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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.edit.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
saveOldColors() - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
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.DistanceValuesByNodeBranchDataEdit
  Saves the old widths in a linear list (ordering is root, child 0..n)
saveOldValues() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
SCALE_BAR_LABEL_FORMAT - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
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
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
ScaleBarPanel - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats
ScaleBarPanel(ElementFormatsDialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
  This is the default constructor
scaleBarPresent - Variable in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
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
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
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
scrollElementToVisible(PaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
scrollPane - Variable in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
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) - 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, 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(Vector<NewickToken>, int, int) - Static 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(Vector<NewickToken>, int, int, TokenType) - Static 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[], String[], TranslTable, boolean) - Method in class info.bioinfweb.treegraph.document.io.DefaultTreeSelector
select(String[], String[], TranslTable, boolean) - Method in interface info.bioinfweb.treegraph.document.io.TreeSelector
select(String[], String[], TranslTable, boolean) - 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.nodedatainput.NodeDataComboBoxModel
selectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NewNodeDataInput
selectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
  Returns the currently selected adapter.
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
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.datatable.DataTableDialog
self - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.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.ApplyNameTableDialog
separatorPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
separatorTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
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.ApplyNameTableDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.AssignImportColumnsDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.IntervalDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.RenameIDDialog
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.EditTextElementDialog
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.ScaleBarPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.JPEGPrefPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.TransparenrtBgPrefPanel
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog
serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceValuesByNodeBranchDataDialog
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.ExportToNewickStringDialog
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.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.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, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.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.LabelPositionFormats
setActionStatusBySelection(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.ActionManagement
setAdapters(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorAdapterListModel
  Creates all color adapters valid for the subtree under `root`.
setAdapters(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceAdapterListModel
  Creates all distance adapters valid for the subtree under `root`.
setAdapters(Tree) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.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.nodedatainput.NodeDataComboBoxModel
setAdapters(Tree) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
  Refeshs the selectable node data adapters.
setAdapters(Tree, boolean, boolean, boolean, boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
  Refeshs the selectable node data adapters.
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.
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
setBackgroundColor(Color) - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats
setBracketPos(PositionData) - Method in class info.bioinfweb.treegraph.document.LegendPositionData
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.datatable.DataTableDialog
setButtonStatus() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters.BranchLineColorAdapter
setColor(Color, Node) - Method in interface info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters.ColorAdapter
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters.LabelTextColorAdapter
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters.NodeLineColorAdapter
setColor(Color, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters.NodeTextColorAdapter
setColumnWidths() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
setConstantWidth(boolean) - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
setCurrentDirectory(File) - Method in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel
setDataType(int, boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
setDataTypeInSubtree(Node, TextElementDataAdapter, boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel
setDecimal(Node, double) - Method in class info.bioinfweb.treegraph.document.nodedata.BranchLengthAdapter
setDecimal(Node, double, int) - Method in class info.bioinfweb.treegraph.document.nodedata.BranchLengthAdapter
setDecimal(Node, double) - Method in interface info.bioinfweb.treegraph.document.nodedata.NodeDataAdapter
setDecimal(Node, double) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter
setDecimal(Node, double) - Method in class info.bioinfweb.treegraph.document.nodedata.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.TextFormats
  Sets a new decimal format object.
setDecimalToAllButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
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.NodePositionData
setDifBelow(float) - Method in class info.bioinfweb.treegraph.document.NodePositionData
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.BranchLineWidthAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.BranchMinLengthAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.BranchSpaceAboveAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.BranchSpaceBelowAdapter
setDistance(float, Node) - Method in interface info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.DistanceAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.LabelTextHeightAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.NodeLineWidthAdapter
setDistance(float, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters.NodeTextHeightAdapter
setDocument(Document) - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
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.
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.DocumentAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.ApplyNameTableAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.AssignLabelIDsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.ChangeLabelIDAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CollapseNodeAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CopyAllLabelsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.CopyElementAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.DeleteElementAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.DeleteSubelementsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchLengthAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchNodeDataAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditTextElementAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.LadderizeAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.MoveSubtreeDownAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.MoveSubtreeUpAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewLegendAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewNodeAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewTextLabelAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.PasteAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.RedoAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.ReplaceInNodeDataAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.RerootAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.SeparateBranchAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.UndoAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.UndoRedoToAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.AddSupportValuesAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.CloseAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExitAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToGraphicAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToNewickNexusAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.NewDocumentAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.OpenAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.SaveAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.file.SaveAsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.ColorsByNodeBranchDataAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.DistanceValuesByNodeBranchDataAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.EditElementFormatsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.EditGlobalFormatsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.ReanchorLegendAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.ScaleBranchLengthsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.ShowHideScaleBarAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.format.ShowRootedAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectAllAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsInSubtreeAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsWithIDAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInDocumentAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInSubtreeAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsWithPosIndexAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectSubtreeAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInDocumentAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInSubtreeAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.view.ChangePainterIDAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetZoomAction
setEnabled(Document, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.window.NextDocumentAction
setEnabled(Document, TreeSelection) - 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.nodedatainput.NewNodeDataInput
setEnabled(boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
setFile(File) - Method in class info.bioinfweb.treegraph.document.Document
setFontName(String) - Method in class info.bioinfweb.treegraph.document.format.TextFormats
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.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.NodePositionData
setHeightBelow(float) - Method in class info.bioinfweb.treegraph.document.NodePositionData
setHelpTopic(int) - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit
setHoldingBranch(Branch) - Method in class info.bioinfweb.treegraph.document.Labels
setID(String) - Method in class info.bioinfweb.treegraph.document.Label
setID(String) - Method in class info.bioinfweb.treegraph.document.nodedata.NewHiddenBranchDataAdapter
setID(String) - Method in class info.bioinfweb.treegraph.document.nodedata.NewHiddenNodeDataAdapter
setID(String) - Method in class info.bioinfweb.treegraph.document.nodedata.NewLabelAdapter
setID(String) - Method in interface info.bioinfweb.treegraph.document.nodedata.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.gui.dialogs.nodedatainput.NewNodeDataInput
  Sets the ID displayed in the contained text field.
