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## S

SaveAction - Class in info.bioinfweb.treegraph.gui.actions.file
SaveAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.SaveAction
SaveAsAction - Class in info.bioinfweb.treegraph.gui.actions.file
SaveAsAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.SaveAsAction
saveDataToFile(File) - Method in class info.bioinfweb.treegraph.document.Document
savedValues - Variable in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
saveLegends() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
SaveLegendsEdit - Class in info.bioinfweb.treegraph.document.undo
  This class should be a superclass of all classes that might delete nodes which are anchors to legends.
SaveLegendsEdit(Document) - Constructor for class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
saveList() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel
  Writes the list of recently used expressions to the TreeGraph configuration directory.
saveOldColors() - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
saveOldLegendValues() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
saveOldSubtreeColors(Node) - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
  Saves the old colors.
saveOldSubtreeValues(Node) - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
  Saves the old widths in a linear list (ordering is root, child 0..n)
saveOldTreeValues() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
ScaleAlignment - Enum in info.bioinfweb.treegraph.document.format
ScaleAlignment() - Constructor for enum info.bioinfweb.treegraph.document.format.ScaleAlignment
ScaleBar - Class in info.bioinfweb.treegraph.document
  This element represents a scale bar for the branch length values.
ScaleBar() - Constructor for class info.bioinfweb.treegraph.document.ScaleBar
scaleBar - Variable in class info.bioinfweb.treegraph.document.Tree
ScaleBarFormats - Class in info.bioinfweb.treegraph.document.format
  Stores the formats of a `ScaleBar`.
ScaleBarFormats() - Constructor for class info.bioinfweb.treegraph.document.format.ScaleBarFormats
ScaleBarFormatsOperator - Class in info.bioinfweb.treegraph.document.format.operate
  There only one operator for all scale bar formats because there can only be one scale bar per document.
ScaleBarFormatsOperator(ScaleBarFormats) - Constructor for class info.bioinfweb.treegraph.document.format.operate.ScaleBarFormatsOperator
ScaleBarIntervalKeyListener - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats
  Used in `ScaleBarPanel` to display the length of the small and long interval in millimeters and points while the user enters a value in branch length units.
ScaleBarIntervalKeyListener(ElementFormatsDialog, JLabel, DecimalInput, DecimalInput) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarIntervalKeyListener
  Creates a `ScaleBarIntervalKeyListener`.
ScaleBarPanel - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats
  Panel of the `ElementFormatsDialog` used to edit the scale bar formats.
ScaleBarPanel(ElementFormatsDialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This is the default constructor
ScaleBranchLengthsAction - Class in info.bioinfweb.treegraph.gui.actions.format
ScaleBranchLengthsAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.ScaleBranchLengthsAction
ScaleBranchLengthsDialog - Class in info.bioinfweb.treegraph.gui.dialogs
  Implementation of the scale branch lengths dialog.
ScaleBranchLengthsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog
ScaleBranchLengthsEdit - Class in info.bioinfweb.treegraph.document.undo.format
ScaleBranchLengthsEdit(Document, float) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ScaleBranchLengthsEdit
ScaleDistanceValuesAction - Class in info.bioinfweb.treegraph.gui.actions.format
ScaleDistanceValuesAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.ScaleDistanceValuesAction
ScaleDistanceValuesDialog - Class in info.bioinfweb.treegraph.gui.dialogs.specialformats
ScaleDistanceValuesDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
ScaleDistanceValuesEdit - Class in info.bioinfweb.treegraph.document.undo.format
ScaleDistanceValuesEdit(Document, Node, float, DistanceAdapter[]) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit
scaleInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
scalePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
ScaleValue - Class in info.bioinfweb.treegraph.document.format
  Stores the length of a branch length scale bar.
ScaleValue() - Constructor for class info.bioinfweb.treegraph.document.format.ScaleValue
ScaleValue(float) - Constructor for class info.bioinfweb.treegraph.document.format.ScaleValue
ScaleValueInput - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats
  Used to edit distance values in millimeters, points or scale bar units.
