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TreeGraph 2
 

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R

RAND_CHARS - Static variable in class info.bioinfweb.treegraph.document.IDManager
 
RAND_LENGTH - Static variable in class info.bioinfweb.treegraph.document.IDManager
 
RAY_ANGLE - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
 
reachElementEnd(XMLEventReader, StartElement) - Method in class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
Delegates to AbstractDocumentReader.reachElementEnd(XMLEventReader, String) where the name of the specified element is passed as elementDescription.
reachElementEnd(XMLEventReader, String) - Method in class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
Delegates to XMLUtils.reachElementEnd(XMLEventReader) and adds a warning to the LoadLogger.
read(File, LoadLogger) - Method in class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
 
read(File, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
 
read(File, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
If you want to implement file specific functionalities you should override this method.
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
 
read(InputStream, LoadLogger) - Method in class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
 
read(InputStream, LoadLogger) - Method in interface info.bioinfweb.treegraph.document.io.DocumentReader
 
read(File, LoadLogger) - Method in interface info.bioinfweb.treegraph.document.io.DocumentReader
 
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter) - Method in interface info.bioinfweb.treegraph.document.io.DocumentReader
 
read(File, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter) - Method in interface info.bioinfweb.treegraph.document.io.DocumentReader
 
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in interface info.bioinfweb.treegraph.document.io.DocumentReader
 
read(File, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in interface info.bioinfweb.treegraph.document.io.DocumentReader
 
read(String, Node) - Method in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
 
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickReader
 
read(File, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickReader
 
read(String) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
read(String, NodeBranchDataAdapter, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
read(String, NodeBranchDataAdapter, NodeBranchDataAdapter, TranslTable, boolean) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
read(String[], NodeBranchDataAdapter, NodeBranchDataAdapter, TranslTable, boolean) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusReader
 
read(File, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusReader
 
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFReader
 
read(InputStream, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
read(File, LoadLogger, NodeBranchDataAdapter, NodeBranchDataAdapter, TreeSelector, boolean) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readAnchor(StartElement, Legend, int) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readBranch(int, int, Node) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
readBranch(StartElement, Branch) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readBranchLength(String, int, NewickToken) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickScanner
Reads a length statement in an Newick string.
readBranchList(int, int, Node) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
readColor() - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readColorValue() - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readComment(String, int, List<NewickToken>) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickScanner
Reads a comment and adds it to last token in the passed list.
readDate(Node) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readDecimalFormat(TextFormats, StartElement, String) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readDelimitedName(String, int, NewickToken) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickScanner
 
readDistance(String, GraphicWriterHints) - Static method in class info.bioinfweb.treegraph.cmd.ImageGenerator
Reads a distance value (width or height) from the specified parameter in millimeters or pixels.
readDistanceDimensionAttr(DistanceDimension, StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readDistanceValueAttr(DistanceValue, StartElement, QName) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readDistribution(Node) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readDocument(StartElement) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readDocument(StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
reader - Variable in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
reader - Variable in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readFreeName(String, int) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickScanner
 
readGlobalFormats(StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readGraphicalLabelDimensions(GraphicalLabelFormats, StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readHiddenData(StartElement, HiddenDataMap) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readIconLabel(StartElement, Labels) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readInternal(int, int) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
readLabelData(StartElement, Label) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
This method also reads the subelements of the root element.
readLeaf(int, int) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
readLegend(StartElement, Legends) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readLineAttr(LineFormats, StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readMargin(Margin, StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readName(int, int, Node, NodeBranchDataAdapter, TranslTable) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
readOnly() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.AbstractIDElementAdapter
 
readOnly() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
 
readOnly() - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
 
readOnly() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
 
readOnly() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
 
readPhylogeny(StartElement) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readPieChartIDs(PieChartLabel) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readPieChartLabel(StartElement, Labels) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readRes(String) - Static method in class info.bioinfweb.treegraph.cmd.ImageGenerator
Reads the resolution from the specified parameter and converts it to pixels per millimeter if necessary.
readScaleBar(StartElement, ScaleBar) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readScaleValueAttr(ScaleValue, StartElement, QName) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readSequence(StartElement, Node) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readStream(InputStream) - Static method in class info.bioinfweb.treegraph.document.io.TextStreamReader
 
