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## A

AboutAction - Class in info.bioinfweb.treegraph.gui.actions.help
AboutAction() - Constructor for class info.bioinfweb.treegraph.gui.actions.help.AboutAction
AboutDialog - Class in info.bioinfweb.treegraph.gui.dialogs
  The about dialog of TreeGraph 2.
AboutDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
above - Variable in class info.bioinfweb.treegraph.document.format.LabelFormats
above - Variable in class info.bioinfweb.treegraph.document.format.operate.LabelAboveOperator
aboveBelowGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
aboveBelowPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
aboveMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
aboveRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
AbstractBranchOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractBranchOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractBranchOperator
AbstractDistanceValueAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
AbstractDistanceValueAdapter() - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractDistanceValueAdapter
AbstractDocumentReader - Class in info.bioinfweb.treegraph.document.io
  Implements basic functionality (especially method delegation) for document readers.
AbstractDocumentReader() - Constructor for class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
AbstractDocumentWriter - Class in info.bioinfweb.treegraph.document.io
AbstractDocumentWriter() - Constructor for class info.bioinfweb.treegraph.document.io.AbstractDocumentWriter
AbstractFilter - Class in info.bioinfweb.treegraph.document.io
AbstractFilter() - Constructor for class info.bioinfweb.treegraph.document.io.AbstractFilter
AbstractGraphicalLabelOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractGraphicalLabelOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractGraphicalLabelOperator
AbstractGraphicWriter - Class in info.bioinfweb.treegraph.graphics.export
AbstractGraphicWriter() - Constructor for class info.bioinfweb.treegraph.graphics.export.AbstractGraphicWriter
AbstractIconLabelDistanceAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
AbstractIconLabelDistanceAdapter(String) - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractIconLabelDistanceAdapter
AbstractIconLabelOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractIconLabelOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractIconLabelOperator
AbstractIDElementAdapter - Class in info.bioinfweb.treegraph.document.nodebranchdata
  Node data adapters that need to store an ID can be inherited from this abstract class.
AbstractIDElementAdapter(String) - Constructor for class info.bioinfweb.treegraph.document.nodebranchdata.AbstractIDElementAdapter
AbstractLabelAdapter - Class in info.bioinfweb.treegraph.gui.dialogs.specialformats
AbstractLabelAdapter(String) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.AbstractLabelAdapter
AbstractLabelDistanceAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
AbstractLabelDistanceAdapter(String) - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLabelDistanceAdapter
AbstractLabelMarginOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractLabelMarginOperator(DistanceValue) - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractLabelMarginOperator
AbstractLabelOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractLabelOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractLabelOperator
AbstractLeafMarginOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractLeafMarginOperator(DistanceValue) - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractLeafMarginOperator
AbstractLegendAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
  This class is the superclass of all distance adapters which have emty implementations of their methods and are only used to be selectable items in an adapter list.
AbstractLegendAdapter() - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLegendAdapter
AbstractLegendMarginOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractLegendMarginOperator(DistanceValue) - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractLegendMarginOperator
AbstractLegendOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractLegendOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractLegendOperator
AbstractLineOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractLineOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractLineOperator
AbstractLoadLogger - Class in info.bioinfweb.treegraph.document.io.log
  Implements basic functionality (especially method delegation) of a load logger.
AbstractLoadLogger() - Constructor for class info.bioinfweb.treegraph.document.io.log.AbstractLoadLogger
AbstractMarginOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractMarginOperator(DistanceValue) - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractMarginOperator
AbstractNodeBranchDataAdapter - Class in info.bioinfweb.treegraph.document.nodebranchdata
  Implements a basic `equals()`-method for all node/branch data adapters.
AbstractNodeBranchDataAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodebranchdata.AbstractNodeBranchDataAdapter
AbstractOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractOperator
AbstractPieChartLabelOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractPieChartLabelOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractPieChartLabelOperator
AbstractSelectionAction - Class in info.bioinfweb.treegraph.gui.actions.select
  Abstract precursor of all actions that manipulate the document selection.
AbstractSelectionAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.AbstractSelectionAction
AbstractTextElement - Class in info.bioinfweb.treegraph.document
  This class can be used as the acestor of all classes that represent document elements which contain text or decimal values.
AbstractTextElement() - Constructor for class info.bioinfweb.treegraph.document.AbstractTextElement
AbstractTextElementDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelement
  Implements basic functionalities for dialogs used to edit a textual document element.