ScaleValueInput(String, JPanel, int) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
scan(String) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
  Splite the passed text into Nexus commands.
scrollElementToVisible(PaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
searchByID(String, boolean) - Method in class info.bioinfweb.treegraph.document.Labels
searchElementToPosition(Node, float, float, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
searchHiddenDataIDs(HiddenDataElement, Vector<String>) - Static method in class info.bioinfweb.treegraph.document.IDManager
searchIDsInSubtree(Node, Vector<String>, boolean, boolean, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.IDManager
searchLabelBlock(Branch, float, float, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner
searchLabelBlock(Labels, boolean) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
searchLabelIDsInLabelBlock(Labels, boolean, boolean, boolean, Vector<String>) - Static method in class info.bioinfweb.treegraph.document.IDManager
  Adds all label IDs to the specified list.
searchLeafNames(Node, Vector<String>) - Method in class info.bioinfweb.treegraph.document.Node
searchLegends(Legends) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
searchPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
searchPattern - Variable in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit
searchScaleBar(Tree) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
searchSubtree(Node) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
searchSubtreeEnd(int, int) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
SearchTextAction - Class in info.bioinfweb.treegraph.gui.actions.edit
SearchTextAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
SearchTextDialog - Class in info.bioinfweb.treegraph.gui.dialogs
SearchTextDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
searchTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
searchToken(int, int, TokenType) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
SECOUND_LINE_POS - Static variable in class info.bioinfweb.treegraph.document.io.tgf.TGFReader
select(String[], Tree[]) - Method in class info.bioinfweb.treegraph.document.io.DefaultTreeSelector
select(String[], Tree[]) - Method in interface info.bioinfweb.treegraph.document.io.TreeSelector
select(String[], Tree[]) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
SelectAllAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectAllAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectAllAction
selected - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel
selected - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
selectedAdapter - Variable in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
selectFrame(boolean) - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
SelectFrameAction - Class in info.bioinfweb.treegraph.gui.actions.window
SelectFrameAction(JInternalFrame, int) - Constructor for class info.bioinfweb.treegraph.gui.actions.window.SelectFrameAction
selectInFontList(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
  Selects an entry in the font list which is equal or similar to the specified string.
selection - Variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
selection - Variable in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
selection - Variable in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
selection - Variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
SELECTION_DISTANCE - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
SELECTION_MARGIN - Static variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
selectionChanged(ChangeEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
selectionChanged(ChangeEvent) - Method in interface info.bioinfweb.treegraph.gui.treeframe.TreeViewPanelListener
selectionColor(Color) - Static method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
selectionPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
SelectLabelsInSubtreeAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectLabelsInSubtreeAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsInSubtreeAction
SelectLabelsWithIDAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectLabelsWithIDAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsWithIDAction
SelectLeafsInDocumentAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectLeafsInDocumentAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInDocumentAction
SelectLeafsInSubtreeAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectLeafsInSubtreeAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInSubtreeAction
SelectLegendsAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectLegendsAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsAction
SelectLegendsInSubtreeAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectLegendsInSubtreeAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsInSubtreeAction
SelectLegendsWithPosIndexAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectLegendsWithPosIndexAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsWithPosIndexAction
selectMenu - Variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
SelectSubtreeAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectSubtreeAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectSubtreeAction
SelectTypeInDocumentAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectTypeInDocumentAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInDocumentAction
SelectTypeInSubtreeAction - Class in info.bioinfweb.treegraph.gui.actions.select
SelectTypeInSubtreeAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInSubtreeAction
self - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
  This field is necessary to acces this intance from the action listeners.
