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## C

calculateAverage(Node) - Method in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler
CalculateColumnAction - Class in info.bioinfweb.treegraph.gui.actions.edit
CalculateColumnAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.CalculateColumnAction
CalculateColumnDialog - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdata
  Used to calculate a node/branch data column as specified by the user defined expression.
CalculateColumnDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
CalculateColumnEdit - Class in info.bioinfweb.treegraph.document.undo.edit
  Calculates a node/branch data column as specified by the passed expression.
CalculateColumnEdit(Document, NodeBranchDataAdapter, String) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
calculateCornerRadiusShift(Node, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner
  This method is overwritten to ensure that no corner radius in painted.
calculateCornerRadiusShift(Node, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
  Returns the space between the right of the node and the real position of the node line dependant of the y position.
calculateLabelBlockDimensions(Labels, boolean) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
calculateMaxNodeData(NodeBranchDataAdapter, Node) - Static method in class info.bioinfweb.treegraph.document.undo.format.NodeBranchDataFormatEdit
  Searches for the maximal node data specified by `adapter` in the subtree under root.
calculatePaintDimension(float, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
calculateScaleByLength(Tree, float) - Static method in class info.bioinfweb.treegraph.document.undo.format.ScaleBranchLengthsEdit
  Returns the branch length scale necessary for the specified tree so that the longest path to a leaf of this tree has the specified length.
calculateSubtree(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
calculateTaxonDimension(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
calculateTextDimension(TextElement) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
  Calculates the Dimensions of this text element.
calculateWidthsHeights(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
canRedo() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
canUndo() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
CAPACITY - Static variable in class info.bioinfweb.treegraph.document.Legends
CAPACITY_INCREMENT - Static variable in class info.bioinfweb.treegraph.document.LabelLine
CAPACITY_INCREMENT - Static variable in class info.bioinfweb.treegraph.document.Labels
CAPACITY_INCREMENT - Static variable in class info.bioinfweb.treegraph.document.Legends
CascadeAction - Class in info.bioinfweb.treegraph.gui.actions.window
CascadeAction() - Constructor for class info.bioinfweb.treegraph.gui.actions.window.CascadeAction
cascadeInternalFrames() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
caseSensitive - Variable in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
caseSensitive() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
caseSensitiveCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
caseSensitiveCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
caseSensitiveCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
changedFormats - Variable in class info.bioinfweb.treegraph.document.undo.format.OperatorsEdit
  Used to store the previous format objects before they are edited to restore them in `OperatorsEdit.undo()`.
changeHappened(DocumentChangeEvent) - Method in interface info.bioinfweb.treegraph.document.DocumentListener
  Called every time changes were made to the document.
changeHappened(DocumentChangeEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
changeHappened(DocumentChangeEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
ChangeIDDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelement
ChangeIDDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
ChangeLabelIDAction - Class in info.bioinfweb.treegraph.gui.actions.edit
ChangeLabelIDAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.ChangeLabelIDAction
ChangeLabelIDEdit - Class in info.bioinfweb.treegraph.document.undo.edit
  Changes the IDs of a specified group of labels.
ChangeLabelIDEdit(Document, String, Label[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.ChangeLabelIDEdit
changeMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
ChangePainterIDAction - Class in info.bioinfweb.treegraph.gui.actions.view
  Allows the user to change the view mode.
ChangePainterIDAction(MainFrame, PositionPaintType) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.ChangePainterIDAction
changeUndefined - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
changeUndefined - Variable in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
changeUndefinedCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
changeUndefinedCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
changeUniqueNames(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.LegendPaster
  Changes the unique names of the subtree under `root` and the anchor names of the legends.
changeUniqueNamesLegends() - Method in class info.bioinfweb.treegraph.document.undo.edit.LegendPaster
changeUniqueNamesSubtree(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.LegendPaster
CHAR_COUNT_AFTER - Static variable in exception info.bioinfweb.treegraph.document.io.newick.NewickException
CHAR_COUNT_BEFORE - Static variable in exception info.bioinfweb.treegraph.document.io.newick.NewickException
checkColor(Color, Color) - Method in class info.bioinfweb.treegraph.document.ContrastManager
  Checks if two colors have an unsifficient contast.
checkInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
  Checks if the input is correct and displays an error dialog if not.
checkInputs() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
checkNameSpace(StartElement) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGReader
  Outputs warnings about the XML namespace and sets the version of `document`.
