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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