SeparateBranchAction - Class in info.bioinfweb.treegraph.gui.actions.edit
SeparateBranchAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.SeparateBranchAction
SeparateBranchEdit - Class in info.bioinfweb.treegraph.document.undo.edit
SeparateBranchEdit(Document, Branch) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.SeparateBranchEdit
separatorGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
separatorPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
separatorPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
separatorTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
serialVersionUID - Static variable in exception info.bioinfweb.treegraph.document.io.newick.NewickException
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditPieChartLabelsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditTextElementDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewGraphicalLabelsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.JPEGPrefPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TransparentBgPrefPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
set(int, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
set(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
  Sets the specified element as the only selected element.
setAbove(boolean) - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
setActionStatusBySelection(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.ActionManagement
setAdapters(Tree) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
  Refeshs the selectable node data adapters.
setAdapters(Tree, boolean, boolean, boolean, boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
  Refreshes the selectable node data adapters.
setAdapters(Tree) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
  Equvilent to a call of `setAdapters(tree, true, false, false)`.
setAdapters(Tree, boolean, boolean, boolean, boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
setAdapters(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorAdapterListModel
  Creates all color adapters valid for the subtree under `root`.
setAdapters(Tree, boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceAdapterListModel
  Creates all distance adapters valid for the whole tree.
setAdapters(Tree, Node, boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceAdapterListModel
  Creates all distance adapters valid for the subtree under `root`.
setAdditionalCount(int) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
setAfferentBranch(Branch) - Method in class info.bioinfweb.treegraph.document.Node
  Sets the specified branch as the afferent branch of this node and additionally sets this node as the target node of the specified branch.
setAlignLegendsToSubtree(boolean) - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
setAlignment(ScaleAlignment) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
setAnchor(int, Node) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
setAnchorName(int, String) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
setAverageScale(Tree, double, float) - Method in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler
  Sets the branch lengths scale of a tree so that the contained branched have the specified average length.
setBackgroundColor(Color) - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
setBranchLengthScale(float) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
  The branch length scale is used to convert millimeters and points to scale values.
setButtonStatus() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
setChild(int, boolean) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.BranchLineColorAdapter
setColor(Color, Node) - Method in interface info.bioinfweb.treegraph.document.format.adapters.color.ColorAdapter
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.LabelLineColorAdapter
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.LabelTextColorAdapter
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.NodeLineColorAdapter
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.NodeTextColorAdapter
setColor(Color) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorIcon
setColor(Color) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorListEntry
SetColumnToDecimalAction - Class in info.bioinfweb.treegraph.gui.actions.edit
  Implements basic functionality to set the data type for all lines of a node/branch data column.
SetColumnToDecimalAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.SetColumnToDecimalAction
SetColumnToTextAction - Class in info.bioinfweb.treegraph.gui.actions.edit
SetColumnToTextAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.SetColumnToTextAction
SetColumnTypeAction - Class in info.bioinfweb.treegraph.gui.actions.edit
  Implements basic functionality to set the data type for all lines of a node/branch data column.
SetColumnTypeAction(MainFrame, boolean) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.SetColumnTypeAction
SetColumnTypeEdit - Class in info.bioinfweb.treegraph.document.undo.edit
SetColumnTypeEdit(Document, TextElementDataAdapter, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.SetColumnTypeEdit
setColumnWidths() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
setComment(String) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
setConstantWidth(boolean) - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
setCurNumberOfParameters(int) - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
setCurrentDirectory(File) - Method in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel
setDataTypeInSubtree(Node, TextElementDataAdapter, boolean) - Method in class info.bioinfweb.treegraph.document.undo.edit.SetColumnTypeEdit
setDecimal(Node, double) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
setDecimal(Node, double, int) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
setDecimal(Node, double) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
setDecimal(Node, double) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
setDecimal(Node, double) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
setDecimal(double) - Method in class info.bioinfweb.treegraph.document.TextElementData
setDecimalCheckBoxStatus() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
setDecimalFormat(DecimalFormat, Locale) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
setDecimalFormat(DecimalFormat, Locale) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
  Sets a new decimal format object.
setDecimalFormat(DecimalFormat, Locale) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
setDefaultAverageScale(Tree) - Method in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler
  Sets the branch lengths scale of a tree so that the contained branched have `BranchFormats.DEFAULT_MIN_LENGTH` as their average length.
setDefaultName(String) - Method in class info.bioinfweb.treegraph.document.Document
setDelimited(boolean) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
setDifAbove(float) - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
setDifBelow(float) - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractDistanceValueAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLabelDistanceAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLegendAdapter
  This method does nothing.
