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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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