readSubtree(int, int) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
readSubtree(StartElement, Node) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readSubtree(StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readTaxonomy(Node) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
readTextElementData(String) - Method in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
 
readTextElementDataAttr(TextElementData, StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readTextFormatsAttr(TextFormats, StartElement, String) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readTextLabel(StartElement, Labels) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readTextStyleAttr(TextFormats, StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
readTranslTable(NexusCommand, TranslTable) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
Reads the content of the passed translation table from the passed command.
readTree() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
readTree(String, NexusDocument) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
Reads a tree from the passed nexus command tokens and adds it to the passed document.
readTree(StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
 
ReadWriteFactory - Class in info.bioinfweb.treegraph.document.io
 
ReadWriteFactory() - Constructor for class info.bioinfweb.treegraph.document.io.ReadWriteFactory
 
ReadWriteFactoryException - Exception in info.bioinfweb.treegraph.document.io
 
ReadWriteFactoryException() - Constructor for exception info.bioinfweb.treegraph.document.io.ReadWriteFactoryException
 
ReadWriteFactoryException(String, Throwable) - Constructor for exception info.bioinfweb.treegraph.document.io.ReadWriteFactoryException
 
ReadWriteFactoryException(String) - Constructor for exception info.bioinfweb.treegraph.document.io.ReadWriteFactoryException
 
ReadWriteFactoryException(Throwable) - Constructor for exception info.bioinfweb.treegraph.document.io.ReadWriteFactoryException
 
ReadWriteFormat - Enum in info.bioinfweb.treegraph.document.io
 
ReadWriteFormat() - Constructor for enum info.bioinfweb.treegraph.document.io.ReadWriteFormat
 
ReanchorLegendAction - Class in info.bioinfweb.treegraph.gui.actions.format
 
ReanchorLegendAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.ReanchorLegendAction
 
ReanchorLegendEdit - Class in info.bioinfweb.treegraph.document.undo.format
 
ReanchorLegendEdit(Document, Legend, String, String) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ReanchorLegendEdit
 
RecentlyUsedExpressionsListModel - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdata
Manages the list of recently used expressions.
RecentlyUsedExpressionsListModel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel
 
recentlyUsedList - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
 
recentlyUsedPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
 
recentlyUsedScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
 
RectangleIcon - Class in info.bioinfweb.treegraph.graphics.positionpaint.labelicons
 
RectangleIcon() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RectangleIcon
 
RectangularCladogramFactory - Class in info.bioinfweb.treegraph.graphics.positionpaint
 
RectangularCladogramFactory() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory
 
RectangularCladogramPainter - Class in info.bioinfweb.treegraph.graphics.positionpaint
Paints the document in the rectangular cladogram view if it was previously positioned.
RectangularCladogramPainter() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
 
RectangularCladogramPositioner - Class in info.bioinfweb.treegraph.graphics.positionpaint
 
RectangularCladogramPositioner() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
 
redFactor - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.BranchLengthEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.ChangeLabelIDEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.CollapseNodeEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.CopyColumnEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteColumnEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteOutsideIntervalEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteSubelementsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.EditNodeBranchDataEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLabelEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLabelsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLegendEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertSiblingEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertSubtreeEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.MoveSubtreeEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteAllLabelsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteLabelEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteLegendEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteRootEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteSiblingEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteSubtreeEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.PieChartLabelIDsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveLabelEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveLegendEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.RenameDataIDEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.SeparateBranchEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.SetColumnTypeEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.edit.TextElementEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.file.ImportTableEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.AutoPositionLabelsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.GlobalFormatsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.OperatorsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.ReanchorLegendEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleBranchLengthsEdit
 
redo() - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit
 
RedoAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
RedoAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.RedoAction
 
