within its encapsulated shape.
contains(int, int) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Returns whether the given coordinates lie within this component and within its encapsulated shape.
contains(long) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Returns true if a particular millisecond is contained in this segment.
contains(long, long) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Returns true if an interval is contained in this segment.
contains(Point2D) - Method in class org.graffiti.plugins.views.defaults.AbstractArrowShape: DOCUMENT ME!
contains(Point2D) - Method in class org.graffiti.plugins.views.defaults.LineEdgeShape: DOCUMENT ME!
contains(Point2D) - Method in class org.graffiti.plugins.views.defaults.RectangularNodeShape: DOCUMENT ME!
contains(Rectangle2D) - Method in class org.graffiti.plugins.views.defaults.AbstractArrowShape: DOCUMENT ME!
contains(Rectangle2D) - Method in class org.graffiti.plugins.views.defaults.LineEdgeShape: DOCUMENT ME!
contains(Rectangle2D) - Method in class org.graffiti.plugins.views.defaults.RectangularNodeShape: DOCUMENT ME!
contains(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
contains(Object) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
contains(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
contains(Object) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
contains(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
contains(Object) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
contains(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
contains(Object) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
contains(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ListOfDataRowsExcelExport
contains(String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.database.dbe.StringScanner
contains(GraphElement) - Method in class org.graffiti.selection.Selection
contains(Node) - Method in class org.vanted.indexednodes.IndexedNodeSet: Adds a node from the super set passed on construction to this set.
contains(SegmentedTimeline.Segment) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Returns true if a segment is contained in this segment.
containsAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
containsAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
containsAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
containsAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
containsAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
containsAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
containsAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
containsAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
containsDomainRange(long, long) - Method in class org.jfree.chart.axis.SegmentedTimeline: Returns true if a range of values are contained in the timeline.
containsDomainRange(long, long) - Method in interface org.jfree.chart.axis.Timeline: Returns true if a range of values are contained in the timeline.
containsDomainRange(Date, Date) - Method in class org.jfree.chart.axis.SegmentedTimeline: Returns true if a range of values are contained in the timeline.
containsDomainRange(Date, Date) - Method in interface org.jfree.chart.axis.Timeline: Returns true if a range of dates are contained in the timeline.
containsDomainValue(long) - Method in class org.jfree.chart.axis.SegmentedTimeline: Returns true if a value is contained in the timeline.
containsDomainValue(long) - Method in interface org.jfree.chart.axis.Timeline: Returns true if a value is contained in the timeline values.
containsDomainValue(Date) - Method in class org.jfree.chart.axis.SegmentedTimeline: Returns true if a value is contained in the timeline.
containsDomainValue(Date) - Method in interface org.jfree.chart.axis.Timeline: Returns true if a date is contained in the timeline values.
containsEdge(Edge) - Method in class org.graffiti.graph.AbstractGraph: Returns true, if the graph contains the specified edge, false otherwise.
containsEdge(Edge) - Method in interface org.graffiti.graph.Graph: Returns true, if the Graph contains the specified Edge, false otherwise.
containsEdge(Edge) - Method in class org.graffiti.graph.OptAdjListGraph: Returns true, if the graph contains the specified edge, false otherwise.
containsNode(Node) - Method in class org.graffiti.graph.AbstractGraph: Returns true, if the graph contains the specified node, false otherwise.
containsNode(Node) - Method in interface org.graffiti.graph.Graph: Returns true, if the Graph contains the specified Node, false otherwise.
containsNode(Node) - Method in class org.graffiti.graph.OptAdjListGraph: Returns true, if the graph contains the specified node, false otherwise.
ContainsTabbedPane - Interface in org.graffiti.plugin.inspector
ContextMenuHelper - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools
ContextMenuHelper() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.ContextMenuHelper
ContextMenuManager - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools: Abstract basis for the context menu managers, not used at the moment.
ContextMenuManager() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.ContextMenuManager
ContinuousAnimation<T extends InterpolatableTimePoint> - Class in org.vanted.animation: Similar to a normal animation but contains an Interpolator so that the animation can transition from one data point value to another data point value in a progressive manner.
ContinuousAnimation(Attributable, List<T>, double) - Constructor for class org.vanted.animation.ContinuousAnimation: Uses a LinearInterpolator
ContinuousAnimation(Attributable, List<T>, double, double) - Constructor for class org.vanted.animation.ContinuousAnimation: Uses a LinearInterpolator
ContinuousAnimation(Attributable, List<T>, double, double, int) - Constructor for class org.vanted.animation.ContinuousAnimation: Uses a LinearInterpolator.
ContinuousAnimation(Attributable, List<T>, double, double, int, Looper) - Constructor for class org.vanted.animation.ContinuousAnimation: Uses a LinearInterpolator
ContinuousAnimation(Attributable, List<T>, double, double, int, Looper, Interpolator) - Constructor for class org.vanted.animation.ContinuousAnimation
ContourDataset - Interface in org.jfree.data: The interface through which JFreeChart obtains data in the form of (x, y, z) items - used for XY and XYZ plots.
ContourEntity - Class in org.jfree.chart.entity: Represents an item on a contour chart.
ContourEntity(Shape, String) - Constructor for class org.jfree.chart.entity.ContourEntity: Constructor for ContourEntity.
ContourEntity(Shape, String, String) - Constructor for class org.jfree.chart.entity.ContourEntity: Constructor for ContourEntity.
ContourPlot - Class in org.jfree.chart.plot: A class for creating shaded contours.
ContourPlot(ContourDataset, ValueAxis, ValueAxis, ColorBar) - Constructor for class org.jfree.chart.plot.ContourPlot: Constructs a contour plot with the specified axes (other attributes take default values).
ContourPlotDemo - Class in org.jfree.chart.demo: A demonstration application to illustrate ContourPlot.
ContourPlotDemo(String) - Constructor for class org.jfree.chart.demo.ContourPlotDemo: Constructs a new demonstration application.
ContourPlotDemo2 - Class in org.jfree.chart.demo: A demonstration application to illustrate ContourPlot.
ContourPlotDemo2(String) - Constructor for class org.jfree.chart.demo.ContourPlotDemo2: Constructs a new demonstration application.
ContourPlotUtilities - Class in org.jfree.chart.plot: Some utility methods for the ContourPlot class.
ContourPlotUtilities() - Constructor for class org.jfree.chart.plot.ContourPlotUtilities
contourRenderer(Graphics2D, Rectangle2D, PlotRenderingInfo, ContourPlot, ValueAxis, ValueAxis, ColorBar, ContourDataset, CrosshairState) - Method in class org.jfree.chart.plot.ContourPlot: Fills the plot.
