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TreeGraph 2
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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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