checkNumberOfParameters(int) - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
checkPopup(MouseEvent, ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeEditlInputListener
checkUpdate() - Method in class info.bioinfweb.treegraph.cmd.CmdProcessor
CHILD_COUNT_KEY - Static variable in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
children - Variable in class info.bioinfweb.treegraph.document.Node
CLADOGRAM_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.ImageGenerator
clear() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
  Clears all stored data (labelList, label, subtree).
clear() - Method in class info.bioinfweb.treegraph.document.format.operate.OperatorMap
clear() - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
clear() - Method in class info.bioinfweb.treegraph.document.io.nexus.TranslTable
clear() - Method in class info.bioinfweb.treegraph.document.Labels
clear() - Method in class info.bioinfweb.treegraph.document.Legends
clear() - Method in class info.bioinfweb.treegraph.document.TextElementData
  Clears this object.
clear() - Method in class info.bioinfweb.treegraph.document.Tree
  Removes all tree elements including all legends from this object.
clear() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
clear() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
clear() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.MessagesListModel
clear() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
clearButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
clearMessages() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
clearValueIDs() - Method in class info.bioinfweb.treegraph.document.PieChartLabel
clipboard - Variable in class info.bioinfweb.treegraph.Main
ClipboardContentType - Enum in info.bioinfweb.treegraph.document.clipboard
ClipboardContentType() - Constructor for enum info.bioinfweb.treegraph.document.clipboard.ClipboardContentType
clone() - Method in class info.bioinfweb.treegraph.document.AbstractTextElement
clone() - Method in class info.bioinfweb.treegraph.document.Branch
  Clones this `Branch` including its `Labels`-object with the included `Label`s.
clone() - Method in class info.bioinfweb.treegraph.document.ConcretePaintableElement
  Implementing classes should not copy the `EnumMap positions` because the copy of this element will be located at another position.
clone() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
clone() - Method in interface info.bioinfweb.treegraph.document.format.CornerRadiusFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension
clone() - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
clone() - Method in interface info.bioinfweb.treegraph.document.format.ElementFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
  Returns a deep copy with the owner `null`.
clone() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  Returns a deep copy of this class.
clone() - Method in interface info.bioinfweb.treegraph.document.format.LineFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.Margin
clone() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
clone() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
clone() - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
  Returns a deep copy of this map and its contents.
clone() - Method in class info.bioinfweb.treegraph.document.IconLabel
  Returns a deep copy of this icon label.
clone() - Method in class info.bioinfweb.treegraph.document.Label
clone() - Method in class info.bioinfweb.treegraph.document.LabelLine
clone() - Method in class info.bioinfweb.treegraph.document.Labels
  Returns a deep copy of this `Labels`-object (including copys of all `LabelLine`-objects and their `Labels`.
clone() - Method in class info.bioinfweb.treegraph.document.Legend
  Returns a deep copy of this legend.
clone() - Method in class info.bioinfweb.treegraph.document.Node
  Returns a deep copy of this node not including the subtrees.
clone(boolean) - Method in class info.bioinfweb.treegraph.document.Node
  Returns a deep copy of this node not including the subtrees.
clone() - Method in class info.bioinfweb.treegraph.document.PieChartLabel
  Returns a deep copy of this pie chart label.
clone() - Method in class info.bioinfweb.treegraph.document.position.PositionData
clone() - Method in class info.bioinfweb.treegraph.document.ScaleBar
clone() - Method in interface info.bioinfweb.treegraph.document.TextElement
clone() - Method in class info.bioinfweb.treegraph.document.TextElementData
clone() - Method in class info.bioinfweb.treegraph.document.TextLabel
  Returns a deep copy of this text label.
cloneLabelBlock(boolean, Labels) - Method in class info.bioinfweb.treegraph.document.Labels
cloneWithSubtree(boolean) - Method in class info.bioinfweb.treegraph.document.Node
  Clones this object and all objects in this subtree and its afferent branch.
close() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
  Asks the user whether to save all opened documents and closes the application if the user did not cancel the process.
CloseAction - Class in info.bioinfweb.treegraph.gui.actions.file
CloseAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.CloseAction
closeButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
closeButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
CmdLoadLogger - Class in info.bioinfweb.treegraph.cmd
  Displays the messages of a `DocumentReader` class on the command line.