ContourToolTipGenerator - Interface in org.jfree.chart.labels: Interface for a tooltip generator for plots that use data from a ContourDataset.
ContourValuePlot - Interface in org.jfree.chart.plot: An interface defining methods related to contour plots.
controlImport(SBMLDocument, Graph, BackgroundTaskStatusProviderSupportingExternalCallImpl) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Model_Reader: Passes the import on to other classes
ContTable - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.exact_fisher_test
ContTable(int, int, int, int, boolean) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.exact_fisher_test.ContTable
CONVERSION_FACTOR - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
convertLVL2Model(Model, Graph, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.LVL2ModelConverter
convertLVL3Model(Model, Graph, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.LVL3ModelConverter
convertToString(ArrayList<IOurl>) - Static method in class org.graffiti.plugin.parameter.MultiFileSelectionParameter
convolveAndTranspose(Kernel, int[], int[], int, int, boolean) - Static method in class org.graffiti.editor.GaussFilter
COORD_PATH - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Path to coordinate attribute
COORDINATE - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
CoordinateAttribute - Class in org.graffiti.graphics: Contains the coordinate graphic attribute.
CoordinateAttribute(String) - Constructor for class org.graffiti.graphics.CoordinateAttribute: Constructor for Coordinate that sets the coordinates to a random number.
CoordinateAttribute(String, double, double) - Constructor for class org.graffiti.graphics.CoordinateAttribute: Constructor for Coordinate.
CoordinateAttribute(String, Point2D) - Constructor for class org.graffiti.graphics.CoordinateAttribute: Constructor for Coordinate.
CoordinateSystem - Enum in org.graffiti.plugin.view
COORDX_PATH - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Path to x-coordinate attribute
COORDY_PATH - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Path to y-coordinate attribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartColorAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundPositionAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.font_label_color.LabelColorAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.font_label_settings.LabelFontAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.font_label_style.LabelStyleAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.font_settings.FontAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggGroupPartAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggIdAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggReactionIdAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggReactionTypeAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggRelationSrcTgtAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggRelationSubTypeAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggRelationTypeAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggTypeAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.label_alignment.LabelAlignmentAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute.URLAttribute
copy() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.xml_attribute.XMLAttribute
copy() - Method in class org.graffiti.attributes.BooleanAttribute: Returns a deep copy of this instance.
copy() - Method in class org.graffiti.attributes.ByteAttribute: Returns a deep copy of this instance.
copy() - Method in class org.graffiti.attributes.DoubleAttribute: Returns a deep copy of this instance.
copy() - Method in class org.graffiti.attributes.FloatAttribute: Returns a deep copy of this instance.
copy() - Method in class org.graffiti.attributes.HashMapAttribute: Copies this CollectionAttribute and returns the copy.
copy() - Method in class org.graffiti.attributes.IntegerAttribute: Returns a deep copy of this instance.
copy() - Method in class org.graffiti.attributes.LinkedHashMapAttribute: Copies this CollectionAttribute and returns the copy.
copy() - Method in class org.graffiti.attributes.LongAttribute: Returns a deep copy of this instance.
copy() - Method in class org.graffiti.attributes.ObjectAttribute
copy() - Method in class org.graffiti.attributes.ShortAttribute: Returns a deep copy of this instance.
copy() - Method in class org.graffiti.attributes.StringAttribute: Returns a deep copy of this instance.
copy() - Method in interface org.graffiti.core.DeepCopy: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graph.AdjListGraph: Creates and returns a copy of the graph.
copy() - Method in class org.graffiti.graph.OptAdjListGraph: Creates and returns a copy of the graph.
copy() - Method in class org.graffiti.graphics.AWTImageAttribute: Copies the image to a new image with the same size.
copy() - Method in class org.graffiti.graphics.ColorAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.CoordinateAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.DimensionAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.DockingAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.EdgeGraphicAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.EdgeLabelPositionAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.GradientFillAttribute
copy() - Method in class org.graffiti.graphics.ImageAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.LineModeAttribute: Returns a deep copy of this Attribute.
copy() - Method in class org.graffiti.graphics.NodeLabelPositionAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.PortAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.PortsAttribute: Returns a deep copy of this object.
copy() - Method in class org.graffiti.graphics.ShapeDescriptionAttribute: Copies this CollectionAttribute and returns the copy.
copy() - Method in class org.graffiti.graphics.SourceDockingAttribute
copy() - Method in class org.graffiti.graphics.TargetDockingAttribute
copy() - Method in class org.graffiti.graphics.ThicknessAttribute
copy() - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Returns a copy of ourselves or null if there was an exception during cloning.
copy() - Method in class org.vanted.indexednodes.IndexAttribute
copy() - Method in class org.vanted.indexednodes.IndexedNodeSet: Creates a subset of this set containing the same nodes with the same basis collection and index space.
CopyAction - Class in org.graffiti.editor.actions: Represents a graph element copy action.
CopyAction(MainFrame) - Constructor for class org.graffiti.editor.actions.CopyAction: Constructs a new copy action.
copyContent(InputStream, OutputStream) - Static method in class org.graffiti.plugin.io.resources.ResourceIOManager
copyContent(InputStream, OutputStream) - Static method in class org.HomeFolder
copyContent(InputStream, OutputStream, long) - Static method in class org.graffiti.plugin.io.resources.ResourceIOManager
copyDataAndReplaceURLPrefix(InputStream, String, ResourceIOConfigObject) - Method in class org.graffiti.plugin.io.resources.FileSystemHandler
copyDataAndReplaceURLPrefix(InputStream, String, ResourceIOConfigObject) - Method in class org.graffiti.plugin.io.resources.FTPhandler
copyDataAndReplaceURLPrefix(InputStream, String, ResourceIOConfigObject) - Method in class org.graffiti.plugin.io.resources.HTTPhandler
copyDataAndReplaceURLPrefix(InputStream, String, ResourceIOConfigObject) - Method in class org.graffiti.plugin.io.resources.HTTPShandler
copyDataAndReplaceURLPrefix(InputStream, String, ResourceIOConfigObject) - Method in interface org.graffiti.plugin.io.resources.ResourceIOHandler
copyDataAndReplaceURLPrefix(String, String, InputStream, ResourceIOConfigObject) - Static method in class org.graffiti.plugin.io.resources.ResourceIOManager
copyDataAndReplaceURLPrefix(String, IOurl, ResourceIOConfigObject) - Static method in class org.graffiti.plugin.io.resources.ResourceIOManager
CopyDataTableAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
CopyDataTableAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.CopyDataTableAlgorithm
copyFile(File, File) - Static method in class org.HomeFolder
copyFile(InputStream, File) - Static method in class org.HomeFolder
copyFile(String, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.FileHelper: Copy file from a folder on the file system to another folder on the file system.
