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.DistanceValuesByNodeBranchDataEdit

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

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

field - Variable in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField

FIELD_END_SYMBOL - Static variable in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader

FIELD_START_SYMBOL - Static variable in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader

FILE_NAME - Static variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel

FILE_PREFIX - Static variable in class info.bioinfweb.treegraph.gui.actions.file.ExportToPDFAction

FILE_SUFFIX - Static variable in class info.bioinfweb.treegraph.gui.actions.file.ExportToPDFAction

fileButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

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

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

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

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

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

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

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

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

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

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

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

FileDialog - Class in info.bioinfweb.treegraph.gui.dialogs.io

All dialogs that deal with files shoud be inherited from this class.

FileDialog(Dialog, FileDialog.Option) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.FileDialog

FileDialog(Frame, FileDialog.Option) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.FileDialog

FileDialog.Option - Enum in info.bioinfweb.treegraph.gui.dialogs.io

FileDialog.Option() - Constructor for enum info.bioinfweb.treegraph.gui.dialogs.io.FileDialog.Option

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

filePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

filePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog

fileTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

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

fill() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap

fill() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel

fillAdapterList(Node) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

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.io.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.treeframe.DocumentTableModel

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

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

findAllocationEnd(String, int) - Method in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader

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 the first occurence of the given command.

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

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

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.

findFieldEnd(String, int) - Method in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader

findHighestConflict(Node, double, Node, NodeInfo) - Method in class info.bioinfweb.treegraph.document.undo.file.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.

findSourceNodeWithAllLeafs(Node, LeafField) - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit

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

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.nodebranchdatainput.NewNodeBranchDataInput

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.labelicons.LabelIconMap

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.io.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.io.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.ConcreteTextFormats

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

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, NodeBranchDataAdapter) - 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.format.operate.ScaleBarFormatsOperator

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

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

formats - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel

FormatsByNodeBranchDataDialog - Class in info.bioinfweb.treegraph.gui.dialogs.specialformats

Superclass of all dialogs which set formats by node/branch data.

FormatsByNodeBranchDataDialog(Dialog, int) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog

FormatsByNodeBranchDataDialog(Frame, int) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog

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

FormatUtils - Class in info.bioinfweb.treegraph.document.format

Provides general format functionalities.

FormatUtils() - Constructor for class info.bioinfweb.treegraph.document.format.FormatUtils

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