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.BranchLineWidthAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.BranchMinLengthAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.BranchSpaceAboveAdapter
setDistance(float, Node) - Method in interface info.bioinfweb.treegraph.document.format.adapters.distance.DistanceAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.NodeLineWidthAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.NodeTextHeightAdapter
setDocument(Document) - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
setDocument(Document) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
  Sets this view to a new model and repaints the element using the data of the new document.
setDocument(Document) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
  Sets this view to a new model and repaints the element using the data of the new document.
setDownwards(boolean) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.DocumentAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CalculateColumnAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.ChangeLabelIDAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CollapseNodeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CopyAllLabelsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CopyColumnAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CopyElementAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.DeleteColumnAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.DeleteElementAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.DeleteOutsideIntervalAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.DeleteSubelementsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchLengthAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditPieChartLabelIDsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditTextElementAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.LadderizeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.MoveSubtreeDownAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.MoveSubtreeUpAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewIconLabelsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewLegendAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewNodeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewPieChartLabelsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewTextLabelAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.PasteAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.RedoAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.RenameDataIDAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.ReplaceInNodeDataAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.RerootAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SeparateBranchAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SetColumnTypeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.UndoAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.edit.UndoRedoToAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.AddSupportValuesAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.ApplyNameTableAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.CloseAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExitAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportTableAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToGraphicAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToNewickNexusAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToPDFAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.NewDocumentAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.OpenAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.SaveAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.file.SaveAsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.AutoPositionLabelsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.ColorsByNodeBranchDataAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.DistanceValuesByNodeBranchDataAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.EditElementFormatsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.EditGlobalFormatsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.ReanchorLegendAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.ScaleBranchLengthsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.ScaleDistanceValuesAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.ShowHideScaleBarAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.format.ShowRootedAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.InvertSelectionAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectAllAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsInSubtreeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsWithIDAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInDocumentAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInSubtreeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsInSubtreeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsWithPosIndexAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectSubtreeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInDocumentAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInSubtreeAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.view.ChangePainterIDAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetZoomAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.window.NextDocumentAction
setEnabled(Document, TreeSelection, NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.actions.window.PreviousDocumentAction
setEnabled(boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput
setEnabled(boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
setEnabled(boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
setFile(File) - Method in class info.bioinfweb.treegraph.document.Document
setFontName(String) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
setFontName(String) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
setFontName(String) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
setFormats(ElementFormats) - Method in class info.bioinfweb.treegraph.document.Branch
setFormats(ElementFormats) - Method in class info.bioinfweb.treegraph.document.IconLabel
setFormats(ElementFormats) - Method in class info.bioinfweb.treegraph.document.Legend
setFormats(ElementFormats) - Method in class info.bioinfweb.treegraph.document.Node
setFormats(ElementFormats) - Method in interface info.bioinfweb.treegraph.document.PaintableElement
setFormats(ElementFormats) - Method in class info.bioinfweb.treegraph.document.PieChartLabel
setFormats(ElementFormats) - Method in class info.bioinfweb.treegraph.document.ScaleBar
setFormats(ElementFormats) - Method in class info.bioinfweb.treegraph.document.TextLabel
setFormats(GlobalFormats) - Method in class info.bioinfweb.treegraph.document.undo.format.GlobalFormatsEdit
setFrame(TreeInternalFrame) - Method in class info.bioinfweb.treegraph.document.Document
setHeight(DistanceValue) - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension
setHeightAbove(float) - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
setHeightBelow(float) - Method in class info.bioinfweb.treegraph.document.position.NodePositionData
setHelpCode(int) - Method in class info.bioinfweb.treegraph.document.io.log.LoggerMessage
setHelpTopic(int) - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
setHoldingBranch(Branch) - Method in class info.bioinfweb.treegraph.document.Labels
setIcon(String) - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
setIcon(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel
setIconFilled(boolean) - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats
setIconFilled(boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel
setIconValues(IconLabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
setID(String) - Method in class info.bioinfweb.treegraph.document.Label
setID(String) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.AbstractIDElementAdapter
setID(String) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.IDElementAdapter
  Sets the ID used to access the returned data.