copyFileFromJar(URI, String, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.FileHelper: Copy file from jar to file system.
copyFileFromStream(String, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.FileHelper: Copy file from resource (as stream) to file system.
copyFiles(String, String, String[]) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.FileHelper: Copy files from a folder on the file system to another folder on the file system.
copyFilesFromJar(URI, String, String, String[]) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.FileHelper: Copy files from jar to file system.
copyFileToTemporaryFolder(File) - Static method in class org.HomeFolder
copyFileToTemporaryFolder(String, File) - Static method in class org.HomeFolder
CopyPatternLayoutAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout
CopyPatternLayoutAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout.CopyPatternLayoutAlgorithm
copyReplaceStringAttribute(Attributable, String, String, String, String, String) - Static method in class org.AttributeHelper
Corner - Enum in org.graffiti.plugins.views.defaults
correlation - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.ResultPair
CorrelationResult - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics
CorrelationResult(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.CorrelationResult
CORRESPONDING_GROUP_ENTRY_NOT_FOUND_FOR_COMPONENT - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Gml2PathwayWarning
coscaleFont(JComponent) - Method in class org.vanted.scaling.scalers.component.AbstractButtonScaler
coscaleFont(JComponent) - Method in class org.vanted.scaling.scalers.component.ComponentScaler: Scales all components that have their font not modified by the LAF-Scalers for one reason or another up to this point.
coscaleFont(JComponent) - Method in class org.vanted.scaling.scalers.component.JLabelScaler
coscaleFont(JComponent) - Method in class org.vanted.scaling.scalers.component.JTabbedPaneScaler
coscaleFont(JComponent) - Method in class org.vanted.scaling.scalers.component.JTextComponentScaler
coscaleHTML(JComponent) - Method in class org.vanted.scaling.scalers.component.AbstractButtonScaler: Interface method for AbstractButtonScaler.modifyHTML(String, AbstractButton).
coscaleHTML(JComponent) - Method in interface org.vanted.scaling.scalers.component.HTMLScaler
coscaleHTML(JComponent) - Method in class org.vanted.scaling.scalers.component.JLabelScaler: Interface method for JLabelScaler.modifyHTML(String, JLabel).
coscaleHTML(JComponent) - Method in class org.vanted.scaling.scalers.component.JTabbedPaneScaler: Interface method for JTabbedPaneScaler.modifyHTML(JTabbedPane, int).
coscaleHTML(JComponent) - Method in class org.vanted.scaling.scalers.component.JTextComponentScaler: Interface method for JTextComponentScaler.modifyHTML(String, JTextComponent).
coscaleIcon(Component) - Method in class org.vanted.scaling.scalers.component.WindowScaler: Scales JFrame and JDialog icons.
coscaleIcon(JComponent) - Method in class org.vanted.scaling.scalers.component.AbstractButtonScaler
coscaleIcon(JComponent) - Method in class org.vanted.scaling.scalers.component.ComponentScaler: Left to subtypes.
coscaleIcon(JComponent) - Method in class org.vanted.scaling.scalers.component.JLabelScaler
coscaleIcon(JComponent) - Method in class org.vanted.scaling.scalers.component.JOptionPaneScaler
coscaleIcon(JComponent) - Method in class org.vanted.scaling.scalers.component.JTabbedPaneScaler
coscaleInsets(JComponent) - Method in class org.vanted.scaling.scalers.component.ComponentScaler: Modifies non-null Insets of JComponent.
CosineInterpolator - Class in org.vanted.animation.interpolators
CosineInterpolator() - Constructor for class org.vanted.animation.interpolators.CosineInterpolator
cost() - Method in class placement.Block
count(String, String) - Method in class qmwi.kseg.som.DataSet: Zuordnung der input-Daten in Ergebnisgruppen cols muss mit den Spalten die beim Training verwendet wurden, �bereinstimmen Z�hlt alle Eintr�ge die innerhalb der Spalte "group" den Wert "entry" haben
countAuspraegungen(Vector<SOMdataEntry>, String) - Method in class qmwi.kseg.som.DataSet: Zählt die verschiedenen Ausprägungen innerhalb einer Spalte Diese Gruppe kann z.B.
CountCircularCrossingsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle
CountCircularCrossingsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CountCircularCrossingsAlgorithm
countCompartments() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartment
countEdges(int, IndexedNodeSet) - Static method in class org.vanted.indexednodes.IndexedGraphOperations
countFunctionDefinitions(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Returns the number of function definitions in the graph
countNodes(int, IndexedNodeSet) - Static method in class org.vanted.indexednodes.IndexedGraphOperations
countOverlapps(Graph, Vector2d, Vector2d) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
cpColA - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
cpColBackground - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
cpColC - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
cpIdxA - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
cpIdxC - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
createAdjacencyMatrix(Graph, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper: Creates the adjacency matrix for a given graph.
createAlgebraicRule(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createAlgebraicRule(Graph, AlgebraicRule) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createAndInitObjectFromString(String) - Static method in class org.ObjectAttributeService
createAndShowContextMenuForAlgorithm(ProvidesNodeContextMenu) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.ContextMenuHelper
createApplicationSettingsFolder(SplashScreenInterface) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.GravistoMainHelper
createAreaChart(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates an area chart with default settings.
createAreaXYChart(String, String, String, XYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Deprecated.
