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## G

g - Variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
generalPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
generate(CommandLineReader) - Static method in class info.bioinfweb.treegraph.cmd.ImageGenerator
generatePattern(String, boolean, boolean) - 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(int) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
get(String, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
get(double, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
get(String) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
get(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel
get(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
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(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
getAdapterComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.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.datatable.ExportNodeDataDialog
  This method initializes addButton
getAddToValuesButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes addToValuesButton
getAfferentBranch() - Method in class info.bioinfweb.treegraph.document.Node
getAlignGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
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
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
getApplyNameTableButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes applyNameTableButton
getArrowDimensions() - Method in class info.bioinfweb.treegraph.document.format.CharShiftFormats
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
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
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.PositionData
getBottomInPixels(float) - Method in class info.bioinfweb.treegraph.document.PositionData
getBraceRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes braceRadioButton
getBracketPos() - Method in class info.bioinfweb.treegraph.document.LegendPositionData
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
getBranchLabelPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
getBranchLengthScale() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getBranchLengthScale() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
getButtonGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
getButtonPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes buttonPanel
getCaseSensitiveCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.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.BranchWidthFromNodeDataDialog
  This method initializes changeUndefinedCheckBox
getChangeUndefinedCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes hCheckBox
getCharShiftLabels(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getChildIndex(Node) - Method in class info.bioinfweb.treegraph.document.Node
getChildren() - Method in class info.bioinfweb.treegraph.document.Node
getClearButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  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
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.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes colorPanel
getColorPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes colorPreviewPanel
getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel
getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getColumnCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel
getColumnCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
getColumnCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel
getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput
getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NewNodeDataInput
getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
getCompressionMethodComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.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
getCopyButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes copyButton
getCopyPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
  This method initializes copyPanel
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenDataAdapter
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.LabelAdapter
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.NodeNameAdapter
getData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter
getData() - Method in class info.bioinfweb.treegraph.document.TextElement
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.BranchLengthAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenBranchDataAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenNodeDataAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.LabelAdapter
getDataElement(Node) - Method in interface info.bioinfweb.treegraph.document.nodedata.NodeDataAdapter
  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.nodedata.NodeNameAdapter
getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.UniqueNameAdapter
getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenBranchDataAdapter
getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenDataAdapter
getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenNodeDataAdapter
getDataSplitPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes dataSplitPane
getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.BranchLengthAdapter
getDecimal(Node) - Method in interface info.bioinfweb.treegraph.document.nodedata.NodeDataAdapter
getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter
getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.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.TextFormats
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenDataAdapter
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.LabelAdapter
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.NodeNameAdapter
getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter
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
getDefaultType() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
getDeleteButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes deleteButton
getDescent() - Method in class info.bioinfweb.treegraph.document.format.TextFormats
getDescent() - Method in class info.bioinfweb.treegraph.document.LabelLine
  Return the maximal descent of all labels in this line.
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.datatable.CopyNodeDataDialog
getDestInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
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.NodePositionData
getDifBelow() - Method in class info.bioinfweb.treegraph.document.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.exporttographic.ExportToGraphicDialog
  This method initializes pngPanel
getDirectionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes directionPanel
getDocument() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
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.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
getDownButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  This method initializes downButton
getDownRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes downRadioButton
getEdgeRadius() - Method in interface info.bioinfweb.treegraph.document.format.EdgeRadiusFormats
getEdgeRadius() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
getEdgeRadius() - 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 edge radius.
getEditButtonsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes editButtonsPanel
getEditMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes editMenu
getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataComboBoxModel
getElementByPosition(MouseEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeEditlInputListener
getElements(Node, T[], boolean, 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
getExamplePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes examplePanel
getExportButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes exportButton
getExpValuesButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes expValuesButton
getFileButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  This method initializes fileButton
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
  This method initializes fileChooser
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
  This method initializes fileChooser.
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.ExportToNewickStringDialog
  This method initializes fileChooser
getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
  This method initializes fileChooser
getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
  This method initializes fileChooserPanel
getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
  This method initializes fileChooserPanel
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.OpenDialog
  This method initializes fileChooserPanel
getFileMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  This method initializes fileMenu
getFilePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  This method initializes filePanel
getFileTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  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
getFirstCharShiftLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
getFirstEdgeRadiusElement() - 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
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() - 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.TextFormats
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.TextFormats
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.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.Branch
getFormats() - Method in class info.bioinfweb.treegraph.document.CharShiftLabel
getFormats() - Method in interface info.bioinfweb.treegraph.document.EdgeRadiusElement
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 class 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
getGeneralPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
  This method initializes generalPanel
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(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.LabelLine
getHeight() - Method in class info.bioinfweb.treegraph.document.LegendPositionData
getHeight() - Method in class info.bioinfweb.treegraph.document.PositionData
getHeightAbove() - Method in class info.bioinfweb.treegraph.document.NodePositionData
getHeightBelow() - Method in class info.bioinfweb.treegraph.document.NodePositionData
getHeightTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.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
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.exporttographic.ExportToGraphicDialog
  Returns the graphic writer hints that have been difined by the user.
