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## G

g - Variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
generalEditorPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
generalPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
generalScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
generate(CommandLineReader) - Static method in class info.bioinfweb.treegraph.cmd.ImageGenerator
generatePattern(String, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit
get(Object) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
get(int) - Method in class info.bioinfweb.treegraph.document.io.nexus.TranslTable
get(String) - Method in class info.bioinfweb.treegraph.document.io.nexus.TranslTable
get(int) - Method in class info.bioinfweb.treegraph.document.LabelLine
get(boolean, int, int) - Method in class info.bioinfweb.treegraph.document.Labels
  Returns the label at the specified position
get(String) - Method in class info.bioinfweb.treegraph.document.Labels
get(int) - Method in class info.bioinfweb.treegraph.document.Legends
get(String) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
get(String) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap
get(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
get(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
GET_VALUE_FUNC - Static variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
getAbove() - Method in class info.bioinfweb.treegraph.document.Label
getAbove(boolean, int, int) - Method in class info.bioinfweb.treegraph.document.Labels
getAboveBelowGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
getAboveBelowPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes labelAboveBelowPanel
getAboveRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes aboveRadioButton
getActionManagement() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
getActionManagement() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel
getActiveTreeFrame() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  Returns the currently avctive Frame where a tree is displayed.
getAdapter() - Method in class info.bioinfweb.treegraph.document.undo.edit.SetColumnTypeEdit
getAdapter(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getAdapterComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes adapterComboBox
getAdapterComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes nodeDataComboBox
getAddButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes addButton
getAdditionalCount() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
getAfferentBranch() - Method in class info.bioinfweb.treegraph.document.Node
getAlignGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
getAlignLegendsToSubtree() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getAlignment() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
getAlignmentPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes anchorPanel
getAlignToSubtreeCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
  This method initializes alignLegendsToSubtreeCheckBox
getAllFilters() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory
getAnchor(int) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getAnchorName(int) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getApachePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes apachePanel
getApacheScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes apacheScrollPane
getApacheTextArea() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes apacheTextArea
getAssignImportColumnsDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction
getAttributeMap() - Method in class info.bioinfweb.treegraph.document.Node
  The attribute map can store data that is specific to special tasks like ladderizing or tree merging.
getBackgroundColor() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getBeginningRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes beginningRadioButton
getBelow() - Method in class info.bioinfweb.treegraph.document.Label
getBelow(boolean, int, int) - Method in class info.bioinfweb.treegraph.document.Labels
getBelowRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes belowRadioButton
getBoldCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes boldCheckBox
getBoolean(String, boolean) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
getBothRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes bothRadioButton
getBottom() - Method in class info.bioinfweb.treegraph.document.format.Margin
getBottom() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
getBottomInMillimeters() - Method in class info.bioinfweb.treegraph.document.position.PositionData
getBottomInPixels(float) - Method in class info.bioinfweb.treegraph.document.position.PositionData
getBraceRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes braceRadioButton
getBracketRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes bracketRadioButton
getBranchDataRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes branchDataRadioButton
getBranches(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getBranchLengthCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
  This method initializes branchLengthCheckBox
getBranchLengthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
getBranchLengthScale() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getBranchLengthScale() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
getBranchLengthsDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
getBranchLengthsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
  This method initializes branchLengthsPanel
getBranchLengthsRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes branchLengthsRadioButton
getButtonPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes buttonPanel
getCaseSensitiveCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes caseSensitiveCheckBox
getCaseSensitiveCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes caseSensitiveCheckBox
getCaseSensitiveCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
  This method initializes caseSensitiveCheckBox
getChangeUndefinedCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes hCheckBox
getChangeUndefinedCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
  This method initializes changeUndefinedCheckBox
getChildren() - Method in class info.bioinfweb.treegraph.document.Node
getClearButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes clearButton
getClipboard() - Method in class info.bioinfweb.treegraph.Main
getCloseButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes closeButton
getCmdProcessor() - Method in class info.bioinfweb.treegraph.Main
getColor(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.coloradapters.BranchLineColorAdapter
getColor(Node) - Method in interface info.bioinfweb.treegraph.gui.dialogs.specialformats.coloradapters.ColorAdapter
getColor(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.coloradapters.LabelLineColorAdapter
getColor(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.coloradapters.LabelTextColorAdapter
getColor(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.coloradapters.NodeLineColorAdapter
getColor(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.coloradapters.NodeTextColorAdapter
getColorChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
  This method initializes lineColorChooser
getColorChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
getColorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes colorPanel
getColorPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes colorPreviewPanel
getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getColumnCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getColumnCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
getColumnCount() - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getColumnInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getColumnPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
  This method initializes columnPanel
getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput
getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
getCommandGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
getCommandPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes commandPanel
getComment() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
  Returns the comment which was located behind this element in the Newick string (if there was any).
getCompressionMethodComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TIFFPrefPanel
  This method initializes compressionMethodComboBox
getConstantWidthCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
  This method initializes constantWidthCheckBox
getContentsTabbedPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes contentsTabbedPane
getContentType() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
getCopyPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
  This method initializes copyPanel
getCornerRadius() - Method in interface info.bioinfweb.treegraph.document.format.CornerRadiusFormats
getCornerRadius() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getCornerRadius() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
  The line wich is dasplayed for an node can be rounded at ist top and bottom end The inner radius (without the line width) of the quater of a circle at the ends of this line is specified by the corner radius.
getCurrentValue(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
  Returns the value of the specified column in the current line (specified by `CalculateColumnEdit.position`).
getData() - Method in class info.bioinfweb.treegraph.document.AbstractTextElement
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter
getData() - Method in interface info.bioinfweb.treegraph.document.TextElement
getData() - Method in class info.bioinfweb.treegraph.document.TextLabel
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenBranchDataAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenNodeDataAdapter
getDataElement(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
  This method should return the tree element which contains the data which is edited with the implementation of the respective adapter.
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenBranchDataAdapter
getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter
getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenNodeDataAdapter
getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
getDecimal(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
getDecimal() - Method in class info.bioinfweb.treegraph.document.TextElementData
  Return the stored decimal value or `Double.NaN` is no decimal is stored.
getDecimalCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
  This method initializes decimalCheckBox
getDecimalFormat() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getDecimalFormat() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
getDecimalFormat() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter
getDecimalFormat() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
getDecimalFormatterFactory() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
getDecimalInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
getDecRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes decRadioButton
getDefaultExtension() - Method in interface info.bioinfweb.treegraph.document.io.DocumentFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.SupportedFormatsFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFilter
getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFilter
getDefaultID() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap
getDefaultType() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getDescent() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getDescent() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
getDescent() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getDescription() - Method in interface info.bioinfweb.treegraph.document.io.DocumentFilter
getDescription() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFilter
getDescription() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFilter
getDescription() - Method in class info.bioinfweb.treegraph.document.io.SupportedFormatsFilter
getDescription() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFilter
getDescription() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFilter
getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFilter
getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter
getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFilter
getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFilter
getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFilter
getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFilter
getDesktopPane() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes desktopPane
getDestAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
getDestInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
getDialog() - Method in class info.bioinfweb.treegraph.gui.actions.EditDialogAction
getDialog() - Method in class info.bioinfweb.treegraph.gui.actions.help.AboutAction
getDifAbove() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
getDifBelow() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
getDimensionsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes widthPanel
getDimensionsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes pngPanel
getDirectionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes directionPanel
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractDistanceValueAdapter
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractLabelDistanceAdapter
  Returns the distance value of the label with the specified ID in millimeters.
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractLegendAdapter
  This method always returns `Float.NaN`.
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.BranchLineWidthAdapter
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.BranchMinLengthAdapter
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.BranchSpaceAboveAdapter
getDistance(Node) - Method in interface info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.DistanceAdapter
  Returns the distance value in millimeters
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.NodeLineWidthAdapter
getDistance(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.NodeTextHeightAdapter
getDistancesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
  This method initializes distancesPanel
getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractDistanceValueAdapter
getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractIconLabelDistanceAdapter
getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractLabelDistanceAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractLegendAdapter
getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.BranchSpaceBelowAdapter
getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.CornerRadiusAdapter
getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LabelMarginBottomAdapter
getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LabelMarginLeftAdapter
getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LabelMarginRightAdapter
getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LabelMarginTopAdapter
getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LabelTextHeightAdapter
getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LeafMarginBottomAdapter
getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LeafMarginLeftAdapter
getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LeafMarginRightAdapter
getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LeafMarginTopAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LegendLineWidthAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LegendMarginBottomAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LegendMarginLeftAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LegendMarginRightAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LegendMarginTopAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LegendSpacingAdapter
getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.LegendTextHeightAdapter
getDocument() - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
getDocument() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
getDocument() - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getDocument() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
getDocument() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
  Returns the currently associated document.
getDocumentMargin() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getDocumentPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
getDocumentRect() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
getDocumentSplitPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  This method initializes documentSplitPane
getDownButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes downButton
getDownRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes downRadioButton
getDownwards() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
getEditMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes editMenu
getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel
getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel
getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorAdapterListModel
getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceAdapterListModel
getElementByPosition(MouseEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeEditlInputListener
getElements(Node, T[], boolean, boolean, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getElementsOfType(Node, PaintableElement, T[], boolean) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getEndRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes endRadioButton
getError() - Method in exception info.bioinfweb.treegraph.document.io.nexus.NexusException
getErrorReporter() - Method in class info.bioinfweb.treegraph.Main
getErrors() - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
  Returns a description of the errors that occured during the last call of `CalculateColumnEdit.redo()` or `CalculateColumnEdit.evaluate()`.
getExamplePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes examplePanel
getExpressionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
  This method initializes expressionPanel
getExpressionTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
  This method initializes expressionTextField
getFileButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes fileButton
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes fileChooser
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes fileChooser
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes fileChooser.