setID(String) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NewHiddenBranchDataAdapter
setID(String) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NewHiddenNodeDataAdapter
setID(String) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NewNodeDataAdapter
  Defines the ID of the node data column that is created by this node data adapter.
setID(String) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NewTextLabelAdapter
setID(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorListEntry
setID(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
  Sets the ID displayed in the contained text field.
setIDs(String[], int) - Method in class info.bioinfweb.treegraph.document.undo.edit.PieChartLabelIDsEdit
setIDs(Document) - Method in class info.bioinfweb.treegraph.gui.dialogs.DataIDComboBox
setIncreasing(boolean) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
setInMillimeters(float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
setInMillimeters(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
setInPixels(float, float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
setInPixels(float, float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
setInPoints(float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue
setInPoints(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
setInUnits(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
setIsSubedit(boolean) - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
  Indicates whether this edit is independent or part of another edit.
setLabelFormats(GraphicalLabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
  Sets the values of a formats object according to the user input.
setLabels(Labels) - Method in class info.bioinfweb.treegraph.document.Label
setLegends(Legends) - Method in class info.bioinfweb.treegraph.document.Legend
setLegendsReanchored(boolean) - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
setLegendsRemoved(boolean) - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
setLegendStyle(LegendStyle) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
setLength(double) - Method in class info.bioinfweb.treegraph.document.Branch
setLength(double) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
setLineColor(Color) - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
setLineColor(Color) - Method in class info.bioinfweb.treegraph.document.format.GraphicalLabelFormats
setLineColor(Color) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
setLineColor(Color) - Method in interface info.bioinfweb.treegraph.document.format.LineFormats
setLineColor(Color) - Method in class info.bioinfweb.treegraph.document.format.NodeFormats
setLineColor(Color) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
setLineNumber(int) - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
setLinePosition(int) - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
setLocale(Locale) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
setLocale(Locale) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
  Sets the local object which is used to
setLocale(Locale) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
setLongInterval(int) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
setMaxColor(Color) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorPreviewPanel
setMessage(String) - Method in class info.bioinfweb.treegraph.document.io.log.LoggerMessage
setMinColor(Color) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorPreviewPanel
setNames() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
setNewColors(Node) - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
  Sets the line colors according to the specified border colors and node data.
setNewDistanceValue(DistanceValue) - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit
setNewLegendValues() - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit
setNewSubtreeValues(Node) - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit
  Sets the branch widths according to the specified rescaling factor.
setNewValues(Node) - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
  Sets the branch widths according to the specified range and node data.
setNode(Node) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
setOldColors(Node, int) - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
  Assigns the previously saved colors in the subtree under `root`.
setOnlyNewAdapters() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
  After the call of this method only adapters which create new data will be available.
setOnlyNewAdapters() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
setOrientation(TextOrientation) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
setOrientation(ToolBarPanel.ToolBarOrientation) - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel
setOwner(Label) - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
setOwner(Legend) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
setPainterType(PositionPaintType) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
setPaintStart(Node) - Method in class info.bioinfweb.treegraph.document.Tree
setParent(Node) - Method in class info.bioinfweb.treegraph.document.Node
setPath(Node, Node) - Method in class info.bioinfweb.treegraph.document.TreePath
setPereferencesPanel(GraphicFormat) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
setPieChartElementsVisible(boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
setPieColor(int, Color) - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
setPosition(int) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  The position of a legend defined in which order vertically overlapping legends are positioned.
setPositionLabelsToLeft(boolean) - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
setResolution(float) - Method in class info.bioinfweb.treegraph.gui.dialogs.ResolutionInput
setScaleBar(ScaleBar) - Method in class info.bioinfweb.treegraph.document.Tree
setScrollPaneBgColor(Color) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
setSelectedAdapter(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
setSelectedAdapter(Class<? extends NodeBranchDataAdapter>) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
  Selects the adapter which is an instance (not instance of a subclass) of the given class.