getHoldingBranch() - Method in class info.bioinfweb.treegraph.document.Labels
getHorizontalLabelSpacing() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getHorizontalRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
  This method initializes horizontalRadioButton
getID() - Method in class info.bioinfweb.treegraph.document.Label
getID() - Method in class info.bioinfweb.treegraph.document.nodedata.IDElementAdapter
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.NewTextLabelDialog
  This method initializes idComboBox
getIdList() - Method in class info.bioinfweb.treegraph.gui.dialogs.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.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.
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.exporttographic.ExportToGraphicDialog
  Return the height entered by the user in pixels or millimeters.
getImageWidth() - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
  Returns the width entered by the user in pixels or millimeters.
getImportButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes importButton
getImportPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.AssignImportColumnsDialog
  This method initializes importPanel
getIncludeHiddenCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
  This method initializes includeHiddenCheckBox
getIncludeLeafs() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
getIncludeLeafsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
  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
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.BranchWidthFromNodeDataDialog
  This method initializes inputPanel
getInputPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes inputPanel
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.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.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
getIntervalPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes decimalPanel
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.ApplyNameTableDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.BranchWidthFromNodeDataDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.AssignImportColumnsDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes jContentPane
getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  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.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.exporttographic.ExportToGraphicDialog
  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.ExportToNewickStringDialog
  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.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.SearchTextDialog
  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.
getLabelBlockDistance() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getLabelBlockMargin() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getLabelIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.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
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
getLeafInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
getLeafList(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
  Returns the leaf list of `node` that is stored in its attribute map.
getLeafMargin() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getLeafNodes(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getLeft() - Method in class info.bioinfweb.treegraph.document.format.Margin
getLeft() - Method in class info.bioinfweb.treegraph.document.LegendPositionData
getLeft() - Method in class info.bioinfweb.treegraph.document.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.
getLegendMargin() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
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
getLegendPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
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
getLegendSpacing() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
  The legend spacing is the distance between the bracket and the text of a legend.
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
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
getLength() - Method in class info.bioinfweb.treegraph.document.Branch
getLength() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
getLineColor() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
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.LineFormatsEntity
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
getLineNoTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
  This method initializes lineNoTextField
getLineNumber() - Method in class info.bioinfweb.treegraph.document.format.LabelPositionFormats
  The number of the line in which this label shall be displayed.
getLinePosition() - Method in class info.bioinfweb.treegraph.document.format.LabelPositionFormats
  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
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
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.LineFormatsEntity
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
getLinkedNode(PaintableElement) - Static method in class info.bioinfweb.treegraph.document.Tree
  Returns the linked node to the given element.
getLocale() - Method in class info.bioinfweb.treegraph.document.format.TextFormats
  Return the local object used in the decimal formats.
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
getLogValuesButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes logButton
getLongInterval() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
  The long interval specifies how often the scale bar is labeles with a value.
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
getMaxColor() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorPreviewPanel
getMaxColorButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes maxColorButton
getMaxWidthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.BranchWidthFromNodeDataDialog
getMinColor() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorPreviewPanel
getMinColorButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes minColorButton
getMinDocumentDimension() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getMinimumSize() - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
getMinLength() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
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.BranchWidthFromNodeDataDialog
getMultiplyValuesButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes multiplyValuesButton
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
getNewID(int) - Method in class info.bioinfweb.treegraph.document.undo.edit.AssignLabelIDsEdit
getNewNameTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.RenameIDDialog
  This method initializes newNameTextField
getNext() - Method in class info.bioinfweb.treegraph.document.Node
getNode() - Method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
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.datatable.ExportNodeDataDialog
  This method initializes nodeDataButtonsPanel
getNodeDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
getNodeDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
  This method initializes nodeDataPanel
getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  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
getNodeMargin() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
getNodePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
getNodes(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
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.exporttographic.ExportToGraphicDialog
  This method initializes preferencesPanel
getOwner() - Method in class info.bioinfweb.treegraph.document.format.LabelPositionFormats
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.exporttographic.PreferencesPanelFactory
getParent() - Method in class info.bioinfweb.treegraph.document.Node
getParseNumericValuesCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
  This method initializes parseNumericValuesCheckBox
getPixelsPerMillimeter() - Method in class info.bioinfweb.treegraph.gui.dialogs.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.