AbstractTextElementDialog(Dialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
AbstractTextElementDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
AbstractTextOperator - Class in info.bioinfweb.treegraph.document.format.operate
AbstractTextOperator() - Constructor for class info.bioinfweb.treegraph.document.format.operate.AbstractTextOperator
AbstractXMLFilter - Class in info.bioinfweb.treegraph.document.io
AbstractXMLFilter(String) - Constructor for class info.bioinfweb.treegraph.document.io.AbstractXMLFilter
accept(File) - Method in class info.bioinfweb.treegraph.document.io.AbstractFilter
accept(File) - Method in class info.bioinfweb.treegraph.document.io.AbstractXMLFilter
accept(File) - Method in interface info.bioinfweb.treegraph.document.io.DocumentFilter
accept(File) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFilter
  Tests if the specified file has a valid extension and starts with `#NEXUS`.
ActionManagement - Class in info.bioinfweb.treegraph.gui.actions
  This class organizes the action objects of TreeGraph.
ActionManagement(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.ActionManagement
actionManagement - Variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.DocumentAction
  Determines the currently active internal frame and passes it to `DocumentAction.onActionPerformed(ActionEvent, TreeInternalFrame)`.
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.file.NewDocumentAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.file.OpenAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.help.AboutAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.help.HelpTopicAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.help.HomepageAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.window.CascadeAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.window.SelectFrameAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.window.TileHorizontalAction
actionPerformed(ActionEvent) - Method in class info.bioinfweb.treegraph.gui.actions.window.TileVerticalAction
adapter - Variable in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit
adapter - Variable in class info.bioinfweb.treegraph.document.undo.edit.RescaleNodeDataEdit
adapter - Variable in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
adapter - Variable in class info.bioinfweb.treegraph.document.undo.NodeBranchDataBackup
adapter - Variable in class info.bioinfweb.treegraph.document.undo.NodeBranchDataEdit
adapterComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
adapterComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
adapterMap - Variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
adapters - Variable in class info.bioinfweb.treegraph.document.undo.file.ImportTableEdit
adapters - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
adapters - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
adapters - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorAdapterListModel
adapters - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceAdapterListModel
adapters - Variable in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
add(DistanceValue) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
add(float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
  Adds the specified value to the stored value in millimeters.
add(String, String) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
add(String, String) - Method in class info.bioinfweb.treegraph.document.io.nexus.TranslTable
add(Label) - Method in class info.bioinfweb.treegraph.document.Labels
  Adds a label to the List.
add(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
add(LoggerMessage) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.MessagesListModel
add(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
addAll(Collection<? extends ConcretePaintableElement>) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
addButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
addButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
addDefaultColors(PieChartLabelFormats, int) - Method in class info.bioinfweb.treegraph.document.PieColorManager
addEdit(UndoableEdit) - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
addElementsOnNode(List<PaintableElement>, Node, Class<T>) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
addend - Variable in class info.bioinfweb.treegraph.document.undo.edit.RescaleNodeDataEdit
addEntry(String, String) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
addError(List<String>) - Method in interface info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatTab
  Adds error messages to the given list, if this tab contains any invalid user inputs.
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
addError(List<String>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
addExpression(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel
  Adds `expression` to the list.
addField(LeafField) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
addHints(GraphicWriterHints) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.JPEGPrefPanel
addHints(GraphicWriterHints) - Method in interface info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.PreferencesPanel
  This method should add the graphic writer hints that are specified by the components contained in the particular implementation
addHints(GraphicWriterHints) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TIFFPrefPanel
addHints(GraphicWriterHints) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TransparentBgPrefPanel
addInputListener(NodeDataInputListener) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
addInternalFrame(JInternalFrame) - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
addInternalFrame(Document) - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
additionalCount - Variable in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
addLabelBlock(List<Label>, boolean, boolean, boolean, boolean) - Method in class info.bioinfweb.treegraph.document.Labels
addLabelBlock(Vector<PaintableElement>, Labels, boolean) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
addLabelsWithID(Vector<Label>, Node, String) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
addLeafFields(Node, TextElementDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
  Adds a boolean field which indicates the leafs located under `root` to the attribute map of `root`.
addLeafList(List<TextElementData>, Node, TextElementDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
  Fills the specified list with the values of all leafs under `root`.
