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TreeGraph 2
 

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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 Labels.
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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