CmdLoadLogger() - Constructor for class info.bioinfweb.treegraph.cmd.CmdLoadLogger
CmdProcessor - Class in info.bioinfweb.treegraph.cmd
CmdProcessor() - Constructor for class info.bioinfweb.treegraph.cmd.CmdProcessor
cmdProcessor - Variable in class info.bioinfweb.treegraph.Main
codeBoolean(boolean) - Static method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
COL_BRANCH_LENGTH_DATA_TYPE - Static variable in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
COL_UNIQUE_NAME_DATA_TYPE - Static variable in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
collapseDone - Variable in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit
CollapseNodeAction - Class in info.bioinfweb.treegraph.gui.actions.edit
CollapseNodeAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.CollapseNodeAction
CollapseNodeEdit - Class in info.bioinfweb.treegraph.document.undo.edit
CollapseNodeEdit(Document, Node, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.CollapseNodeEdit
collapseNodeEdit - Variable in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit
color - Variable in class info.bioinfweb.treegraph.document.format.operate.LineColorOperator
color - Variable in class info.bioinfweb.treegraph.document.format.operate.TextColorOperator
color - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorIcon
color - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorListEntry
ColorAdapter - Interface in info.bioinfweb.treegraph.document.format.adapters.color
ColorAdapterListModel - Class in info.bioinfweb.treegraph.gui.dialogs.specialformats
ColorAdapterListModel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorAdapterListModel
colorChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
colorChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
colorForIndex(int) - Method in class info.bioinfweb.treegraph.document.PieColorManager
colorLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
colorList - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
colorListScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
colorMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel
colorMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
colorPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
ColorPreviewPanel - Class in info.bioinfweb.treegraph.gui.dialogs.specialformats
ColorPreviewPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorPreviewPanel
colorPreviewPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
colors - Variable in class info.bioinfweb.treegraph.document.format.operate.PieColorOperator
colors - Variable in class info.bioinfweb.treegraph.document.PieColorManager
ColorsByNodeBranchDataAction - Class in info.bioinfweb.treegraph.gui.actions.format
ColorsByNodeBranchDataAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.ColorsByNodeBranchDataAction
ColorsByNodeBranchDataDialog - Class in info.bioinfweb.treegraph.gui.dialogs.specialformats
ColorsByNodeBranchDataDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
ColorsByNodeBranchDataEdit - Class in info.bioinfweb.treegraph.document.undo.format
ColorsByNodeBranchDataEdit(Document, NodeBranchDataAdapter, Color, Color, boolean, boolean, ColorAdapter[]) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
columnInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
columnPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
comboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput
comboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
COMMAND_PATTERN - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
COMMAND_SEPARATOR - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
commandGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
commandPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
comment - Variable in class info.bioinfweb.treegraph.document.io.newick.NewickToken
COMMENT_END - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
COMMENT_END - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
COMMENT_START - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
COMMENT_START - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
CommentDataReader - Class in info.bioinfweb.treegraph.document.io.newick
  Reads hidden node data from a comment in a Newick string like it is generated by BEAST.
CommentDataReader() - Constructor for class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
commentDataReader - Variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
compareLeafs() - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
comparePosition(TreePath) - Method in class info.bioinfweb.treegraph.document.TreePath
  Calculates which of the two target nodes is further upwards in the tree.
compareTo(NodeLadderizeComparable) - Method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
  Compares which node has more (or less) nodes in its subtree.
compareTo(LeafField, boolean) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
  Compares this field or its complement to another.
complement() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
ComplexDocumentEdit - Class in info.bioinfweb.treegraph.document.undo
  This class is the ancestor to all edits that are too complex to have an own `undo()` method.
ComplexDocumentEdit(Document) - Constructor for class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit
compressionMethodComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TIFFPrefPanel
compressionMethodLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TIFFPrefPanel
ConcretePaintableElement - Class in info.bioinfweb.treegraph.document
ConcretePaintableElement() - Constructor for class info.bioinfweb.treegraph.document.ConcretePaintableElement
ConcreteTextFormats - Class in info.bioinfweb.treegraph.document.format
ConcreteTextFormats() - Constructor for class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
CONFIG_DIR - Static variable in class info.bioinfweb.treegraph.Main
confirmChange() - Method in class info.bioinfweb.treegraph.document.ContrastManager
  Asks the user whether to change any colors if this was not already done.