setSelectedAdapter(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
  Selects the adapter which is an instance (not instance of a subclass) of same class as the given adapter and has the same ID (if it is an adapter for ID elements).
setSelectedAdapter(Class<? extends NodeBranchDataAdapter>) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
  Selects the adapter which is an instance (not instance of a subclass) of the given class.
setSelectedAdapter(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
  Selects the adapter which is an instance (not instance of a subclass) of same class as the given adapter and has the same ID (if it is an adapter for ID elements).
setSelectedItem(Object) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel
setSelectedItem(Object) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
setSelection(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
setShowInternalLines(boolean) - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
setShowNullLines(boolean) - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
setShowRooted(boolean) - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
setShowScaleBar(boolean) - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
setShowWarnings(boolean) - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
setShowWarnings(boolean) - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
setShowWarnings(boolean) - Method in interface info.bioinfweb.treegraph.document.undo.WarningEdit
setSmallInterval(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
setStartLeft(boolean) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
setTargetNode(Node) - Method in class info.bioinfweb.treegraph.document.Branch
setText(String) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken
setText(Node, String) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
setText(Node, String) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
setText(Node, String) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
setText(Node, String) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
setText(String) - Method in class info.bioinfweb.treegraph.document.TextElementData
setTextColor(Color) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
setTextColor(Color) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
setTextColor(Color) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
setTextElement(TextElement) - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
setTextStyle(int) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats
setTextStyle(int) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats
setTextStyle(int) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
setTree(Tree) - Method in class info.bioinfweb.treegraph.document.Document
setType(LoggerMessageType) - Method in class info.bioinfweb.treegraph.document.io.log.LoggerMessage
setType(Node, boolean) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
setUniqueName(String) - Method in class info.bioinfweb.treegraph.document.Node
  The unique name is used to identify nodes in the XML-file which are associated with legends.
setUnit(RulerUnit) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
setUnit(RulerUnit) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRulerUnitField
SetUserZoomAction - Class in info.bioinfweb.treegraph.gui.actions.view
SetUserZoomAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.SetUserZoomAction
setValue(DistanceValue) - Method in class info.bioinfweb.treegraph.gui.dialogs.DistanceValueInput
  Assigns the given value to the text-field.
setValue(TextElement) - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
setValue(TextFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
setValue(ScaleValue) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput
setValue(Margin) - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
  Assigns the given value to the text-fields.
setValueAt(Object, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
setValueID(int, String) - Method in class info.bioinfweb.treegraph.document.PieChartLabel
setValueIsAdjusting(boolean) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
  Sets the `valueIsAdjusting` property, which indicates whether or not upcoming selection changes should be considered part of a single change.
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
setValues(TreeSelection) - Method in interface info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatTab
  The values of the first compatible element in the selection should be set to the input components of this tab.
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
setValues(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
setValues(GlobalFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
setVersion(FormatVersion) - Method in class info.bioinfweb.treegraph.document.Document
setWidth(DistanceValue) - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension
setZoom(float) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
SetZoomAction - Class in info.bioinfweb.treegraph.gui.actions.view
SetZoomAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.SetZoomAction
SetZoomToOriginalAction - Class in info.bioinfweb.treegraph.gui.actions.view
SetZoomToOriginalAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.SetZoomToOriginalAction
ShapeLabelIcon - Class in info.bioinfweb.treegraph.graphics.positionpaint.labelicons
ShapeLabelIcon() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.ShapeLabelIcon
sharedInstance - Static variable in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler
sharedInstance - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
sharedInstance - Static variable in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
sharedInstance - Static variable in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
sharedInstance - Static variable in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
SHORT_DASH_SCALE_FACTOR - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
show - Variable in class info.bioinfweb.treegraph.document.format.operate.InternalPieChartLinesOperator
show - Variable in class info.bioinfweb.treegraph.document.format.operate.NullPieChartLinesOperator
show(NewickException) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
ShowHideScaleBarAction - Class in info.bioinfweb.treegraph.gui.actions.format
ShowHideScaleBarAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.ShowHideScaleBarAction
ShowHideScaleBarEdit - Class in info.bioinfweb.treegraph.document.undo.format
ShowHideScaleBarEdit(Document, GlobalFormats) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ShowHideScaleBarEdit
showInternalLines - Variable in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
showInternalLinesCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
showNullLines - Variable in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats
showNullLinesCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
showRooted - Variable in class info.bioinfweb.treegraph.document.format.GlobalFormats
ShowRootedAction - Class in info.bioinfweb.treegraph.gui.actions.format
ShowRootedAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.ShowRootedAction
showRootedCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
ShowRootedEdit - Class in info.bioinfweb.treegraph.document.undo.format
ShowRootedEdit(Document, GlobalFormats) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ShowRootedEdit
showScaleBar - Variable in class info.bioinfweb.treegraph.document.format.GlobalFormats
showScaleBarCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
showWarningDialog() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
showWarnings - Variable in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit
showWarnings() - Method in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit
showWarnings - Variable in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
SIN_RAY_36 - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
SIN_RAY_72 - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
SinglePositionPaintFactory - Interface in info.bioinfweb.treegraph.graphics.positionpaint
  This interface should be implmeneted by all factory classes for view modes in TreeGraph 2.
