A B C D E F G H I J K L M N O P Q R S T U V W X Z

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

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

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

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.EditTextElementDialog

serialVersionUID - Static variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog

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.TransparenrtBgPrefPanel

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.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

Refeshs 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) - Method in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler

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

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

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.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.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.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

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

setID(String) - Method in class info.bioinfweb.treegraph.document.Label

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.nodebranchdatainput.NewNodeBranchDataInput

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.IconLabelFormats

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

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

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

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(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

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.IconLabelPanel

setValues(IconLabelFormats) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

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(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

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

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

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

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.

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

sourceComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog

sourceInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog

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

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

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

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