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
getPositionFormats() - Method in class info.bioinfweb.treegraph.document.CharShiftLabel
getPositionFormats() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
getPositionFormats() - Method in class info.bioinfweb.treegraph.document.Label
getPositionFormats() - Method in class info.bioinfweb.treegraph.document.TextLabel
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.AddSupportValuesEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.ApplyNameTableEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.AssignLabelIDsEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.BranchLengthEdit
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.CutEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
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.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.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.TextElementEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.BranchWidthsFromNodeDataEdit
getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsFromNodeDataEdit
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.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.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.Node
getQualitySlider() - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.JPEGPrefPanel
  This method initializes qualitySlider
getRaiseToButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes raiseToButton
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
getRedoPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
getRemoveButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  This method initializes removeButton
getRenameButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.RenameIDDialog
  This method initializes renameButton
getRenameIDButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes renameIDButton
getReplaceButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes replaceButton
getReplaceButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  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
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.PositionData
getRightInPixels(float) - Method in class info.bioinfweb.treegraph.document.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
getRowCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel
getRowCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
getRowCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
getScaleBar() - Method in class info.bioinfweb.treegraph.document.Tree
getScaleBar() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
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
getScrollPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
  This method initializes scrollPane
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
getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
  Returns the selected file with a valid extension.
getSelectedItem() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.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
getSeparatorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
  This method initializes separatorPanel
getSeparatorTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
  This method initializes separatorTextField
getSetDecimalToAllButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes setDecimalToAllButton
getSetTextToAllButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes setTextToAllButton
getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.nodedata.NodeNameAdapter
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.nodedatainput.NodeDataComboBoxModel
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.BranchWidthFromNodeDataDialog
  This method initializes nodeDataComboBox
getSourceComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
  This method initializes sourceComboBox
getSourceComboBoxModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.BranchWidthFromNodeDataDialog
getSourceComboBoxModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.colorfrombranchwidth.ColorsFromNodeDataDialog
getSrcAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
getSrcInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
getStartPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This method initializes startPanel
getStateAfter() - Method in class info.bioinfweb.treegraph.document.CharShiftLabel
getStateAfterFormats() - Method in class info.bioinfweb.treegraph.document.format.CharShiftFormats
getStateBefore() - Method in class info.bioinfweb.treegraph.document.CharShiftLabel
getStateBeforeFormats() - Method in class info.bioinfweb.treegraph.document.format.CharShiftFormats
getStoredValue() - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
  Returns the stored value in millimeters or in branch length units.
getString() - Method in class info.bioinfweb.treegraph.document.TextElementData
  Returns the stored string value or `null` is no string is stored.
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.ApplyNameTableDialog
  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.
getSupportValue(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
getTable() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes table
getTable() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  This method initializes table
getTableModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
getTableModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes tableScrollPane
getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  This method initializes tableScrollPane
getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
  This method initializes tableScrollPane
getTabRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
  This method initializes tabRadioButton
getTabs() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
getTargetNode() - Method in class info.bioinfweb.treegraph.document.Branch
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.nodedata.BranchLengthAdapter
getText(Node) - Method in interface info.bioinfweb.treegraph.document.nodedata.NodeDataAdapter
getText(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter
getText(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.UniqueNameAdapter
getText() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
getTextColor() - Method in class info.bioinfweb.treegraph.document.format.TextFormats
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.nodedatainput.NewNodeDataInput
getTextHeight() - Method in class info.bioinfweb.treegraph.document.format.TextFormats
getTextLabels(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
getTextPos() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
getTextPos() - Method in class info.bioinfweb.treegraph.document.LegendPositionData
getTextStyle() - Method in class info.bioinfweb.treegraph.document.format.TextFormats
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.LegendPositionData
getTop() - Method in class info.bioinfweb.treegraph.document.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.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.dialogs.datatable.NodeDataTableModel
getTreeScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes treeScrollPane
getTreeViewInputListener() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
getTreeViewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
  This method initializes treeViewPanel
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
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.exporttographic.ExportToGraphicDialog
  This method initializes unitComboBox
getUnterminedNameException(int) - Static method in exception info.bioinfweb.treegraph.document.io.newick.NewickException
getUpButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
  This method initializes upButton
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.gui.dialogs.DistanceValueInput
getValue() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel
getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
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) - Static method in class info.bioinfweb.treegraph.document.IDManager
getVersion() - Method in class info.bioinfweb.treegraph.document.Document
getVersion() - Method in class info.bioinfweb.treegraph.Main
getVerticalLabelSpacing() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
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.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(PositionPaintType, float) - Method in class info.bioinfweb.treegraph.document.LabelLine
getWidth() - Method in class info.bioinfweb.treegraph.document.LegendPositionData
getWidth() - Method in class info.bioinfweb.treegraph.document.PositionData
getWidthTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.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.ColorsFromNodeDataEdit

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