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
  This method initializes fileChooser
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.FileDialog
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
  This method initializes fileChooser
getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes fileChooserPanel
getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes fileChooserPanel
getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes fileChooserPanel
getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
  This method initializes fileChooserPanel
getFileMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes fileMenu
getFileName() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel
getFilePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes filePanel
getFilePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
  This method initializes filePanel
getFileTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes fileTextField
getFilter() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFactory
getFilter() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFactory
getFilter(ReadWriteFormat) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory
getFilter() - Method in interface info.bioinfweb.treegraph.document.io.SingleReadWriteFactory
getFilter() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFactory
getFilter() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFactory
getFilter() - Method in interface info.bioinfweb.treegraph.graphics.export.GraphicsFactory
getFilter(GraphicFormat) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory
getFilter() - Method in class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory
getFindTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes findTextField
getFirstBranch() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstEdgeRadiusElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstIconLabel(Node, String) - Static method in class info.bioinfweb.treegraph.document.IDManager
getFirstIconLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstLabel(Node, String) - Static method in class info.bioinfweb.treegraph.document.IDManager
getFirstLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstLeaf() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstLegend() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstLineElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstNode() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstTextElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstTextLabel(Node, String) - Static method in class info.bioinfweb.treegraph.document.IDManager
getFirstTextLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstTreeElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFloat(String, float) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
getFont(float) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getFont(float) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
getFont(float) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getFontFamilyList() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes fontFamilyList
getFontFamilyPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes fontFamilyPanel
getFontFamilyTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes fontFamilyTextField
getFontHeightInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
getFontHeightPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes fontHeightPanel
getFontName() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getFontName() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
getFontName() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getFontStylePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes fontStylePanel
getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFilter
getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicFilter
getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter
getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFilter
getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFilter
getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFilter
getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFilter
getFormat() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  Returns the graphic format the user selected.
getFormatMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes formatMenu
getFormatPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes formatPanel
getFormats() - Method in class info.bioinfweb.treegraph.document.AbstractTextElement
getFormats() - Method in class info.bioinfweb.treegraph.document.Branch
getFormats() - Method in interface info.bioinfweb.treegraph.document.CornerRadiusElement
getFormats() - Method in class info.bioinfweb.treegraph.document.IconLabel
getFormats() - Method in class info.bioinfweb.treegraph.document.Label
getFormats() - Method in class info.bioinfweb.treegraph.document.Legend
getFormats() - Method in interface info.bioinfweb.treegraph.document.LineElement
getFormats() - Method in class info.bioinfweb.treegraph.document.Node
getFormats() - Method in interface info.bioinfweb.treegraph.document.PaintableElement
getFormats() - Method in class info.bioinfweb.treegraph.document.ScaleBar
getFormats() - Method in interface info.bioinfweb.treegraph.document.TextElement
getFormats() - Method in class info.bioinfweb.treegraph.document.TextLabel
getFormats() - Method in class info.bioinfweb.treegraph.document.Tree
getFormatsTabbedPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
  This method initializes formatsTabbedPane
getFormatsTabbedPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
  This method initializes formatsTabbedPane
getFormatTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes formatTextField
getFrame() - Method in class info.bioinfweb.treegraph.document.Document
getGeneralEditorPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes generalEditorPane
getGeneralPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes generalPanel
getGeneralScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes generalScrollPane
getGplEditorPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes gplTextArea
getGPLPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes gplPanel
getGplScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes gplScrollPane
getHasLengthCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
  This method initializes hasLengthCheckBox
getHeight() - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension
getHeight() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
  Defines the height of the long dashes (the height of the text below is not included.)
getHeight() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
getHeight() - Method in class info.bioinfweb.treegraph.document.position.PositionData
getHeightAbove() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
getHeightBelow() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
getHeightTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes heightTextField
getHelpMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes helpMenu
getHelpTopic() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
getHiddenBranchDataIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Searches for all the IDs of hidden data that is assigned to a branch present in the subtree under root.
getHiddenBranchDataIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
getHiddenDataAdded() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
  Returns whether hidden data has been read from commetns in the newick string (e.g. from BEAST) during the last call of `NewickStringReader.read(String, NodeBranchDataAdapter, NodeBranchDataAdapter, TranslTable, boolean)` or one of its convenience methods.
getHiddenDataMap() - Method in class info.bioinfweb.treegraph.document.Branch
getHiddenDataMap() - Method in interface info.bioinfweb.treegraph.document.HiddenDataElement
getHiddenDataMap() - Method in class info.bioinfweb.treegraph.document.Node
getHiddenNodeDataIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Searches for all the IDs of hidden data that is assigned to a node present in the subtree under root.
getHiddenNodeDataIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
getHighestChild() - Method in class info.bioinfweb.treegraph.document.Node
  Returns the upper most subnode of this node (e.g. needed for legend positioning).
getHints() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  Returns the graphic writer hints that have been specified by the user.