setIDs(Document) - Method in class info.bioinfweb.treegraph.gui.dialogs.LabelIDComboBox
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
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.LegendFormats
setLineColor(Color) - Method in interface info.bioinfweb.treegraph.document.format.LineFormats
setLineColor(Color) - Method in class info.bioinfweb.treegraph.document.format.LineFormatsEntity
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.LabelPositionFormats
setLinePosition(int) - Method in class info.bioinfweb.treegraph.document.format.LabelPositionFormats
setLocale(Locale) - Method in class info.bioinfweb.treegraph.document.format.TextFormats
  Sets the local object which is used to
setLongInterval(int) - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
setMaxColor(Color) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorPreviewPanel
setMinColor(Color) - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorPreviewPanel
setNames() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.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.
setNewValues(Node) - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
  Sets the branch widths according to the specified range and node data.
setOldColors(Node, int) - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
  Assigns the previously saved colors in the subtree under `root`.
setOldWidths(Node, int) - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
  Assigns the previously saved line widths to the branches in the subtree under root.
setOnlyNewAdapters() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataComboBoxModel
setOnlyNewAdapters() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
  After the call of this method only adapters which create new data will be available.
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.LabelPositionFormats
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) - Method in class info.bioinfweb.treegraph.document.TreePath
setPereferencesPanel(GraphicFormat) - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog
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.
setPositionFormats(LabelPositionFormats) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
setPositionFormats(LabelPositionFormats) - Method in class info.bioinfweb.treegraph.document.IconLabel
setPositionFormats(LabelPositionFormats) - Method in class info.bioinfweb.treegraph.document.Label
setPositionFormats(LabelPositionFormats) - Method in class info.bioinfweb.treegraph.document.TextLabel
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(Class<? extends NodeDataAdapter>) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataComboBoxModel
  Selects the adapter which is an instance (not instance of a subclass) of the given class.
setSelectedAdapter(Class<? extends NodeDataAdapter>) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput
  Selects the adapter which is an instance (not instance of a subclass) of the given class.
setSelectedItem(Object) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataComboBoxModel
setSelection(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog
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
setString(String) - Method in class info.bioinfweb.treegraph.document.TextElementData
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.nodedata.BranchLengthAdapter
setText(Node, String) - Method in interface info.bioinfweb.treegraph.document.nodedata.NodeDataAdapter
setText(Node, String) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter
setText(Node, String) - Method in class info.bioinfweb.treegraph.document.nodedata.UniqueNameAdapter
setTextColor(Color) - Method in class info.bioinfweb.treegraph.document.format.TextFormats
setTextElement(TextElement) - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
setTextPos(PositionData) - Method in class info.bioinfweb.treegraph.document.LegendPositionData
setTextStyle(int) - Method in class info.bioinfweb.treegraph.document.format.TextFormats
setTextToAllButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog
setTree(Tree) - Method in class info.bioinfweb.treegraph.document.Document
setType(Node, boolean) - Method in class info.bioinfweb.treegraph.document.nodedata.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.dialogs.datatable.NodeDataTableModel
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.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.ScaleBarPanel
setValues(GlobalFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
setVersion(int) - 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
sharedInstance - Static variable in class info.bioinfweb.treegraph.document.nodedata.BranchLengthAdapter
sharedInstance - Static variable in class info.bioinfweb.treegraph.document.nodedata.NodeNameAdapter
SHORT_DASH_SCALE_FACTOR - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter
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
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
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.edit.AddSupportValuesEdit.LeafList
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.PositionPaintFactory
size() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel
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.ScaleBarPanel
sortAnchors(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats
  Sorts the anchors by the y-coordinates of their according terminal subnodes.
sourceAdapter - Variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
sourceAdapter - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
sourceAdapter - Variable in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
sourceComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.FormatsByNodeBranchDataDialog
sourcePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.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.exporttographic.ExportToGraphicDialog
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
src - Variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
srcInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
srcLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog
START_MIN_SIZE - Static variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel
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.EdgeRadiusFormats
STD_LEGEND_STYLE - Static variable in class info.bioinfweb.treegraph.document.format.LegendFormats
STD_MIN_LENGTH - Static variable in class info.bioinfweb.treegraph.document.format.BranchFormats
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
STREAM_ENCODING - Static variable in class info.bioinfweb.treegraph.document.io.xtg.XTGWriter
string - Variable in class info.bioinfweb.treegraph.document.TextElementData
stringFormatterFactory - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog
stringRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog
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
subtreeRoot - Variable in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
SUPPORT_DECIMAL_FORMAT - Static variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
SUPPORT_NAME - Static variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
supportAdapter - Variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit
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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