CONFLICT_DECIMAL_FORMAT - Static variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
CONFLICT_NAME - Static variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
conflictAdapter - Variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
  The node/branch data column to write imported conflict values to
constantWidth - Variable in class info.bioinfweb.treegraph.document.format.BranchFormats
constantWidth - Variable in class info.bioinfweb.treegraph.document.format.operate.ConstantWidthOperator
constantWidthCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
constantWidthMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
ConstantWidthOperator - Class in info.bioinfweb.treegraph.document.format.operate
ConstantWidthOperator(boolean) - Constructor for class info.bioinfweb.treegraph.document.format.operate.ConstantWidthOperator
containedInSubtree(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.document.Node
  Tests whether an element is contained in the subtree under this node.
containedLabelIDs() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
  Returns a list of the IDs of the labels that are currently selected.
contains(Label) - Method in class info.bioinfweb.treegraph.document.LabelLine
contains(boolean, Label) - Method in class info.bioinfweb.treegraph.document.Labels
  Tests if the specified label is contained in the specified block (above or below the branch).
contains(Label) - Method in class info.bioinfweb.treegraph.document.Labels
  Tests if the specified label is contained in this object.
contains(Legend) - Method in class info.bioinfweb.treegraph.document.Legends
contains(float, float, float) - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData
contains(DistanceValue, DistanceValue, float) - Method in class info.bioinfweb.treegraph.document.position.PositionData
contains(float, float, float) - Method in class info.bioinfweb.treegraph.document.position.PositionData
contains(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.document.Tree
  Tests if the given element is present in the tree.
contains(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsAnyAndOther(LeafField, boolean) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
  Tests if this field (or its complement) contains at least one element from the specified field and at least one which is not contained in `other`.
containsDecimal(NodeBranchDataAdapter, Node) - Static method in class info.bioinfweb.treegraph.document.Tree
  Tests if the subtree under `root` contains a node which would be able to return a decimal value to the given adapter.
containsDecimal(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.Tree
  Tests if the tree contains a node which would be able to return a decimal value to the given adapter.
containsIDElements(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Test whether the subtree under `root` contains at least one ID element (label or hidden data)
containsKey(Object) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
containsKey(String) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
containsLegendFormats() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
  Returns whether legend formats have been stored.
containsOnlyType(Class<? extends PaintableElement>) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
  Tests if only elements of the specified type are selected.
containsParent(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
containsSameID(HiddenDataMap) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
  Tests if the specified map contains one or more IDs that are also contained in this map.
containsSameID(Labels, boolean) - Method in class info.bioinfweb.treegraph.document.Labels
containsSameID(Labels) - Method in class info.bioinfweb.treegraph.document.Labels
containsType(Class<? extends PaintableElement>) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
  Tests if at least one elements of the specified type is selected.
containsValue(Object) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
contentsTabbedPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
ContrastManager - Class in info.bioinfweb.treegraph.document
  Ensures that document elements (that are e.g. pasted from the clipboard) have a sufficient contrast to the document background.
ContrastManager() - Constructor for class info.bioinfweb.treegraph.document.ContrastManager
contrastManager - Variable in class info.bioinfweb.treegraph.gui.actions.edit.PasteAction
ContrastManager.State - Enum in info.bioinfweb.treegraph.document
ContrastManager.State() - Constructor for enum info.bioinfweb.treegraph.document.ContrastManager.State
convert(CommandLineReader) - Method in class info.bioinfweb.treegraph.cmd.CmdProcessor
CONVERT_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.CmdProcessor
convertToPixels(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
convertValue(JTextField, ItemEvent) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
CopyAllLabelsAction - Class in info.bioinfweb.treegraph.gui.actions.edit
CopyAllLabelsAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.CopyAllLabelsAction
copyBranchData(Branch, Branch) - Method in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit
CopyColumnAction - Class in info.bioinfweb.treegraph.gui.actions.edit
CopyColumnAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.CopyColumnAction
CopyColumnDialog - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdata
CopyColumnDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
CopyColumnEdit - Class in info.bioinfweb.treegraph.document.undo.edit
  Copies a node/branch data column.