redoMenu - Variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
 
RedoToAction - Class in info.bioinfweb.treegraph.gui.actions.edit
Undoes all edit to the specified edit.
RedoToAction(MainFrame, UndoableEdit) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.RedoToAction
 
reduceLabelLineVectors() - Method in class info.bioinfweb.treegraph.document.Labels
 
refreshActionStatus() - Method in class info.bioinfweb.treegraph.gui.actions.ActionManagement
Enables or disables all action objects by calling their setEnabled(Document, TreeSelection)-methods.
refreshText() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarIntervalKeyListener
Refreshes the label text depending of the value of the small and long interval decimal input.
registerChange() - Method in class info.bioinfweb.treegraph.document.Document
 
registerPositioner(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.Document
 
reinsert() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
If this object has an owner-Label this is reinserted into its Labels-object.
reinsert() - Method in class info.bioinfweb.treegraph.document.Label
Reinserts this label into its owning Labels-object of one is linked.
reinsert(Label) - Method in class info.bioinfweb.treegraph.document.Labels
 
reinsert() - Method in class info.bioinfweb.treegraph.document.Legend
 
reinsert(Legend) - Method in class info.bioinfweb.treegraph.document.Legends
Reinserts a legend to ensure the correct order of the stored legends.
remove(Object) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
 
remove(Label) - Method in class info.bioinfweb.treegraph.document.LabelLine
 
remove(Label) - Method in class info.bioinfweb.treegraph.document.Labels
 
remove(Legend) - Method in class info.bioinfweb.treegraph.document.Legends
 
remove() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveLabelEdit
 
remove() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveLegendEdit
 
remove() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveSubtreeEdit
 
remove(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
 
remove(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
 
removeButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
 
removeButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
removeComments(String) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
Returns the specified string without any comments (seperated by "[" and "]").
removeInputListener(NodeDataInputListener) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
 
RemoveLabelEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
RemoveLabelEdit(Document, Label, Labels) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.RemoveLabelEdit
 
RemoveLegendEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
RemoveLegendEdit(Document, Legend) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.RemoveLegendEdit
 
removeLegends() - Method in class info.bioinfweb.treegraph.document.undo.edit.LegendPaster
 
RemoveSubtreeEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
RemoveSubtreeEdit(Document, Node, Node, int, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit
 
removeTextStyle(int) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
 
removeTextStyle(int) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
 
removeTextStyle(int) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
 
removeTreeViewListener(TreeViewPanelListener) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
 
removeValueID(int) - Method in class info.bioinfweb.treegraph.document.PieChartLabel
 
removeView(DocumentListener) - Method in class info.bioinfweb.treegraph.document.Document
 
rename(Node, List<String>, List<String>) - Method in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
 
renameButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
 
RenameDataIDAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
RenameDataIDAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.RenameDataIDAction
 
RenameDataIDEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
RenameDataIDEdit(Document, String[], String[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.RenameDataIDEdit
 
renameHiddenDataID(HiddenDataElement, String, String) - Static method in class info.bioinfweb.treegraph.document.IDManager
 
renameID(String, String, Tree) - Static method in class info.bioinfweb.treegraph.document.IDManager
Renames a data ID in the specified tree and updates possible links to this ID in pie chart labels.
RenameIDDialog - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdata
 
RenameIDDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
 
renameIDSubtree(String, String, Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
Changes all occurrences of the given ID in the subtree under root.
renameLabelIDInLabelBlock(String, String, Labels, boolean) - Static method in class info.bioinfweb.treegraph.document.IDManager
 
replace(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit
 
replaceButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
 
replaceButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
replaceEdit(UndoableEdit) - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
 
ReplaceInNodeDataAction - Class in info.bioinfweb.treegraph.gui.actions.edit
Action in the edit menu.
ReplaceInNodeDataAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.ReplaceInNodeDataAction
 
ReplaceInNodeDataDialog - Class in info.bioinfweb.treegraph.gui.dialogs
 
ReplaceInNodeDataDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
ReplaceInNodeDataDialog(Dialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
ReplaceInNodeDataEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
ReplaceInNodeDataEdit(Document, NodeBranchDataAdapter, ReplaceInNodeDataEdit.InsertPosition, String, String, boolean, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit
 