Use createXYAreaChart(...).
createAssignmentRule(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createAssignmentRule(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createAssignmentRule(Graph, AssignmentRule) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createAttribute - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.ModeOfAttributeOperation
createBarChart(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a bar chart.
createBarChart3D(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a bar chart with a 3D effect.
createBoxAndWhiskerChart(String, String, String, BoxAndWhiskerXYDataset, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates and returns a default instance of a box and whisker chart.
createBubbleChart(String, String, String, XYZDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a bubble chart with default settings.
createBufferedImage(int, int) - Method in class org.jfree.chart.JFreeChart: Creates and returns a buffered image into which the chart has been drawn.
createBufferedImage(int, int, double, double, ChartRenderingInfo) - Method in class org.jfree.chart.JFreeChart: Creates and returns a buffered image into which the chart has been drawn.
createBufferedImage(int, int, int, ChartRenderingInfo) - Method in class org.jfree.chart.JFreeChart: Creates and returns a buffered image into which the chart has been drawn.
createBufferedImage(int, int, ChartRenderingInfo) - Method in class org.jfree.chart.JFreeChart: Creates and returns a buffered image into which the chart has been drawn.
createCandlestickChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a candlestick chart.
createCandlestickChart(String, String, String, HighLowDataset, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates and returns a default instance of a candlesticks chart.
createCategoryDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates and returns a CategoryDataset for the demo charts.
createCategoryDataset(String[], String[], double[][]) - Static method in class org.jfree.data.DatasetUtilities: Creates a CategoryDataset that contains a copy of the data in an array (instances of Double are created to represent the data items).
createCategoryDataset(String, String, double[][]) - Static method in class org.jfree.data.DatasetUtilities: Creates a CategoryDataset that contains a copy of the data in an array (instances of Double are created to represent the data items).
createCategoryDataset(String, String, Number[][]) - Static method in class org.jfree.data.DatasetUtilities: Creates a CategoryDataset that contains a copy of the data in an array.
createCategoryDataset(String, KeyedValues) - Static method in class org.jfree.data.DatasetUtilities: Creates a CategoryDataset by copying the data from the supplied KeyedValues instance.
createCentroidNodesGraph(Map, String[]) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOMguiHelper
createChart(CategoryDataset) - Method in class org.jfree.chart.demo.StackedAreaChartDemo: Creates a sample chart.
createChartPrintJob() - Method in class org.jfree.chart.ChartPanel: Creates a print job for the chart.
createCircleOrder(Collection<Node>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterAlgorithm: Creates an ordered list of a given list of nodes for creation of circular layouts, without the disruption of the order of nodes.
CreateClusterGraphAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
CreateClusterGraphAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.CreateClusterGraphAlgorithm
createClusterReferenceGraph(Graph, HashMap<String, Integer>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
createCombinedAndOverlaidChart1() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a combined and overlaid chart.
createCombinedAndOverlaidDynamicXYChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Displays an XY chart that is periodically updated by a background thread.
createCompartment(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Creates an compartment in the graph tab with an specific id
createCompartment(Graph, Compartment) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createCompassChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a compass chart.
createCompatibleDestImage(BufferedImage, ColorModel) - Method in class org.graffiti.editor.GaussFilter
createConstraint(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createConstraint(Graph, Constraint) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createCopy(int, int) - Method in class org.jfree.data.time.TimePeriodValues: Creates a new instance by copying a subset of the data in this collection.
createCopy(int, int) - Method in class org.jfree.data.time.TimeSeries: Creates a new timeseries by copying a subset of the data in this time series.
createCopy(int, int) - Method in class org.jfree.data.XYSeries: Creates a new series by copying a subset of the data in this time series.
createCopy(RegularTimePeriod, RegularTimePeriod) - Method in class org.jfree.data.time.TimeSeries: Creates a new timeseries by copying a subset of the data in this time series.
CREATED - org.graffiti.event.AbstractEvent.EVENTTYPE
createDataset() - Static method in class org.jfree.chart.demo.GanttDemo1: Creates a sample dataset for a Gantt chart.
createDataset() - Method in class org.jfree.chart.demo.MovingAverageDemo: Creates a dataset, one series containing unit trust prices, the other a moving average.
createDataset() - Method in class org.jfree.chart.demo.StackedAreaChartDemo: Creates a sample dataset.
createDataset() - Method in class org.jfree.chart.demo.SymbolicChartDemo1: Creates a dataset, consisting of two series of monthly data.
createDataset() - Method in class org.jfree.chart.demo.TimePeriodValuesDemo2: Creates a dataset, consisting of two series of monthly data.
createDataset() - Method in class org.jfree.chart.demo.TimePeriodValuesDemo3: Creates a dataset, consisting of two series of monthly data.
createDataset() - Method in class org.jfree.chart.demo.TimeSeriesDemo6: Creates a dataset, consisting of two series of monthly data.
createDataset() - Method in class org.jfree.chart.demo.TimeSeriesDemo9: Creates a sample dataset.
createDataset1() - Method in class org.jfree.chart.demo.CombinedCategoryPlotDemo1: Creates a dataset.
createDataset1() - Method in class org.jfree.chart.demo.CombinedCategoryPlotDemo2: Creates a dataset.
createDataset1() - Method in class org.jfree.chart.demo.TimePeriodValuesDemo: Creates a dataset, consisting of two series of monthly data.
createDataset2() - Method in class org.jfree.chart.demo.CombinedCategoryPlotDemo1: Creates a dataset.
createDataset2() - Method in class org.jfree.chart.demo.CombinedCategoryPlotDemo2: Creates a dataset.
createDataset2() - Method in class org.jfree.chart.demo.TimePeriodValuesDemo: Creates a dataset, consisting of two series of monthly data.
createDefaultPaintArray() - Static method in class org.jfree.chart.ChartColor: Convenience method to return an array of Paint objects that represent the pre-defined colors in the Color and ChartColor objects.
CreateDirectChildrenClustersHistogramAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram
CreateDirectChildrenClustersHistogramAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram.CreateDirectChildrenClustersHistogramAlgorithm
CreateDistanceMatrixAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms
CreateDistanceMatrixAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.CreateDistanceMatrixAlgorithm
createDownRotationLabelPositions(double) - Static method in class org.jfree.chart.axis.CategoryLabelPositions: Creates a new instance where the category labels angled downwards by the specified amount.
createDynamicXYChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Displays an XY chart that is periodically updated by a background thread.
createEURTimeSeries() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a time series of the daily EUR/GBP exchange rates in 2001 (to date), for use in the JFreeChart demonstration application.
createEvent(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createEvent(Graph, Event) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createExternalFrame(String, String, EditorSession, boolean, boolean, int, int, int, int) - Method in class org.graffiti.editor.MainFrame
createExternalFrame(String, EditorSession, boolean, boolean, int, int, int, int) - Method in class org.graffiti.editor.MainFrame
createFolderPaneErrors(boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.gui.KGMLerrorWindow
createFolderPaneWarnings(boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.gui.KGMLerrorWindow
createForAlgorithms(boolean, List<Algorithm>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.algorithms.AlgorithmPanelFactory
CreateFuncatGraphAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe
CreateFuncatGraphAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.CreateFuncatGraphAlgorithm
createFunctionDefinition(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createFunctionDefinition(Graph, FunctionDefinition) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createGanttChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a gantt chart.
createGanttChart(String, String, String, IntervalCategoryDataset, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a Gantt chart using the supplied attributes plus default values where required.
CreateGOchildrenAverageDataDiagramAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram
CreateGOchildrenAverageDataDiagramAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram.CreateGOchildrenAverageDataDiagramAlgorithm
CreateGOchildrenClustersHistogramAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram
CreateGOchildrenClustersHistogramAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram.CreateGOchildrenClustersHistogramAlgorithm
CreateGOchildrenTtestHistogramAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram
CreateGOchildrenTtestHistogramAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram.CreateGOchildrenTtestHistogramAlgorithm
CreateGOtreeAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go
CreateGOtreeAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go.CreateGOtreeAlgorithm
createGraph(int, boolean, double, boolean, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation.ErdosRenyiGraphGenerator
createGraph(int, boolean, int, double) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation.WattsStrogatzGraphGenerator
createHeatMapLegend() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.AddDiagramLegendAlgorithm
CreateHierarchyTree - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands: Deprecated.
CreateHierarchyTree() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.CreateHierarchyTree: Deprecated.
createHighLowChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Displays a vertical bar chart in its own frame.
createHighLowChart(String, String, String, HighLowDataset, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates and returns a default instance of a high-low-open-close chart.
createHighLowChart(String, String, String, HighLowDataset, Timeline, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates and returns a default instance of a high-low-open-close chart with a special timeline.
createHighLowDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates a sample high low dataset.
createHistogram(String, String, String, IntervalXYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a histogram chart.
createHorizontalBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Create a horizontal bar chart.
createHorizontallyCombinedChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a horizontally combined chart.
createHTMLfor(String, String, Collection<String>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm
createHyperLinkListener(JEditorPane) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.info_dialog_dbe.MenuItemInfoDialog
createHyperLinkListener(JEditorPane) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.info_dialog_example.MenuItemInfoDialog: Deprecated.
createInitialAssignment(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createInitialAssignment(Graph, InitialAssignment) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createInputSerializer(InputStream, String) - Method in class org.graffiti.managers.DefaultIOManager
createInputSerializer(InputStream, String) - Method in interface org.graffiti.managers.IOManager: Creates an instance of an input serializer from the given extension.
createInstance(Class<?>) - Static method in class org.graffiti.util.InstanceLoader: Returns a new instance of the specified class.
createInstance(Class<?>, Object) - Static method in class org.graffiti.util.InstanceLoader: Returns a new instance of the specified class.
createInstance(Class<?>, String, Object) - Static method in class org.graffiti.util.InstanceLoader: Returns a new instance of the specified class.
createInstance(String) - Static method in class org.graffiti.util.InstanceLoader: Returns a new instance of the specified class.
createInstance(String, Object) - Static method in class org.graffiti.util.InstanceLoader: Returns a new instance of the specified class.
createInstance(URL) - Method in class org.graffiti.managers.pluginmgr.DefaultPluginManager: Returns a new instance of the plugin "main" class with the given plugin name.
createInstance(URL) - Method in interface org.graffiti.managers.pluginmgr.PluginManager: Returns a new instance of the plugin "main" class with the given plugin name.
createInstance(URL, ProgressViewer) - Method in class org.graffiti.managers.pluginmgr.DefaultPluginManager: Returns a new instance of the plugin "main" class with the given plugin name.
createInstance(JFreeChart) - Static method in class org.jfree.chart.Legend: Static factory method that returns a concrete subclass of Legend.
createIntegerTickUnits() - Static method in class org.jfree.chart.axis.NumberAxis: Returns a collection of tick units for integer values.
createIntegerTickUnits() - Static method in class org.jfree.chart.axis.TickUnits: Deprecated.
this method has been moved to the NumberAxis class.
createIntegerTickUnits(Locale) - Static method in class org.jfree.chart.axis.NumberAxis: Returns a collection of tick units for integer values.
createIntegerTickUnits(Locale) - Static method in class org.jfree.chart.axis.TickUnits: Deprecated.
this method has been moved to the NumberAxis class.
createInternalFrame(String, String, boolean, boolean) - Method in class org.graffiti.editor.MainFrame: Creates and adds a new internal frame to the desktop within an existing session.
createInternalFrame(String, String, EditorSession, boolean) - Method in class org.graffiti.editor.MainFrame
createInternalFrame(String, String, EditorSession, boolean, boolean, boolean) - Method in class org.graffiti.editor.MainFrame
createInternalFrame(String, String, EditorSession, boolean, boolean, boolean, ConfigureViewAction, boolean) - Method in class org.graffiti.editor.MainFrame: Creates and adds a new internal frame to the desktop within a new session.
createInternalFrame(String, String, EditorSession, boolean, boolean, ConfigureViewAction) - Method in class org.graffiti.editor.MainFrame
createInternalFrame(String, EditorSession, boolean) - Method in class org.graffiti.editor.MainFrame
createIntervalCategoryDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a null interval category dataset.
createJPYTimeSeries() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a time series of the daily EUR/GBP exchange rates in 2001 (to date), for use in the JFreeChart demonstration application.
CreateKEGGOrthologyGraphAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.hierarchies: This class replaces the CreateFuncatGraphAlgorithm, The first class created KEGG hierarchies based on direct given hierarchies (using alternative labels in the nodes), or
CreateKEGGOrthologyGraphAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.hierarchies.CreateKEGGOrthologyGraphAlgorithm
CreateKeggReactionNetworkAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction
CreateKeggReactionNetworkAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction.CreateKeggReactionNetworkAlgorithm
createLicenseFile(String) - Static method in class org.vanted.KeggAccess: Create a new empty file, indicating the state of the KEGG license agreement.
createLineChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample line chart.
createLineChart(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a line chart with default settings.
createLines(int) - Method in class org.jfree.chart.demo.Performance: Creates lines in a loop.
createLineXYChart(String, String, String, XYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Deprecated.
Use createXYLineChart(...).
createMeterChartChord() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample meter chart.
createMeterChartCircle() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample meter chart.
createMeterChartPie() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample meter chart.
createMovingAverage(TimeSeriesCollection, String, int, int) - Static method in class org.jfree.data.MovingAverage: Creates a new TimeSeriesCollection containing a moving average series for each series in the source collection.
createMovingAverage(TimeSeries, String, int, int) - Static method in class org.jfree.data.MovingAverage: Creates a new TimeSeries containing moving average values for the given series.
createMovingAverage(XYDataset, int, String, double, double) - Static method in class org.jfree.data.MovingAverage: Creates a new XYSeries containing the moving averages of one series in the source dataset.
createMovingAverage(XYDataset, int, String, long, long) - Static method in class org.jfree.data.MovingAverage: Deprecated.