CopyColumnEdit(Document, NodeBranchDataAdapter, NodeBranchDataAdapter, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.CopyColumnEdit
CopyElementAction - Class in info.bioinfweb.treegraph.gui.actions.edit
CopyElementAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.CopyElementAction
copyLabel(Label) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
copyLabelBlock(Labels, boolean) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
copyLabels(Labels) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
copyLabels(Labels, Labels) - Method in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit
copyLegend(Legend) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
copyPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
copySubtree(Tree, Node) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
copySubtree(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.CopyColumnEdit
cornerRadius - Variable in class info.bioinfweb.treegraph.document.format.LegendFormats
cornerRadius - Variable in class info.bioinfweb.treegraph.document.format.NodeFormats
cornerRadius - Variable in class info.bioinfweb.treegraph.document.format.operate.CornerRadiusOperator
cornerRadius - Variable in class info.bioinfweb.treegraph.document.io.tgf.TGFReader
CornerRadiusAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
CornerRadiusAdapter() - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.CornerRadiusAdapter
CornerRadiusElement - Interface in info.bioinfweb.treegraph.document
CornerRadiusFormats - Interface in info.bioinfweb.treegraph.document.format
cornerRadiusInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
CornerRadiusOperator - Class in info.bioinfweb.treegraph.document.format.operate
CornerRadiusOperator(DistanceValue) - Constructor for class info.bioinfweb.treegraph.document.format.operate.CornerRadiusOperator
COS_RAY_36 - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
COS_RAY_72 - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
count - Variable in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler
countNodes(Node) - Static method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
  Sets all the `childCount` values of the contained `Node`-objects.
createAdapterMap() - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
createBackups() - Method in class info.bioinfweb.treegraph.document.undo.file.ImportTableEdit
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
  This method should create the data object if does not already exist.
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.CalculateColumnAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.ChangeLabelIDAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.CopyColumnAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.DeleteOutsideIntervalAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchLengthAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditPieChartLabelIDsAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditTextElementAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewIconLabelsAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewPieChartLabelsAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewTextLabelAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.RenameDataIDAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.ReplaceInNodeDataAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.EditDialogAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.AddSupportValuesAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ApplyNameTableAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportTableAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToGraphicAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToNewickNexusAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.OpenAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.ColorsByNodeBranchDataAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.DistanceValuesByNodeBranchDataAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.EditElementFormatsAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.EditGlobalFormatsAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.ScaleBranchLengthsAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.ScaleDistanceValuesAction
createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFactory
createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFactory
createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFactory
createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFactory
createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory
createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFactory
createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFactory
createGraphics(OutputStream, Dimension) - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFWriter
createGraphics(OutputStream, Dimension) - Method in class info.bioinfweb.treegraph.graphics.export.FreeHEPWriter
createInputs(int, Tree) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
createInstance(Document, Document, TextElementDataAdapter, AddSupportValuesEdit.TargetType, String, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
  Returns a new instance of `AddSupportValuesEdit` or `null` if the given source document contains internal node names that are not decimal.
createInstance(Document, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.format.ShowHideScaleBarEdit
createInstance(Document, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.format.ShowRootedEdit
createLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewGraphicalLabelsDialog
  Descendant classes should return a label object here which if formatted according to the user input.
createLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
createLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
createLegend(Node, Legends) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils
  Creates a legend to be inserted in the specified document.
createNode(Node) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils
  Creates a node with an afferent branch to be inserted in the specified document.
createNode(Document) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils
  Creates a node with an afferent branch to be inserted in the specified document.
createParser() - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
createSubedits() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
  Implementing classes can specify their target list model here.
createTrees(NodeBranchDataAdapter, NodeBranchDataAdapter, boolean) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
  Creates a `Tree` object from each stored Newick string.
createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFactory
createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFactory
createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFactory
createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFactory
createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory
createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFactory
createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFactory
CrossIcon - Class in info.bioinfweb.treegraph.graphics.positionpaint.labelicons
CrossIcon() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.CrossIcon
curNumberOfParameters - Variable in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
CURRENT_DIR_PREF_KEY - Static variable in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel
CURRENT_VALUE_VAR - Static variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
CurrentDirectoryModel - Class in info.bioinfweb.treegraph.gui
  Manages the working directory of TreeGraph 2.
CurrentDirectoryModel() - Constructor for class info.bioinfweb.treegraph.gui.CurrentDirectoryModel
currentTree - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
customizeComboBox(JComboBox) - Method in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput
customizeComboBox(JComboBox) - Method in class info.bioinfweb.treegraph.gui.dialogs.DistanceValueInput
customizeComboBox(JComboBox) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
customizeComboBox(JComboBox) - Method in class info.bioinfweb.treegraph.gui.dialogs.ResolutionInput
customizeSpashScreen() - Method in class info.bioinfweb.treegraph.Main
customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
  This method is called from `SpecialFormatsDialog.onExecute()`.
CutAction - Class in info.bioinfweb.treegraph.gui.actions.edit
CutAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.CutAction
CutEdit - Class in info.bioinfweb.treegraph.document.undo.edit
  The impelemention of this edit is the same as it is at `DeleteEdit`.
CutEdit(Document, ConcretePaintableElement[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.CutEdit
cutToSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel

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