ReplaceInNodeDataEdit.InsertPosition - Enum in info.bioinfweb.treegraph.document.undo.edit
 
ReplaceInNodeDataEdit.InsertPosition() - Constructor for enum info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit.InsertPosition
 
replaceLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
replacePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
replaceRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
replaceTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
replaceTextLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
reroot(Branch) - Method in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit
 
RerootAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
RerootAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.RerootAction
 
RerootEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
RerootEdit(Document, Branch) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.RerootEdit
 
rescale(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.RescaleNodeDataEdit
 
rescaleBranchWidth(Branch, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner
This method is overwritten to regard the stored branch lengths.
rescaleBranchWidth(Branch, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
This methode can be overwritten by extending classes to define a different rescaling process.
RescaleNodeDataEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
RescaleNodeDataEdit(Document, NodeBranchDataAdapter, double, double) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.RescaleNodeDataEdit
 
rescaleNodeWidth(Node, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner
This method is overwritten to ensure that no corner radius in painted.
rescaleNodeWidth(Node, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
This methode can be overwritten by extending classes to define a different rescaling process.
rescaleSubtree(Node, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
Rescales the subtree under root.
rescalingFactorX - Variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
 
reset() - Method in class info.bioinfweb.treegraph.document.Document
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
 
resetChangeMonitors() - Method in interface info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatTab
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
 
resetChangeMonitors() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
 
RESOLUTION_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.ImageGenerator
 
resolutionInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
 
ResolutionInput - Class in info.bioinfweb.treegraph.gui.dialogs
 
ResolutionInput(String, JPanel, int) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.ResolutionInput
 
RESOURCES_PATH - Static variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
 
restore(Node) - Method in class info.bioinfweb.treegraph.document.undo.NodeBranchDataBackup
Restores the previous values of the specified column if it previously exsited.
restoreFormats() - Method in class info.bioinfweb.treegraph.document.undo.format.AutoPositionLabelsEdit
 
restoreLegends() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
 
restoreNames(Node, int) - Method in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
 
restoreSubtree(Node, int) - Method in class info.bioinfweb.treegraph.document.undo.NodeBranchDataBackup
 
restoreSubtreeValues(Node, int) - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
Assigns the previously saved line widths to the branches in the subtree under root.
restoreValues() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
 
right - Variable in class info.bioinfweb.treegraph.document.format.Margin
 
right - Variable in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
 
rightRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
 
root - Variable in class info.bioinfweb.treegraph.document.undo.edit.DeleteSubelementsEdit
 
root - Variable in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveSubtreeEdit
 
root - Variable in class info.bioinfweb.treegraph.document.undo.edit.LadderizeEdit
 
root - Variable in class info.bioinfweb.treegraph.document.undo.edit.MoveSubtreeEdit
 
root - Variable in class info.bioinfweb.treegraph.document.undo.edit.PasteSubtreeEdit
 
root - Variable in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
 
root - Variable in class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit
 
ROOTED_COMMAND - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
rootingPoint - Variable in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit
 
rootName - Variable in class info.bioinfweb.treegraph.document.io.AbstractXMLFilter
 
RoundRectangleIcon - Class in info.bioinfweb.treegraph.graphics.positionpaint.labelicons
 
RoundRectangleIcon() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RoundRectangleIcon
 
RulerOrientation - Enum in info.bioinfweb.treegraph.gui.treeframe.ruler
Defines the orientation of a ruler.
RulerOrientation() - Constructor for enum info.bioinfweb.treegraph.gui.treeframe.ruler.RulerOrientation
 
RulerUnit - Enum in info.bioinfweb.treegraph.gui.treeframe.ruler
Enumerates the units displayable by the ruler.
RulerUnit() - Constructor for enum info.bioinfweb.treegraph.gui.treeframe.ruler.RulerUnit
 
run(Stack) - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
 
run() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
 

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