Use similar method with 'double' parameters.
createMovingAverage(XYDataset, String, double, double) - Static method in class org.jfree.data.MovingAverage: Creates a new XYDataset containing the moving averages of each series in the source dataset.
createMovingAverage(XYDataset, String, long, long) - Static method in class org.jfree.data.MovingAverage: Creates a new XYDataset containing the moving averages of each series in the source dataset.
createMultiplePieChart(String, CategoryDataset, TableOrder, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a chart that displays multiple pie plots.
createMultiplePieChart3D(String, CategoryDataset, TableOrder, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a chart that displays multiple pie plots.
createNewSession() - Method in class org.graffiti.editor.MainFrame: Creates and returns a new editor session.
createNewSession(Graph) - Method in class org.graffiti.editor.MainFrame
createNewShape(CoordinateSystem) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayLinkVisualizationComponent
createNewShape(CoordinateSystem) - Method in class org.graffiti.plugin.attributecomponent.AbstractAttributeComponent: Called to initialise the component of this attribute correctly.
createNewShape(CoordinateSystem) - Method in interface org.graffiti.plugin.view.GraffitiViewComponent: Called to initialise the shape of the NodeComponent correctly.
createNewShape(CoordinateSystem) - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface: Called to initialise the shape of the NodeComponent correctly.
createNewShape(CoordinateSystem) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Called to initialize the shape of the NodeComponent correctly.
createNullXYPlot() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample XY chart with null data.
createNumberArray(double[]) - Static method in class org.jfree.data.DatasetUtilities: Constructs an array of Number objects from an array of double primitives.
createNumberArray(double[]) - Static method in class org.jfree.data.DefaultHighLowDataset: Constructs an array of Number objects from an array of doubles.
createNumberArray2D(double[][]) - Static method in class org.jfree.data.DatasetUtilities: Constructs an array of arrays of Number objects from a corresponding structure containing double primitives.
createOpenFileChooser() - Method in class org.graffiti.managers.DefaultIOManager
createOpenFileChooser() - Method in interface org.graffiti.managers.IOManager: Modifies the given file chooser by registering file extensions from the input serializers.
CreateOrgSpecificSuperGraphsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar
CreateOrgSpecificSuperGraphsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.CreateOrgSpecificSuperGraphsAlgorithm
createOutputSerializer(String) - Method in class org.graffiti.managers.DefaultIOManager
createOutputSerializer(String) - Method in interface org.graffiti.managers.IOManager: Creates an instance of an output serializer from the given extension.
createOutputSerializer(String, String) - Method in class org.graffiti.managers.DefaultIOManager
createOutputSerializer(String, String) - Method in interface org.graffiti.managers.IOManager: Creates an instance of an output serializer from the given extension and file type description.
createOverlaidChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample overlaid chart.
createParameter(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createParameter(Graph, Parameter) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createPie3DChart(String, PieDataset, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Deprecated.
Use createPieChart3D(...).
createPieChart(String, PieDataset, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a pie chart with default settings.
createPieChart(String, PieDataset, PieDataset, int, boolean, boolean, boolean, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a pie chart with default settings that compares 2 datasets.
createPieChart3D(String, PieDataset, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a 3D pie chart using the specified dataset.
createPieChartOne() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample pie chart.
createPieChartThree() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample pie chart which compares 2 datasets.
createPieChartTwo() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample pie chart.
createPieDatasetForColumn(CategoryDataset, int) - Static method in class org.jfree.data.DatasetUtilities: Creates a pie dataset from a table dataset by taking all the values for a single column.
createPieDatasetForColumn(CategoryDataset, Comparable) - Static method in class org.jfree.data.DatasetUtilities: Creates a pie dataset from a table dataset by taking all the values for a single column.
createPieDatasetForRow(CategoryDataset, int) - Static method in class org.jfree.data.DatasetUtilities: Creates a pie dataset from a table dataset by taking all the values for a single row.
createPieDatasetForRow(CategoryDataset, Comparable) - Static method in class org.jfree.data.DatasetUtilities: Creates a pie dataset from a table dataset by taking all the values for a single row.
createPNGimageFromGraph(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm
createPNGimageFromGraph(Graph, String, PngJpegAlgorithmParams) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm
createPointMovingAverage(TimeSeries, String, int) - Static method in class org.jfree.data.MovingAverage: Creates a new TimeSeries containing moving average values for the given series, calculated by number of points (irrespective of the 'age' of those points).
createPolarChart(String, XYDataset, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a polar plot for the specified dataset (x-values interpreted as angles in degrees).
createRandomWaferMapDataset(int) - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates a random wafermap dataset
createRateRule(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createRateRule(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createRateRule(Graph, RateRule) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createReaction(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createReaction(Graph, Reaction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createSampleDataset() - Static method in class org.jfree.chart.demo.XYBoxAndWhiskerDemo: Creates a sample BoxAndWhiskerXYDataset.
createSampleSignalDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a sample signal dataset.
createSampleXYDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a sample XY dataset.
createSaveFileChooser() - Method in class org.graffiti.managers.DefaultIOManager
createSaveFileChooser() - Method in interface org.graffiti.managers.IOManager: Creates and returns a file open chooser dialog with the registered file extensions from the output serializers.
createSaveFileChooser(Graph) - Method in class org.graffiti.managers.DefaultIOManager
createSaveFileChooser(Graph) - Method in interface org.graffiti.managers.IOManager: Creates and returns a file open chooser dialog with the registered file extensions from the output serializers and checking, if output serializer is capable of writing the graph.
createScatterPlot() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample scatter plot.
createScatterPlot(String, String, String, XYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a scatter plot with default settings.
createScatterPlotBlock(boolean, boolean, boolean, boolean, double, float, boolean, double, boolean, double, Color, Color, Color, Collection<GraphElement>, Graph, boolean, Component, JComponent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.TabStatistics
createScenario() - Static method in class scenario.ScenarioService
createSegmentedHighLowDataset(SegmentedTimeline, Date) - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates a sample high low dataset for a SegmentedTimeline
createSignalChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample signal chart.
createSignalChart(String, String, String, SignalsDataset, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates and returns a default instance of a signal chart.
createSingleCategoryDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates and returns a category dataset with JUST ONE CATEGORY for the demo charts.
createSingleSeriesBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample bar chart with just one series.
createSingleSeriesCategoryDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates and returns a category dataset for the demo charts.
createSpecies(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Creates a new species node and sets its id
createSpecies(Graph, Species) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createStackedAreaChart(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a stacked area chart with default settings.
createStackedAreaXYChart(String, String, String, TableXYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Deprecated.