getHoldingBranch() - Method in class info.bioinfweb.treegraph.document.Label
getHoldingBranch() - Method in class info.bioinfweb.treegraph.document.Labels
getHorizontalRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes horizontalRadioButton
getIcon() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
getIconComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
  This method initializes iconComboBox
getIconComboBoxModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
getIconDistanceValue(IconLabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.AbstractIconLabelDistanceAdapter
getIconDistanceValue(IconLabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.IconHeightAdapter
getIconDistanceValue(IconLabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.distanceadapters.IconWidthAdapter
getIconFilled() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
getIconFilledCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
  This method initializes iconFilledCheckBox
getIconFormatsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
getIconHeight() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
getIconHeight() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel
getIconHeightInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
getIconLabelIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
getIconPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
  This method initializes iconPanel
getIconPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
  This method initializes iconPreviewPanel
getIconWidth() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
getIconWidth() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel
getIconWidthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
getID() - Method in class info.bioinfweb.treegraph.document.Label
getID() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.AbstractIDElementAdapter
getID() - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.IDElementAdapter
getID() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.AbstractLabelAdapter
getIDComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
  This method initializes idComboBox
getIDComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
  This method initializes idComboBox
getIDComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
  This method initializes idComboBox
getIdList() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
  This method initializes idList
getIdNamePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes idNamePanel
getIDNameTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes idNameTextField
getIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
  This method initializes idPanel
getIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
  This method initializes idPanel
getIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
  This method initializes idPanel
getIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Searches for all IDs (hidden data and label IDs) present in the subtree under root.
getIDValue(String) - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
  Returns the value of the current line in the column specified the passed id present.
getIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Searches for all IDs present in the subtree under root.
getImageHeight() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  Return the height entered by the user in pixels or millimeters.
getImageWidth() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  Returns the width entered by the user in pixels or millimeters.
getImportButtonGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
getImportPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes importPanel
getImportPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
  This method initializes importPanel
getImportTableDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction
getIncludeHiddenCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
  This method initializes includeHiddenCheckBox
getIncludeLeafs() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
getIncludeLeafsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
  This method initializes includeLeafsCheckBox
getIncRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes incRadioButton
getIncreaseGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
getInheritToTerminalsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes inheritToTerminalsCheckBox
getInheritToTerminalsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
  This method initializes inheritToTerminalsCheckBox
getInitialFile() - Method in class info.bioinfweb.treegraph.cmd.CmdProcessor
getInMillimeters() - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
getInMillimeters(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
getInPixels(float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
getInPixels(float, float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
getInPoints() - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
  Returns the value in DTP-Points (1 pt = 0.3527777 mm).
getInPoints(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
getInputPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
  This method initializes InputPanel
getInstance() - Static method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory
getInstance() - Static method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory
getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap
getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPainter
getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner
getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
getInstance() - Static method in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel
getInstance() - Static method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.PreferencesPanelFactory
getInstance() - Static method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
getInstance() - Static method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
getInstance() - Static method in class info.bioinfweb.treegraph.Main
getInstanceWithBranch() - Static method in class info.bioinfweb.treegraph.document.Node
getInternalFrameByFile(File) - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
getInternalFrameListener() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
getInternalInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
getInternalNodesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
  This method initializes internalNodesPanel
getInternalsRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes InternalsRadioButton
getIntervalPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes decimalPanel
getIntervalPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
  This method initializes intervalPanel
getInUnits(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
getItalicCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes italicCheckBox
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditTextElementDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  This method initializes jContentPane
getLabel() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
  Returns a deep copy of the label in the clipboard.
getLabelIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
  This method initializes labelIDPanel
getLabelIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Searches for all label IDs present in the subtree under root.
getLabelIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
getLabelingPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes labelingPanel
getLabelList() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
  Returns a deep copy of the label list in the clipboard.
getLabelNumbersPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes labelNumbersPanel
getLabelRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes labelRadioButton
getLabels() - Method in class info.bioinfweb.treegraph.document.Branch
getLabels() - Method in class info.bioinfweb.treegraph.document.Label
getLabels(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
  Returns all labels in the subtree under root.
getLabels(Labels) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
  Returns all labels of this labels-object.
getLabelsToLeftCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
  This method initializes labelsToLeftCheckBox
getLabelsWithID(Node, String) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getLabelsWithIDInBlock(Vector<Label>, Labels, boolean, String) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getLeafField(Node) - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
getLeafIndex(TextElementData) - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
getLeafInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
getLeafMargin() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
getLeafNodes(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getLeafNodesBetween(Node, Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getLeafsRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes LeafsRadioButton
getLeft() - Method in class info.bioinfweb.treegraph.document.format.Margin
getLeft() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
getLeft() - Method in class info.bioinfweb.treegraph.document.position.PositionData
getLeft() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
getLeftRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes leftRadioButton
getLegend() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
  Returns a deep copy of the legend in the clipboard.
getLegendBottom(LegendFormats) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
getLegendNumbersPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes legendNumbersPanel
getLegendOrientationPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes legendOrientationPanel
getLegendPositionTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes positionTextField
getLegends() - Method in class info.bioinfweb.treegraph.document.Legend
getLegends() - Method in class info.bioinfweb.treegraph.document.Tree
getLegends() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
getLegendsInSubtree(Tree, Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
  Returns an array of all legends which are completely anchored inside the subtree under `root`.
