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## C

calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.AddCalculator
calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.ExpCalculator
calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.LogCalculator
calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.MultiplyCalculator
calculate(double) - Method in interface info.bioinfweb.treegraph.gui.dialogs.datatable.math.NodeDataCalculator
calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.PowerCalculator
calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.RescaleCalculator
calculateEdgeRadiusShift(Node, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner
  This method is overwritten to ensure that no edge radius in painted.
calculateEdgeRadiusShift(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.
calculateElementFlags() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
calculateLabelBlockDimensions(Labels, boolean) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
calculateMaxNodeData(NodeDataAdapter, 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
calculateScale(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.
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
canUndo() - Method in class info.bioinfweb.treegraph.document.undo.edit.AssignLabelIDsEdit
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.edit.ApplyNameTableEdit
caseSensitive() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
caseSensitiveCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.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(ChangeEvent) - Method in interface info.bioinfweb.treegraph.document.DocumentView
changeHappened(ChangeEvent) - 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
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.formatbynodedata.ColorsByNodeBranchDataDialog
changeUndefinedCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceValuesByNodeBranchDataDialog
checkColor(Color, Color) - Method in class info.bioinfweb.treegraph.document.ContrastManager
  Checks if two colors have an unsifficient contast.
checkInputs() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
checkPopup(MouseEvent, ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeEditlInputListener
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.datatable.ExportNodeDataTableModel
clear() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
clearButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
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.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.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.LabelPositionFormats
clone() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  Returns a deep copy of this class.
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.ScaleBarFormats
clone() - Method in class 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
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.PositionData
clone() - Method in class info.bioinfweb.treegraph.document.ScaleBar
clone() - Method in class 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.
cloneWithSubtree(boolean) - Method in class info.bioinfweb.treegraph.document.Node
  Clones this object and all objects in this subtree and its afferent branch.
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
CmdProcessor - Class in info.bioinfweb.treegraph.cmd
CmdProcessor() - Constructor for class info.bioinfweb.treegraph.cmd.CmdProcessor
cmdProcessor - Variable in class info.bioinfweb.treegraph.Main
COL_BRANCH_LENGTH_DATA_TYPE - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
COL_UNIQUE_NAME_DATA_TYPE - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
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
ColorAdapter - Interface in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters
ColorAdapterListModel - Class in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata
ColorAdapterListModel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorAdapterListModel
colorChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
colorChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
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.formatbynodedata.ColorsByNodeBranchDataDialog
ColorPreviewPanel - Class in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata
ColorPreviewPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorPreviewPanel
colorPreviewPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog
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.formatbynodedata
ColorsByNodeBranchDataDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog
ColorsByNodeBranchDataEdit - Class in info.bioinfweb.treegraph.document.undo.format
ColorsByNodeBranchDataEdit(Document, NodeDataAdapter, Color, Color, boolean, boolean, ColorAdapter[]) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
comboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput
comboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
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.exporttographic.ExportToGraphicDialog
commandPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
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
compareLists(NodeDataAdapter, AddSupportValuesEdit.LeafList, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
  Checks if the elements in the given lists have the same names as the elements of this list.
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.
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.exporttographic.TIFFPrefPanel
compressionMethodLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.TIFFPrefPanel
ConcretePaintableElement - Class in info.bioinfweb.treegraph.document
ConcretePaintableElement() - Constructor for class info.bioinfweb.treegraph.document.ConcretePaintableElement
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.edit.AddSupportValuesEdit
CONFLICT_NAME - Static variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
conflictAdapter - Variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
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 of this node including all of its `Node`s, `Branch`es and `Label`s.
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(float, float, float) - Method in class info.bioinfweb.treegraph.document.LegendPositionData
contains(Legend) - Method in class info.bioinfweb.treegraph.document.Legends
contains(DistanceValue, DistanceValue, float) - Method in class info.bioinfweb.treegraph.document.PositionData
contains(float, float, float) - Method in class info.bioinfweb.treegraph.document.PositionData
contains(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.document.Tree
  Tests if the given element is present in the tree.
contains(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
contains(double, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
contains(String, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
contains(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsAllNames(NodeDataAdapter, AddSupportValuesEdit.LeafList, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
  Tests if the given list contains elements with the same text values as this list.
containsAnyNameAndOther(NodeDataAdapter, AddSupportValuesEdit.LeafList, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList
  Tests if the given list contains at least one element that has the same text value as one element in this list and additionally contains at least one element with a text value that is not contained in this list.
containsBranch() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsDecimal(NodeDataAdapter, Node) - Static method in class info.bioinfweb.treegraph.document.Tree
  Tests if the subtree unter `root` contains a node which would be able to return a decimal value to the given adapter.
containsDecimal(NodeDataAdapter) - 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.
containsEdgeRadiusElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsIconLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsKey(Object) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
containsKey(String) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
containsLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsLegend() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsLineElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsNode() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyBranches() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyEdgeRadiusElements() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyIconLabels() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyLabels() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyLegends() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyLineElements() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyNodes() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyScaleBar() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyTextElements() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyTextLabels() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsOnlyTreeElements() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
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
containsScaleBar() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsTextElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsTextLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
containsTreeElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
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_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.CmdProcessor
convertToPixels(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
convertValue(JTextField, ItemEvent) - Method in class info.bioinfweb.treegraph.gui.dialogs.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
copyButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
copyColumn(boolean, NodeDataAdapter, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
copyDialog - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
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
copyLegend(Legend) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
CopyNodeDataDialog - Class in info.bioinfweb.treegraph.gui.dialogs.datatable
CopyNodeDataDialog(Dialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
copyPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
copyrightLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
copySubtree(Node) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
copySubtree(Node, boolean, NodeDataAdapter, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
cornerRadiusInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
count() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
countNodes(Node) - Static method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
  Sets all the `childCount` values of the contained `Node`-objects.
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenDataAdapter
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.LabelAdapter
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.NodeNameAdapter
createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter
  This method should create the data object if does not already exist.
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.ApplyNameTableAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.ChangeLabelIDAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchLengthAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchNodeDataAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditTextElementAction
createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewTextLabelAction
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.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
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.datatable.AssignImportColumnsDialog
createInstance(Document, Document, NodeDataAdapter, AddSupportValuesEdit.TargetType, String, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.edit.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
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.
createSubedits() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog
createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceValuesByNodeBranchDataDialog
createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.FormatsByNodeBranchDataDialog
  Implementing classes can specify their target list model here.
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
CURRENT_DIR_PREF_KEY - Static variable in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel
CurrentDirectoryModel - Class in info.bioinfweb.treegraph.gui
CurrentDirectoryModel() - Constructor for class info.bioinfweb.treegraph.gui.CurrentDirectoryModel
currentIDs - Variable in class info.bioinfweb.treegraph.document.undo.edit.AssignLabelIDsEdit
currentMin - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.RescaleCalculator
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.formatbynodedata.ColorsByNodeBranchDataDialog
customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceValuesByNodeBranchDataDialog
customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.FormatsByNodeBranchDataDialog
  This method is called from `FormatsByNodeBranchDataDialog.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

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