Method renamed - use createStackedXYAreaChart().
createStackedBarChart(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a stacked bar chart with default settings.
createStackedBarChart3D(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a stacked bar chart with a 3D effect and default settings.
createStackedHorizontalBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample stacked horizontal bar chart.
createStackedXYAreaChart(String, String, String, TableXYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a stacked XY area plot.
createStandardDateTickUnits() - Static method in class org.jfree.chart.axis.DateAxis: Returns a collection of standard date tick units that uses the default time zone.
createStandardDateTickUnits(TimeZone) - Static method in class org.jfree.chart.axis.DateAxis: Returns a collection of standard date tick units.
createStandardSeriesShapes(float) - Static method in class org.jfree.chart.plot.DefaultDrawingSupplier: Creates an array of standard shapes to display for the items in series on charts.
createStandardShape() - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface: Called to initialise and draw a standard shape, if the specified shapeclass could not be found.
createStandardShape() - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Called to initialize and draw a standard shape, if the specified shape class could not be found.
createStandardShape() - Method in class org.graffiti.plugins.views.defaults.EdgeComponent: Sets a standard shape for this edge.
createStandardShape() - Method in class org.graffiti.plugins.views.defaults.NodeComponent: Creates a standard NodeShape (in this case a rectangle) and draws it.
createStandardTickUnits() - Static method in class org.jfree.chart.axis.NumberAxis: Creates the standard tick units.
createStandardTickUnits() - Static method in class org.jfree.chart.axis.TickUnits: Deprecated.
this method has been moved to the NumberAxis class.
createStandardTickUnits(Locale) - Static method in class org.jfree.chart.axis.NumberAxis: Creates a collection of standard tick units.
createStandardTickUnits(Locale) - Static method in class org.jfree.chart.axis.TickUnits: Deprecated.
this method has been moved to the NumberAxis class.
createStepXYDataset() - Static method in class org.jfree.chart.demo.XYStepChartDemo: Creates and returns a sample dataset for the XY 'Step' chart.
createSunriseSeries() - Method in class org.jfree.chart.demo.DifferenceChartDemo2: Creates a time series containing sunrise times for London in 2004.
createSunsetSeries() - Method in class org.jfree.chart.demo.DifferenceChartDemo2: Creates a time series containing sunset times for London in 2004.
createThermometerChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample thermometer chart.
createTimeSeries(int, int) - Method in class org.jfree.chart.demo.TimeSeriesDemo9: Creates a time series containing random daily data.
createTimeSeries1Chart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample time series chart.
createTimeSeries2Chart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample time series chart.
createTimeSeriesChart(String, String, String, XYDataset, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates and returns a time series chart.
createTimeSeriesChartInScrollPane() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample time series chart that will be displayed in a scroll pane.
createTimeSeriesCollection1() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a dataset consisting of one annual series.
createTimeSeriesCollection2() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates a time series collection containing JPY/GBP exchange rates.
createTimeSeriesCollection3() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates a time series collection containing USD/GBP and EUR/GBP exchange rates.
createTimeSeriesCollection4() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a time series dataset using millisecond data.
createTimeSeriesWithMAChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample time series chart.
createTypedHashMapAttributes(Graph) - Static method in class org.graffiti.plugins.ios.importers.TypedAttributeService
createUnitDefinition(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createUnitDefinition(Graph, UnitDefinition) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
createUpRotationLabelPositions(double) - Static method in class org.jfree.chart.axis.CategoryLabelPositions: Creates a new instance where the category labels angled upwards by the specified amount.
createUSDTimeSeries() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Returns a time series of the daily USD/GBP exchange rates in 2001 (to date), for use in the JFreeChart demonstration application.
createVertical3DBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample vertical 3D bar chart.
createVerticalBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample vertical bar chart.
createVerticallyCombinedChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample vertically combined chart.
createVerticalStacked3DBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample stacked vertical 3D bar chart.
createVerticalStackedBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample stacked vertical bar chart.
createVerticalXYBarChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample vertical XY bar chart.
createView(String) - Method in class org.graffiti.managers.DefaultViewManager
createView(String) - Method in interface org.graffiti.managers.ViewManager: Returns a new instance of the specified view.
createWaferMapChart() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a basic wafermap chart with a random dataset
createWaferMapChart(String, WaferMapDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a wafer map chart.
createWaferMapChartPositionIndexed() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a basic wafermap chart with a random dataset
createWaferMapChartValueIndexed() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a basic wafermap chart with a random dataset
createWaferMapDataset() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates a sample wafermap dataset.
createWaterfallChart(String, String, String, CategoryDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a waterfall chart.
createWindDataset1() - Static method in class org.jfree.chart.demo.DemoDatasetFactory: Creates a sample wind dataset.
createWindPlot() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample wind plot.
createWindPlot(String, String, String, WindDataset, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a wind plot with default settings.
createXYAreaChart(String, String, String, XYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates an area chart using an XYDataset.
createXYBarChart(String, String, boolean, String, IntervalXYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates and returns a default instance of an XY bar chart.
createXYBarChart(String, String, String, IntervalXYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Deprecated.