getLegendsReanchored() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit
getLegendsReanchored() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
getLegendsRemoved() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit
getLegendsRemoved() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
getLegendsSave() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
getLegendStartX(LegendFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
getLegendStyle() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getLegendStylePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes legendStylePanel
getLegendTop(LegendFormats) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
getLength() - Method in class info.bioinfweb.treegraph.document.Branch
getLength() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
getLengthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog
  Returns the length input and creates it if necessary.
getLengthPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog
  This method initializes lengthPanel
getLineColor() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
getLineColor(Document) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils
  Returns the default line color or its inversion depending in the backgound color of the specified document.
getLineColor() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
getLineColor() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getLineColor() - Method in interface info.bioinfweb.treegraph.document.format.LineFormats
getLineColor() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
getLineColor() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
getLineColorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
  This method initializes lineColorPanel
getLineElements(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getLineFormats() - Method in class info.bioinfweb.treegraph.document.Branch
getLineIndex() - Method in class info.bioinfweb.treegraph.document.Label
  Returns the line index of the label or -1 if it is not linked to a `Labels`-object.
getLineIndex(Label) - Method in class info.bioinfweb.treegraph.document.Labels
getLineIndex(boolean, Label) - Method in class info.bioinfweb.treegraph.document.Labels
  Returns the index of the specified label in its line.
getLineIndex(boolean, int, Label) - Method in class info.bioinfweb.treegraph.document.Labels
  Returns the index of the specified label in its line.
getLineNo() - Method in class info.bioinfweb.treegraph.document.Label
  Returns the line number of this label or -1 if it is not linked to a `Labels`-object.
getLineNo(boolean, Label) - Method in class info.bioinfweb.treegraph.document.Labels
  Returns the line number this label is located in.
getLineNoTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes lineNoTextField
getLineNumber() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
  The number of the line in which this label shall be displayed.
getLinePos() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
  The position if the icon (for labels) or the bracket (for legends).
getLinePosition() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
  If more than one element is located in the same line the line position is used to determine the order of the elements.
getLinePosTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes linePosTextField
getLines(boolean) - Method in class info.bioinfweb.treegraph.document.Labels
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getLineWidth() - Method in interface info.bioinfweb.treegraph.document.format.LineFormats
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
getLinkedNode() - Method in class info.bioinfweb.treegraph.document.Branch
getLinkedNode() - Method in class info.bioinfweb.treegraph.document.Label
getLinkedNode() - Method in class info.bioinfweb.treegraph.document.Node
getLinkedNode(PaintableElement) - Static method in class info.bioinfweb.treegraph.document.Tree
  Returns the linked node to the given element.
getLinkedNode() - Method in interface info.bioinfweb.treegraph.document.TreeElement
getLocale() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getLocale() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
  Return the local object used in the decimal formats.
getLocale() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getLocaleComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes localeComboBox
getLocaleValue() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
getLongInterval() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
  The long interval specifies how often the scale bar is labeles with a value.
getLowerBorder() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
getLowerToolBar() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel
  This method initializes editFormatToolBar
getLowestChild() - Method in class info.bioinfweb.treegraph.document.Node
  Returns the lowest subnode of this node (e.g. needed for legend positioning).
getMainFrame() - Method in class info.bioinfweb.treegraph.gui.actions.DocumentAction
getMainMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes mainMenu
getMargin() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
getMargin() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getMarginInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
getMarginInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
getMarginInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
getMarginPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes marginPanel
getMarginPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes marginPanel
getMarginPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
  This method initializes marginPanel
getMaxColor() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorPreviewPanel
getMaxColorButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes maxColorButton
getMaxWidthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
getMinColor() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorPreviewPanel
getMinColorButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes minColorButton
getMinimumSize() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getMinLength() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
getMinMaxPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This method initializes minMaxPanel
getMinSpaceAbove() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
getMinSpaceBelow() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
getMinTreeDistance() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getMinWidthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
getModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
getName() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusCommand
getName(int) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
getName(PositionPaintType) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getNameManager() - Method in class info.bioinfweb.treegraph.Main
getNegativeExampleLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
getNewMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes newMenu
getNewNameTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
  This method initializes newNameTextField
getNext() - Method in class info.bioinfweb.treegraph.document.Label
getNext(List<LabelLine>, int, int, int) - Method in class info.bioinfweb.treegraph.document.Labels
getNext() - Method in class info.bioinfweb.treegraph.document.Node
getNextLeaf() - Method in class info.bioinfweb.treegraph.document.Node
getNode() - Method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
getNode() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
getNodeBranchDataMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes nodeBranchDataMenu
getNodeByUniqueName(String) - Method in class info.bioinfweb.treegraph.document.Tree
  Searches for a node with the given unique name in this tree.