addLeafNodesBetween(Vector<Node>, Node, int, TreePath, TreePath) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
addMessage(LoggerMessage) - Method in class info.bioinfweb.treegraph.cmd.CmdLoadLogger
addMessage(String, int) - Method in class info.bioinfweb.treegraph.document.io.log.AbstractLoadLogger
addMessage(String) - Method in class info.bioinfweb.treegraph.document.io.log.AbstractLoadLogger
addMessage(LoggerMessage) - Method in interface info.bioinfweb.treegraph.document.io.log.LoadLogger
  Outputs a usual message to the user.
addMessage(String) - Method in interface info.bioinfweb.treegraph.document.io.log.LoadLogger
  Outputs a usual message to the user.
addMessage(String, int) - Method in interface info.bioinfweb.treegraph.document.io.log.LoadLogger
  Outputs a usual message to the user.
addMessage(LoggerMessage) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
addMessage(String, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
addMessage(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
addNewAdapters() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
addOperator(FormatOperator) - Method in class info.bioinfweb.treegraph.document.format.operate.OperatorMap
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
addOperators(List<FormatOperator>) - Method in interface info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatTab
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
addOperators(List<FormatOperator>) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
addPieColor(Color) - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
addPieColor(int, Color) - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
addSpacer(JPanel, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
  This method initializes this
addSubtree(Vector<PaintableElement>, Node, boolean, Class<? extends PaintableElement>) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer
AddSupportValuesAction - Class in info.bioinfweb.treegraph.gui.actions.file
AddSupportValuesAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.AddSupportValuesAction
AddSupportValuesDialog - Class in info.bioinfweb.treegraph.gui.dialogs.io
AddSupportValuesDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
AddSupportValuesEdit - Class in info.bioinfweb.treegraph.document.undo.file
AddSupportValuesEdit(Document, Document, TextElementDataAdapter, AddSupportValuesEdit.TargetType, String, NodeBranchDataAdapter, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
AddSupportValuesEdit.TargetType - Enum in info.bioinfweb.treegraph.document.undo.file
AddSupportValuesEdit.TargetType() - Constructor for enum info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit.TargetType
addTextStyle(int) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
addTextStyle(int) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
addTextStyle(int) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
addToNode(NodeLadderizeComparable[], Node) - Static method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
  This method is used to reinsert sorted elements in the a subtree.
addTranscodingHints(Transcoder, GraphicWriterHints) - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGWriter
addTranscodingHints(Transcoder, GraphicWriterHints) - Method in class info.bioinfweb.treegraph.graphics.export.SVGTranscodeWriter
  This method can be overwritten to add more transcoding hints to the transcoder.
addTranscodingHints(Transcoder, GraphicWriterHints) - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFWriter
addTreeViewListener(TreeViewPanelListener) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
addValueID(int, String) - Method in class info.bioinfweb.treegraph.document.PieChartLabel
addValueID(String) - Method in class info.bioinfweb.treegraph.document.PieChartLabel
addView(DocumentListener) - Method in class info.bioinfweb.treegraph.document.Document
addWarning(String, int) - Method in class info.bioinfweb.treegraph.document.io.log.AbstractLoadLogger
addWarning(String) - Method in class info.bioinfweb.treegraph.document.io.log.AbstractLoadLogger
addWarning(String) - Method in interface info.bioinfweb.treegraph.document.io.log.LoadLogger
  Outputs a warning message to the user.
addWarning(String, int) - Method in interface info.bioinfweb.treegraph.document.io.log.LoadLogger
  Outputs a warning message to the user.
addWarning(String, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
addWarning(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
afferentBranch - Variable in class info.bioinfweb.treegraph.document.Node
alertPositioners() - Method in class info.bioinfweb.treegraph.document.Document
  Alerts all registered positioners to reposition the tree elements becuase of made changes.
