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

F

factor - Variable in class info.bioinfweb.treegraph.document.undo.edit.RescaleNodeDataEdit

factor - Variable in class info.bioinfweb.treegraph.document.undo.format.BranchWidthsFromNodeDataEdit

factories - Variable in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

factories - Variable in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

factories - Variable in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

fileButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog

fileChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog

fileChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog

fileChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog

fileChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog

fileChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

fileChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

fileChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

fileChooserPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog

fileChooserPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog

fileChooserPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

fileChooserPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

fileMenu - Variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

filePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog

fileTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog

fileViewWindowGBC - Variable in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel

fillAdapterList(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel

fillEntryList() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel

fillFactoryList() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

fillList() - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

fillList() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

fillList() - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.PreferencesPanelFactory

fillMap() - Method in class info.bioinfweb.treegraph.gui.actions.ActionManagement

All Action objects used in TreeGraph 2 added to the HashMap in this mehtod.

fillNodeList(Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel

fillPopupActions() - Method in class info.bioinfweb.treegraph.gui.actions.ActionManagement

filter - Variable in class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory

findBlockEnd(NexusCommand[], int, int) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

findCommand(NexusCommand[], int, int, Pattern, Pattern) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

Searches for thr first occurence of the given command.

findDecimal(List<String>, double) - Method in class info.bioinfweb.treegraph.document.undo.edit.ApplyNameTableEdit

Returns the index of the first string that represents the specified double value.

findDeepestNodeWithLeafs(AddSupportValuesEdit.LeafList) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

Finds the deepest node in the source document which has a subtree that contains all the specified leafs.

findEquivilant(Node) - Method in class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit

Returns the node in the new tree (copy of the old) with the equivilant position to old.

findEquivilant(Branch) - Method in class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit

Returns the branch in the new tree (copy of the old) with the equivilant position to old.

findHighestConflict(Node, AddSupportValuesEdit.LeafList) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

Finds the highest conflicting support value in the subtree under root.

findHighestConflictRek(Node, double, AddSupportValuesEdit.LeafList) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

This method is the recursive part called by findHighestConflict.

findNode(Node) - Method in class info.bioinfweb.treegraph.document.TreePath

Finds the node specidied by the stored path relative to the given root node.

findString(List<String>, String) - Method in class info.bioinfweb.treegraph.document.undo.edit.ApplyNameTableEdit

findSubnodeWithLeafs(AddSupportValuesEdit.LeafList, Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

Finds the direct subnode under root that contains all the specified leafs.

findTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

fireChangeHappened() - Method in class info.bioinfweb.treegraph.document.Document

Alerts all registered views to display made changes.

fireNewIDSelected(boolean) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NewNodeDataInput

fireSelectionChanged() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

fireSizeChanged() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

fireZoomChanged() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

firstInstance - Static variable in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

firstInstance - Static variable in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

firstInstance - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPainter

firstInstance - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner

firstInstance - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

firstInstance - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

firstInstance - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

firstInstance - Static variable in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel

firstInstance - Static variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.PreferencesPanelFactory

firstInstance - Static variable in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

firstInstance - Static variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

firstInstance - Static variable in class info.bioinfweb.treegraph.Main

firstLineLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.AssignImportColumnsDialog

firstRedone - Variable in class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit

firstSibling - Variable in class info.bioinfweb.treegraph.document.undo.edit.InsertSiblingEdit

FitZoomToHeightAction - Class in info.bioinfweb.treegraph.gui.actions.view

FitZoomToHeightAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.FitZoomToHeightAction

FitZoomToWidthAction - Class in info.bioinfweb.treegraph.gui.actions.view

FitZoomToWidthAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.FitZoomToWidthAction

FitZoomToWidthHeightAction - Class in info.bioinfweb.treegraph.gui.actions.view

FitZoomToWidthHeightAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.FitZoomToWidthHeightAction

FONT - Static variable in interface info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRulerConstants

The font used to label the ruler

FontColorPanel - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats

FontColorPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel

fontFamilyList - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

fontFamilyMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

fontFamilyPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

fontFamilyTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

FontFormatsPanel - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats

FontFormatsPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

This is the default constructor

fontHeightInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

fontHeightPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

fontName - Variable in class info.bioinfweb.treegraph.document.format.operate.FontNameOperator

fontName - Variable in class info.bioinfweb.treegraph.document.format.TextFormats

FontNameOperator - Class in info.bioinfweb.treegraph.document.format.operate

FontNameOperator(String) - Constructor for class info.bioinfweb.treegraph.document.format.operate.FontNameOperator

fontStylePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

FORMAT_EXAMPLE - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

formatByFile(File) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

formatByFileName(String) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

formatByFileName(String) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

formatColor(Color) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGWriter

formatColorByte(int) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGWriter

formatLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

formatMenu - Variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

formatName(Node, NodeDataAdapter) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringWriter

FormatOperator - Interface in info.bioinfweb.treegraph.document.format.operate

formatPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

formats - Variable in class info.bioinfweb.treegraph.document.Branch

formats - Variable in class info.bioinfweb.treegraph.document.CharShiftLabel

formats - Variable in class info.bioinfweb.treegraph.document.format.operate.ScaleBarFormatsOperator

formats - Variable in class info.bioinfweb.treegraph.document.Legend

formats - Variable in class info.bioinfweb.treegraph.document.Node

formats - Variable in class info.bioinfweb.treegraph.document.ScaleBar

formats - Variable in class info.bioinfweb.treegraph.document.TextLabel

formats - Variable in class info.bioinfweb.treegraph.document.Tree

formatsTabbedPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog

formatsTabbedPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

formatTextElement(TextElement) - Static method in class info.bioinfweb.treegraph.document.TextElementData

Returns the formatted value of the given text element.

formatTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

formatTextStyle(TextFormats) - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGWriter

formatValue(DecimalFormat) - Method in class info.bioinfweb.treegraph.document.TextElementData

Return the contained string or the contained formated decimal value or an empty string is the object contains no data.

frame - Variable in class info.bioinfweb.treegraph.document.Document

frame - Variable in class info.bioinfweb.treegraph.gui.actions.window.SelectFrameAction

FREE_NAME_BLANK - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars

FreeHEPWriter - Class in info.bioinfweb.treegraph.graphics.export

FreeHEPWriter() - Constructor for class info.bioinfweb.treegraph.graphics.export.FreeHEPWriter