getNodeByUniqueName(Node, String) - Static method in class info.bioinfweb.treegraph.document.Tree
  Searches for a node with the given unique name in the subtree under root.
getNodeDataButtonsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes nodeDataButtonsPanel
getNodeDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes nodeDataPanel
getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes nodeDataPanel
getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
  This method initializes nodeDataPanel
getNodeDataRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes nodeDataRadioButton
getNodeNamesDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
getNodeNamesRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes nodeNamesRadioButton
getNodes(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getNodesGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
getNodesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes NodesPanel
getNoneRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes noneRadioButton
getNumberOfParameters() - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
getOpenRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes openRadioButton
getOrientation() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getOrientation() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel
getOrientation() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getOrientationGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
getOtherLineFormatsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
  This method initializes otherLineFormatsPanel
getOuterPreferencesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes preferencesPanel
getOwner() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
getOwner() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getPaintableElements(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getPaintDimension(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.Tree
  Returnes the stored paint dimension (the size of the document) for the given painter ID.
getPainter() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory
getPainter(PositionPaintType) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getPainter() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory
getPainter() - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory
getPainterType() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
getPaintStart() - Method in class info.bioinfweb.treegraph.document.Tree
getPanel(GraphicFormat) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.PreferencesPanelFactory
getParent() - Method in class info.bioinfweb.treegraph.document.Node
getParseNumericValuesCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes parseNumericValuesCheckBox
getPixelsPerMillimeter() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
getPixelsPerMillimeter() - Method in class info.bioinfweb.treegraph.gui.dialogs.ResolutionInput
getPopupMenu(PaintableElement) - Method in class info.bioinfweb.treegraph.gui.actions.ActionManagement
getPosBeforeLinePos(int) - Method in class info.bioinfweb.treegraph.document.LabelLine
  Returns the index of the label at the given line position.
getPosition(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.ConcretePaintableElement
getPosition() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  The position of a legend defined in which order vertically overlapping legends are positioned.
getPosition() - Method in exception info.bioinfweb.treegraph.document.io.newick.NewickException
getPosition(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.Legend
getPosition(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.Node
getPosition(PositionPaintType) - Method in interface info.bioinfweb.treegraph.document.PaintableElement
  Returns the stored `DataPosition`-object of an for an positioner- identifier.
getPosition(int) - Method in class info.bioinfweb.treegraph.document.TreePath
  Returns the position in this path on the specified level.
getPositioner() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory
getPositioner(PositionPaintType) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getPositioner() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory
getPositioner() - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory
getPositionLabelsToLeft() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getPositionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes positionPanel
getPositiveExampleLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
getPredifinedTable() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes predifinedTable
getPreferences() - Method in class info.bioinfweb.treegraph.Main
getPreferredScrollableViewportSize() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getPreferredScrollableViewportSize() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.BranchLengthEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.ChangeLabelIDEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CollapseNodeEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CopyColumnEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CutEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteColumnEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteOutsideIntervalEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteSubelementsEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.EditNodeBranchDataEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLabelEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLabelsEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLegendEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertSiblingEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertSubtreeEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.LadderizeEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.MoveSubtreeEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteAllLabelsEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteLabelEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteLegendEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteRootEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteSiblingEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteSubtreeEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveLabelEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveLegendEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RenameDataIDEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RescaleNodeDataEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.SeparateBranchEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.SetColumnTypeEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.TextElementEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.file.ImportTableEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.GlobalFormatsEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.OperatorsEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ReanchorLegendEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleBranchLengthsEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ShowHideScaleBarEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ShowRootedEdit
getPreviewLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
getPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
  This method initializes previewPanel
getPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes previewPanel
getPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel
  This method initializes previewPanel
getPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
  This method initializes previewPanel
getPreviewScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
  This method initializes previewScrollPane
getPreviewTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes previewTextField
getPrevious() - Method in class info.bioinfweb.treegraph.document.Label
getPrevious() - Method in class info.bioinfweb.treegraph.document.Node
getPreviousLeaf() - Method in class info.bioinfweb.treegraph.document.Node
getPrintRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes printRadioButton
getQualitySlider() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.JPEGPrefPanel
  This method initializes qualitySlider
getReader() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFactory
getReader() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFactory
getReader(File) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory
getReader(ReadWriteFormat) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory
getReader() - Method in interface info.bioinfweb.treegraph.document.io.SingleReadWriteFactory
getReader() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFactory
getReader() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFactory
getRecentlyUsedList() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
  This method initializes recentlyUsedList
getRecentlyUsedListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
getRecentlyUsedPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
  This method initializes recentlyUsedPanel
getRecentlyUsedScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
  This method initializes recentlyUsedScrollPane
getRedoMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes redoMenu
getRedoPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
getRemoveButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes removeButton
getRenameButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
  This method initializes renameButton
getReplaceButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes replaceButton
getReplacePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes replacePanel
getReplaceRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes replaceRadioButton
getReplaceTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes replaceTextField
getResourcePath(String) - Static method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
getRight() - Method in class info.bioinfweb.treegraph.document.format.Margin
getRight() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
getRightInMillimeters() - Method in class info.bioinfweb.treegraph.document.position.PositionData
getRightInPixels(float) - Method in class info.bioinfweb.treegraph.document.position.PositionData
getRightRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes leafsRadioButton
getRoundedInPixels(float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
  Gives the uprounded value in pixels
getRoundedInPixels(float, float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
getRow(Node) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getRowCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getRowCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
getRowCount() - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getScaleBar() - Method in class info.bioinfweb.treegraph.document.Tree
getScaleBar() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getScaleInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
getScalePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
  This method initializes rescalePanel
getScrollableBlockIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getScrollableBlockIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
getScrollableTracksViewportHeight() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getScrollableTracksViewportHeight() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
getScrollableTracksViewportWidth() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getScrollableTracksViewportWidth() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
getScrollableUnitIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getScrollableUnitIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
getSearchPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
  This method initializes searchPanel
getSearchTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
  This method initializes searchTextField
getSelctedIndex() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
  Returns the currently selected adapter.
getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  Returns the selected adapter in the node/branch data table.
getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  Returns the selected file with a valid extension.
getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.FileDialog
  Override this method if you e.g. want to add a default extension.
getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
getSelectedItem() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel
getSelectedItem() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
getSelectedNode(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.MoveSubtreeAction
  Returns the node that should be moved if the selection contains this node or its afferent branch as the first element.
getSelection() - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
getSelection() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
getSelectionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
  This method initializes selectionPanel
getSelectMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes selectMenu
getSeparator() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
getSeparator() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
getSeparatorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes separatorPanel
getSeparatorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
  This method initializes separatorPanel
getSeparatorTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
  This method initializes separatorTextField
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.CrossIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.EllipseIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.HexagonIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.OctagonIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RectangleIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RoundRectangleIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.ShapeLabelIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TitedCrossIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TitedHexagonIcon
getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TriangleIcon
getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler
getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
getShowRooted() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getShowRootedCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
  This method initializes showRootedCheckBox
getShowScaleBar() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getShowScaleBarCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
  This method initializes showScaleBarCheckBox
getShowWarnings() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
getShowWarnings() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
getShowWarnings() - Method in interface info.bioinfweb.treegraph.document.undo.WarningEdit
getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel
getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel
getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorAdapterListModel
getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceAdapterListModel
getSlider() - Method in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup
  This method initializes slider
getSmallInterval() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
  The small interval speccifies the distance between the small dashes of the branch length scale bar in branch length units.
getSourceComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog
  This method initializes sourceComboBox
getSourceComboBoxModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog
getSourceInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
  Creates the source input if necessary.
getSourcePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
  This method initializes sourcePanel
getSourcePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog
  This method initializes sourcePanel
getSpacing() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  The legend spacing is the distance between the bracket and the text of a legend.
getSpacing() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
  The spacing between the icon or bracket and the text.
getSrcAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
getSrcInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
getStartPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes startPanel
getStoredValue() - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
  Returns the stored value in millimeters or in branch length units.
getString(String, String) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
getStringFormatterFactory() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
getStringRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
  This method initializes stringRadioButton
getStyleGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
getSubtree() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
  Returns a deep copy of the subtree in the clipboard.
getSubtreeLegends() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
  Returns a deep copies of the legends attached to the ubtree in the clipboard.
getSupportValue(Node) - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
getTable() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes table
getTable() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  This method initializes table
getTableModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
getTableModel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes tableScrollPane
getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes tableScrollPane
getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  This method initializes tableScrollPane
getTabRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
  This method initializes tabRadioButton
getTabs() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
getTargetDataButtonGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
getTargetList() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
  This method initializes targetList
getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
getTargetNode() - Method in class info.bioinfweb.treegraph.document.Branch
getTargetPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
  This method initializes targetPanel
getTargetScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
  This method initializes targetScrollPane
getTargetTypePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes targetTypePanel
getTerminalDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
getTerminalsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes terminalsPanel
getText() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
getText(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
getText(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
getText(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
getText(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
getText() - Method in class info.bioinfweb.treegraph.document.TextElementData
  Returns the stored string value or `null` is no string is stored.
getText() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
getTextColor() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getTextColor(Document) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils
  Returns the default text color or its inversion depending in the backgound color of the specified document.
getTextColor() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
getTextColor() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getTextElement() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
getTextElements(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
getTextHeight() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getTextHeight() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
getTextHeight() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getTextLabelIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
getTextLabelIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
getTextPos() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
getTextPos() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
getTextStyle() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
getTextStyle() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
getTextStyle() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getTitleLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
getTokens() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusCommand
getToolBarPanel() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes toolBarPanel
getToolTipText(MouseEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
  This method is overwriten to show the internal node names or label IDs as tooltip text.