ALIGN_LEFT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ALIGN_RIGHT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ALIGN_TREE_WIDTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
alignGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
alignLegendsToSubtree - Variable in class info.bioinfweb.treegraph.document.format.GlobalFormats
alignment - Variable in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
alignmentPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
alignMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
alignToOtherLegends(Legends, int, int, float, float, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
alignToSubtreeCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
ALLOCATION_SEPARATOR_SYMBOL - Static variable in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
ALLOCATION_SYMBOL - Static variable in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
ALTERNATIVE_EXTENSION - Static variable in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFilter
ALTERNATIVE_EXTENSION_1 - Static variable in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter
ALTERNATIVE_EXTENSION_2 - Static variable in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter
ALTERNATIVE_SELECTION_COLOR - Static variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
anchor - Variable in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveLegendEdit
anchorNames - Variable in class info.bioinfweb.treegraph.document.format.LegendFormats
apachePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
apacheScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
apacheTextArea - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditPieChartLabelsDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditTextElementDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewGraphicalLabelsDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.FileDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
apply() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
applyElements - Variable in class info.bioinfweb.treegraph.document.undo.format.OperatorsEdit
ApplyNameTableAction - Class in info.bioinfweb.treegraph.gui.actions.file
ApplyNameTableAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.ApplyNameTableAction
ApplyNameTableDialog - Class in info.bioinfweb.treegraph.gui.dialogs.io
ApplyNameTableDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
ApplyNameTableDialog(Dialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
ApplyNameTableEdit - Class in info.bioinfweb.treegraph.document.undo.file
ApplyNameTableEdit(Document, NodeBranchDataAdapter, List<String>, List<String>, boolean, boolean, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
applyTo(ElementFormats) - Method in class info.bioinfweb.treegraph.document.format.operate.AbstractLabelMarginOperator
applyTo(ElementFormats) - Method in class info.bioinfweb.treegraph.document.format.operate.AbstractLeafMarginOperator
applyTo(ElementFormats) - Method in class info.bioinfweb.treegraph.document.format.operate.AbstractLegendMarginOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.AbstractMarginOperator
applyTo(ElementFormats) - Method in class info.bioinfweb.treegraph.document.format.operate.AbstractOperator
applyTo(ElementFormats) - Method in interface info.bioinfweb.treegraph.document.format.operate.FormatOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LabelMarginBottomOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LabelMarginLeftOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LabelMarginRightOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LabelMarginTopOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LeafMarginBottomOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LeafMarginLeftOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LeafMarginRightOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LeafMarginTopOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LegendMarginBottomOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LegendMarginLeftOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LegendMarginRightOperator
applyTo(Margin) - Method in class info.bioinfweb.treegraph.document.format.operate.LegendMarginTopOperator
aspectRatio - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
assign(BranchFormats) - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
assign(DistanceDimension) - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension
assign(DistanceValue) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
assign(GlobalFormats) - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
assign(IconLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
assign(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
assign(Margin) - Method in class info.bioinfweb.treegraph.document.format.Margin
assign(NodeFormats) - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
assign(PieChartLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
assign(ScaleBarFormats) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
assign(ScaleValue) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
assign(TextLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
assign(HiddenDataMap) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
  Clears the current contents of the map and fills it with copies of the contents of the given map.
assign(TextElementData) - Method in class info.bioinfweb.treegraph.document.TextElementData
assignBranchFormats(BranchFormats) - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
assignCornerRadiusFormats(CornerRadiusFormats) - Method in interface info.bioinfweb.treegraph.document.format.CornerRadiusFormats
assignCornerRadiusFormats(CornerRadiusFormats) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
assignCornerRadiusFormats(CornerRadiusFormats) - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
assignData(Node, TextElementData) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter
assignData(Node, TextElementData) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
assignData(Node, TextElementData) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
assignData(Node, TextElementData) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter
assignGraphicalLabelFormats(GraphicalLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.GraphicalLabelFormats
  Assigns the graphical labels formats to this object.
assignIconLabelFormats(IconLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
assignImportColumnsDialog - Variable in class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction
AssignImportColumnsDialog - Class in info.bioinfweb.treegraph.gui.dialogs.io
AssignImportColumnsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
assignLabelData(Label) - Method in class info.bioinfweb.treegraph.document.Label
  Assigns the values of the passed label to this class.
assignLabelFormats(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
assignLegendData(Legend) - Method in class info.bioinfweb.treegraph.document.Legend
  This method currently does not do anything but should be called in the `clone()`-method of derived classes anyway because `Legend` might contain data that needs to be copied in future versions.
assignLegendFormats(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
assignLegendPosition(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  Adopts the position values and the anchors but not the owning legend object.