SingleReadWriteFactory - Interface in info.bioinfweb.treegraph.document.io
SingletonGraphicsFactory - Class in info.bioinfweb.treegraph.graphics.export
SingletonGraphicsFactory() - Constructor for class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory
size() - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
size() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
size() - Method in class info.bioinfweb.treegraph.document.io.nexus.TranslTable
size() - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory
size() - Method in class info.bioinfweb.treegraph.document.LabelLine
size() - Method in class info.bioinfweb.treegraph.document.Legends
size() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
size() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory
size() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints
size() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap
size() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
size() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
size() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
  Returns the number of selected elements.
sizeChanged(ChangeEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
sizeChanged(ChangeEvent) - Method in interface info.bioinfweb.treegraph.gui.treeframe.TreeViewPanelListener
slider - Variable in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup
SMALL_FACTOR - Static variable in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler
  The factor to calculate the length of the smallest dashes from the maximal length
SMALL_LENGTH - Static variable in interface info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRulerConstants
  The width of a vertical or the height of a horizontal ruler in pixels
smallInterval - Variable in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
smallIntervalInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarIntervalKeyListener
smallIntervalInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
smallIntervalKeyListener - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
smallIntervalLengthLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
sortAnchors(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  Sorts the anchors by the y-coordinates of their according terminal subnodes.
source - Variable in class info.bioinfweb.treegraph.document.undo.edit.CopyColumnEdit
SOURCE_LEAFS_ADAPTER - Static variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
sourceAdapter - Variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
  The node/branch data to be imported (node names or branch lengths)
sourceAdapter - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
sourceAdapter - Variable in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
sourceAfter - Variable in exception info.bioinfweb.treegraph.document.io.newick.NewickException
sourceAfterLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
sourceBefore - Variable in exception info.bioinfweb.treegraph.document.io.newick.NewickException
sourceBeforeLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
sourceComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog
sourceInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
sourceLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
sourcePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
sourcePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog
spaceAbove - Variable in class info.bioinfweb.treegraph.document.format.operate.MinSpaceAboveOperator
spaceAboveInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
spaceBelow - Variable in class info.bioinfweb.treegraph.document.format.operate.MinSpaceBelowOperator
spaceBelowInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
spacer - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
spacerLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
spacing - Variable in class info.bioinfweb.treegraph.document.format.LegendFormats
spacing - Variable in class info.bioinfweb.treegraph.document.position.LegendPositionData
SpecialFormatsDialog - Class in info.bioinfweb.treegraph.gui.dialogs.specialformats
  Superclass of all dialogs which set special formats (e.g. formats by node/branch data).