getTop() - Method in class info.bioinfweb.treegraph.document.format.Margin
getTop() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
getTop() - Method in class info.bioinfweb.treegraph.document.position.PositionData
getTop() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
getTranslateInternalNodesCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
  This method initializes translateInternalNodesCheckBox
getTranslateInternalsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
  This method initializes translateInternalsCheckBox
getTranslTable() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
getTransparentCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TransparenrtBgPrefPanel
  This method initializes transparentCheckBox
getTree() - Method in class info.bioinfweb.treegraph.document.Document
getTree(int) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
getTree() - Method in class info.bioinfweb.treegraph.document.Legends
getTreeComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
  This method initializes treeComboBox
getTreeDistance() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
getTreeElement(int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getTreeScrollPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  This method initializes scrollPane
getTreeViewInputListener() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
getTreeViewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
  This method initializes treeViewPanel
getTreeViewPanel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  This method initializes treeViewPanel
getTreeWidthRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes rightRadioButton
getType() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
getType(TreePositioner) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getType(TreePainter) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getUnderlineCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  This method initializes underlineCheckBox
getUndoManager() - Method in class info.bioinfweb.treegraph.document.Document
getUndoMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes undoMenu
getUndoPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
getUniqueName() - Method in class info.bioinfweb.treegraph.document.Node
  The unique name is used to identify nodes in the XML-file which are associated with legends.
getUnit() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getUnit() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRulerUnitField
getUnitComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes unitComboBox
getUnterminatedCommentException(int) - Static method in exception info.bioinfweb.treegraph.document.io.newick.NewickException
getUnterminatedNameException(int) - Static method in exception info.bioinfweb.treegraph.document.io.newick.NewickException
getUpButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
  This method initializes upButton
getUpperBorder() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
getUpperToolBar() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel
  This method initializes fileviewWindowToolBar
getUpRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes upRadioButton
getValue() - Method in class info.bioinfweb.treegraph.document.format.operate.AbstractMarginOperator
getValue(String) - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
getValue(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
getValue() - Method in class info.bioinfweb.treegraph.gui.dialogs.DistanceValueInput
getValue() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
getValue(NodeBranchDataAdapter, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
getValues() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
getValuesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
  This method initializes valuesPanel
getValueTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
  This method initializes textTextField
getVector(Node, boolean, boolean, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Returns a vector of IDs which is sorted alphabetically.
getVersion() - Method in class info.bioinfweb.treegraph.document.Document
getVersion() - Method in class info.bioinfweb.treegraph.Main
getViewMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes viewMenu
getWarningsMessages() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
getWhitespaceCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
  This method initializes whitespaceCheckBox
getWidth() - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension
getWidth() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
getWidth() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
getWidth() - Method in class info.bioinfweb.treegraph.document.position.PositionData
getWidthTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
  This method initializes widthTextField
getWikiHelp() - Method in class info.bioinfweb.treegraph.Main
getWindowListener() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
getWindowMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes windowMenu
getWordsOnlyCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
  This method initializes wordsOnlyCheckBox
getWordsOnlyCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
  This method initializes wordsOnlyCheckBox
getWriter() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFactory
getWriter() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFactory
getWriter(ReadWriteFormat) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory
getWriter() - Method in interface info.bioinfweb.treegraph.document.io.SingleReadWriteFactory
getWriter() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFactory
getWriter() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFactory
getWriter() - Method in interface info.bioinfweb.treegraph.graphics.export.GraphicsFactory
getWriter(GraphicFormat) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory
getWriter() - Method in class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory
getZeroLeftRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes zeroLeftRadioButton
getZeroPosGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
getZeroRightRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes ueroRightRadioButton
getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.FitZoomToHeightAction
getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.FitZoomToWidthAction
getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.FitZoomToWidthHeightAction
getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetUserZoomAction
getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetZoomAction
getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetZoomToOriginalAction
getZoom() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
GlobalFormats - Class in info.bioinfweb.treegraph.document.format
GlobalFormats() - Constructor for class info.bioinfweb.treegraph.document.format.GlobalFormats
GlobalFormatsDialog - Class in info.bioinfweb.treegraph.gui.dialogs
GlobalFormatsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
GlobalFormatsEdit - Class in info.bioinfweb.treegraph.document.undo.format
GlobalFormatsEdit(Document, GlobalFormats) - Constructor for class info.bioinfweb.treegraph.document.undo.format.GlobalFormatsEdit
gplEditorPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
gplPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
gplScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
GraphicFilter - Class in info.bioinfweb.treegraph.graphics.export
GraphicFilter() - Constructor for class info.bioinfweb.treegraph.graphics.export.GraphicFilter
GraphicFormat - Enum in info.bioinfweb.treegraph.graphics.export
GraphicFormat() - Constructor for enum info.bioinfweb.treegraph.graphics.export.GraphicFormat
GraphicsFactory - Interface in info.bioinfweb.treegraph.graphics.export
GraphicWriter - Interface in info.bioinfweb.treegraph.graphics.export
GraphicWriterFactory - Class in info.bioinfweb.treegraph.graphics.export
GraphicWriterFactory() - Constructor for class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory
GraphicWriterHints - Class in info.bioinfweb.treegraph.graphics.export
GraphicWriterHints() - Constructor for class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
greenFactor - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit

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