Use createXYBarChart() method with additional parameter.
createXYLineChart(String, String, String, XYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a line chart (based on an XYDataset) with default settings.
createXYPlot() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates and returns a sample XY plot.
createXYPlotZeroData() - Method in class org.jfree.chart.demo.JFreeChartDemoBase: Creates a sample XY plot with an empty dataset.
createXYStepAreaChart(String, String, String, XYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a filled stepped XY plot with default settings.
createXYStepChart(String, String, String, XYDataset, PlotOrientation, boolean, boolean, boolean) - Static method in class org.jfree.chart.ChartFactory: Creates a stepped XY plot with default settings.
createXYSymbolicPlot(String, String, String, XYDataset, boolean) - Static method in class org.jfree.chart.demo.SymbolicXYPlotDemo: Creates a XY graph with symbolic value on X and Y axis.
createXYSymbolicSample1() - Static method in class org.jfree.chart.demo.SymbolicXYPlotDemo: Creates a sample dataset.
createXYSymbolicSample2() - Static method in class org.jfree.chart.demo.SymbolicXYPlotDemo: Creates a sample dataset.
createYSymbolicPlot(String, String, String, XYDataset, boolean) - Static method in class org.jfree.chart.demo.SymbolicYPlotDemo: Creates a XY graph with symbolic value on Y axis.
createYSymbolicSample1() - Static method in class org.jfree.chart.demo.SymbolicXYPlotDemo: Creates a sample dataset.
createYSymbolicSample1() - Static method in class org.jfree.chart.demo.SymbolicYPlotDemo: Creates a sample symbolic dataset.
createYSymbolicSample2() - Static method in class org.jfree.chart.demo.SymbolicXYPlotDemo: Creates a sample dataset.
createYSymbolicSample2() - Static method in class org.jfree.chart.demo.SymbolicYPlotDemo: Creates a sample symbolic dataset.
CREATOR - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathGene
CREATOR - Static variable in class org.graffiti.plugins.ios.importers.gml.sym
CRITICAL - Static variable in class org.jfree.chart.plot.ThermometerPlot: A constant for the 'critical' range.
CRITICAL_DATA - Static variable in interface org.jfree.data.MeterDataset: Deprecated.

A constant representing the 'critical' level.
CRITICAL_DATA_RANGE - Static variable in class org.jfree.chart.plot.MeterPlot: Constant to indicate the critical data range.
CRITICAL_TEXT - Static variable in class org.jfree.chart.plot.MeterPlot: The default text for the critical level.
CrosshairDemo1 - Class in org.jfree.chart.demo: A simple demonstration of the crosshairs that can be displayed in an XYPlot.
CrosshairDemo1(String) - Constructor for class org.jfree.chart.demo.CrosshairDemo1: Creates a new demo.
CrosshairState - Class in org.jfree.chart.plot: Maintains state information about crosshairs on a plot.
CrosshairState() - Constructor for class org.jfree.chart.plot.CrosshairState: Default constructor.
CrosshairState(boolean) - Constructor for class org.jfree.chart.plot.CrosshairState: Creates a new info object.
CSV_SOM_dataEntry - Class in qmwi.kseg.som
CSV_SOM_dataEntry(int) - Constructor for class qmwi.kseg.som.CSV_SOM_dataEntry
CSV_SOM_dataEntry(int, Object) - Constructor for class qmwi.kseg.som.CSV_SOM_dataEntry
CSVreader - Class in qmwi.kseg.som
CSVreader() - Constructor for class qmwi.kseg.som.CSVreader
CubicInterpolator - Class in org.vanted.animation.interpolators: Provides true continuity throughout the animation.
CubicInterpolator() - Constructor for class org.vanted.animation.interpolators.CubicInterpolator
CUBICSPLINE - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
CUBICSPLINE_CLASSNAME - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: cubic spline edge shape class name; not yet implemented.
cursorDown(double) - Method in class org.jfree.chart.axis.AxisState: Moves the cursor down by the specified number of Java 2D units.
cursorLeft(double) - Method in class org.jfree.chart.axis.AxisState: Moves the cursor left by the specified number of Java 2D units.
cursorRight(double) - Method in class org.jfree.chart.axis.AxisState: Moves the cursor right by the specified number of Java 2D units.
cursorUp(double) - Method in class org.jfree.chart.axis.AxisState: Moves the cursor up by the specified number of Java 2D units.
CUSTOM - org.graffiti.plugins.views.defaults.DockingAttributeEditor.DockingModes
CustomFullscreenView - Interface in org.graffiti.plugin.view
CustomPieURLGenerator - Class in org.jfree.chart.urls: A custom URL generator for pie charts.
CustomPieURLGenerator() - Constructor for class org.jfree.chart.urls.CustomPieURLGenerator: Default constructor.
customRangeSteps - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
CustomXYToolTipGenerator - Class in org.jfree.chart.labels: A tool tip generator that stores custom tooltips.
CustomXYToolTipGenerator() - Constructor for class org.jfree.chart.labels.CustomXYToolTipGenerator: Default constructor.
CustomXYURLGenerator - Class in org.jfree.chart.urls: A custom URL generator.
CustomXYURLGenerator() - Constructor for class org.jfree.chart.urls.CustomXYURLGenerator: Default constructor.
CutAction - Class in org.graffiti.editor.actions: Represents a cut of graph elements action.
CutAction(MainFrame) - Constructor for class org.graffiti.editor.actions.CutAction: Constructs a new cut action.
CyclicNumberAxis - Class in org.jfree.chart.axis: This class extends NumberAxis and handles cycling.
CyclicNumberAxis(double) - Constructor for class org.jfree.chart.axis.CyclicNumberAxis: Creates a CycleNumberAxis with the given period.
CyclicNumberAxis(double, double) - Constructor for class org.jfree.chart.axis.CyclicNumberAxis: Creates a CycleNumberAxis with the given period and offset.
CyclicNumberAxis(double, double, String) - Constructor for class org.jfree.chart.axis.CyclicNumberAxis: Creates a named CycleNumberAxis with the given period and offset.
CyclicNumberAxis(double, String) - Constructor for class org.jfree.chart.axis.CyclicNumberAxis: Creates a named CycleNumberAxis with the given period.
CyclicXYItemRenderer - Class in org.jfree.chart.renderer: The Cyclic XY item renderer is specially designed to handle cyclic axis.
CyclicXYItemRenderer() - Constructor for class org.jfree.chart.renderer.CyclicXYItemRenderer: Default constructor.
CyclicXYItemRenderer(int) - Constructor for class org.jfree.chart.renderer.CyclicXYItemRenderer: Creates a new renderer.
CyclicXYItemRenderer(int, XYToolTipGenerator) - Constructor for class org.jfree.chart.renderer.CyclicXYItemRenderer: Creates a new renderer.
CyclicXYItemRenderer(int, XYToolTipGenerator, XYURLGenerator) - Constructor for class org.jfree.chart.renderer.CyclicXYItemRenderer: Creates a new renderer.
CyclicXYPlotDemo - Class in org.jfree.chart.demo: Demo for an XY plot, with a cyclic axis and renderer
CyclicXYPlotDemo(String) - Constructor for class org.jfree.chart.demo.CyclicXYPlotDemo: A demonstration application showing an XY plot, with a cyclic axis and renderer


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