SpecialFormatsDialog(Dialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
SpecialFormatsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog
SPLASH_SCREEN_BORDER - Static variable in class info.bioinfweb.treegraph.Main
SPLASH_SCREEN_FONT - Static variable in class info.bioinfweb.treegraph.Main
SPLASH_SCREEN_FONT_COLOR - Static variable in class info.bioinfweb.treegraph.Main
splitDocument(String) - Method in class info.bioinfweb.treegraph.document.io.newick.NewickReader
SQRT_OF_2 - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.OctagonIcon
src - Variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
srcInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
srcLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
StarIcon - Class in info.bioinfweb.treegraph.graphics.positionpaint.labelicons
StarIcon() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
START_MIN_SIZE - Static variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
START_SYMBOL - Static variable in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
startApplication(String[]) - Method in class info.bioinfweb.treegraph.Main
startLeft - Variable in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
startMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
startPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
startUI() - Method in class info.bioinfweb.treegraph.cmd.CmdProcessor
state - Variable in class info.bioinfweb.treegraph.document.ContrastManager
STD_CONSTANT_WIDTH - Static variable in class info.bioinfweb.treegraph.document.format.BranchFormats
STD_EDGE_RADIUS_IN_MM - Static variable in interface info.bioinfweb.treegraph.document.format.CornerRadiusFormats
STD_LEGEND_STYLE - Static variable in class info.bioinfweb.treegraph.document.format.LegendFormats
STD_MIN_SPACE_ABOVE - Static variable in class info.bioinfweb.treegraph.document.format.BranchFormats
STD_MIN_SPACE_BELOW - Static variable in class info.bioinfweb.treegraph.document.format.BranchFormats
STD_ORIENTATION - Static variable in class info.bioinfweb.treegraph.document.format.LegendFormats
STD_POSITION - Static variable in class info.bioinfweb.treegraph.document.format.LegendFormats
storeHiddenData(HiddenDataMap, String, StartElement) - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
storeLegendFormats - Variable in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup
storePositionInfo(int, String) - Method in exception info.bioinfweb.treegraph.document.io.newick.NewickException
STREAM_ENCODING - Static variable in class info.bioinfweb.treegraph.document.io.xtg.XTGWriter
STRING_COMPARATOR - Static variable in class info.bioinfweb.treegraph.document.IDManager
stringFormatterFactory - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
stringRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
style - Variable in class info.bioinfweb.treegraph.document.format.operate.LegendStyleOperator
style - Variable in class info.bioinfweb.treegraph.document.format.operate.TextStyleOperator
STYLE_BOLD - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
STYLE_BRACE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
STYLE_BRACKET - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
STYLE_ITALIC - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
STYLE_UNDERLINE - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
styleGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
styleMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
subnodes - Variable in class info.bioinfweb.treegraph.document.undo.edit.DeleteSubelementsEdit
SUBTREE_END - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
SUBTREE_START - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
subtreeLegends - Variable in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
subtreeRoot - Variable in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
subtreeVisible(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
sum - Variable in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler
SUPPORT_DECIMAL_FORMAT - Static variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
SUPPORT_NAME - Static variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
supportAdapter - Variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
  The node/branch data column to write imported support values to
SupportedFormatsFilter - Class in info.bioinfweb.treegraph.document.io
SupportedFormatsFilter() - Constructor for class info.bioinfweb.treegraph.document.io.SupportedFormatsFilter
SVGFactory - Class in info.bioinfweb.treegraph.graphics.export.svg
SVGFactory() - Constructor for class info.bioinfweb.treegraph.graphics.export.svg.SVGFactory
SVGFilter - Class in info.bioinfweb.treegraph.graphics.export.svg
SVGFilter() - Constructor for class info.bioinfweb.treegraph.graphics.export.svg.SVGFilter
SVGTranscodeWriter - Class in info.bioinfweb.treegraph.graphics.export
  This class generates an image file from a tree document.
SVGTranscodeWriter(Class<? extends Transcoder>) - Constructor for class info.bioinfweb.treegraph.graphics.export.SVGTranscodeWriter
SVGWriter - Class in info.bioinfweb.treegraph.graphics.export.svg
SVGWriter() - Constructor for class info.bioinfweb.treegraph.graphics.export.svg.SVGWriter

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