assignLineFormats(LineFormats) - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
assignLineFormats(LineFormats) - Method in class info.bioinfweb.treegraph.document.format.GraphicalLabelFormats
assignLineFormats(LineFormats) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
assignLineFormats(LineFormats) - Method in interface info.bioinfweb.treegraph.document.format.LineFormats
assignLineFormats(LineFormats) - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
assignLineFormats(LineFormats) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
assignNodeFormats(NodeFormats) - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
assignPaintSize() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
assignPieChartData(PieChartLabel) - Method in class info.bioinfweb.treegraph.document.PieChartLabel
assignPieChartLabelFormats(PieChartLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
assignScaleBarData(ScaleBar) - Method in class info.bioinfweb.treegraph.document.ScaleBar
  This method currently does not do anything but should be called in the `clone()`-method of derived classes anyway because `ScaleBar` might contain data that needs to be copied in future versions.
assignScaleBarFormats(ScaleBarFormats) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
assignTextElementData(TextElement) - Method in class info.bioinfweb.treegraph.document.AbstractTextElement
assignTextElementData(TextElement) - Method in interface info.bioinfweb.treegraph.document.TextElement
assignTextElementData(TextElement) - Method in class info.bioinfweb.treegraph.document.TextLabel
assignTextFormats(TextFormats) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
assignTextFormats(TextFormats) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
assignTextFormats(TextFormats) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
assignUniqueNames() - Method in class info.bioinfweb.treegraph.document.Tree
  Assigns unique names to all nodes in the tree currently without one.
assignUniqueNamesToSubtree(Node) - Method in class info.bioinfweb.treegraph.document.Tree
  Assigns unique names to all nodes in the subtree under root currently without one.
assignValue(TextFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
assignValueTo(DistanceValue) - Method in class info.bioinfweb.treegraph.gui.dialogs.DistanceValueInput
  Assigns the current value of the text-field to the given `DistanceValue`.
assignValueTo(ScaleValue) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
assignValueTo(Margin) - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
  Assigns the current values of the text-fields to the given `Margin`.
ATTR_ALIGN_TO_SUBTREE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_BG_COLOR - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_BOTTOM - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLConstants
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_BRANCH_LENGTH_SCALE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_BRANCH_LENGTH_UNIT - Static variable in interface info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLConstants
ATTR_CONSTANT_WIDTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_DECIMAL_FORMAT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_EDGE_RADIUS - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_FONT_FAMILY - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_HEIGHT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_ICON - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_ICON_FILLED - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_ICON_HEIGHT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_ICON_WIDTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_ID - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LABEL_ABOVE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LABEL_HEIGHT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LABEL_SPACING - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LABEL_WIDTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LEFT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LEGEND_POS - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LEGEND_SPACING - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LEGEND_STYLE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LINE_COLOR - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LINE_NO - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LINE_POS - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LINE_WIDTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LOCALE_COUNTRY - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LOCALE_LANG - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LOCALE_VARIANT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_LONG_INTERVAL - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_MIN_BRANCH_LENGTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_MIN_SPACE_ABOVE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_MIN_SPACE_BELOW - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_MIN_TREE_DISTANCE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_POSITION_LABELS_TO_LEFT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_RIGHT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_ROOTED - Static variable in interface info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLConstants
ATTR_SCALE_BAR_ALIGN - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SCALE_BAR_DISTANCE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SCALE_BAR_HEIGHT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SCALE_BAR_INCREASE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SCALE_BAR_START - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SCALE_BAR_WIDTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SHOW_INTERNAL_LINES - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SHOW_NULL_LINES - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SHOW_ROOTED - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SHOW_SCALE_BAR - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_SMALL_INTERVAL - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TEXT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TEXT_COLOR - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TEXT_HEIGHT - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TEXT_IS_DECIMAL - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TEXT_ORIENTATION - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TEXT_STYLE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TOP - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_TYPE - Static variable in interface info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLConstants
ATTR_UNIQUE_NAME - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ATTR_WIDTH - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
attributeMap - Variable in class info.bioinfweb.treegraph.document.Node
AutoPositionLabelsAction - Class in info.bioinfweb.treegraph.gui.actions.format
AutoPositionLabelsAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.AutoPositionLabelsAction
AutoPositionLabelsEdit - Class in info.bioinfweb.treegraph.document.undo.format
AutoPositionLabelsEdit(Document, Branch[]) - Constructor for class info.bioinfweb.treegraph.document.undo.format.AutoPositionLabelsEdit
AWTExceptionHandler - Class in info.bioinfweb.treegraph
  This class is used to handle exceptions during the processing of modal dialogs.
AWTExceptionHandler() - Constructor for class info.bioinfweb.treegraph.AWTExceptionHandler

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