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TreeGraph 2
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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
Adds all available icons to the map.
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
 
first() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
 
firstInstace - Static variable in class info.bioinfweb.treegraph.cmd.CmdLoadLogger
 
firstInstance - Static variable in class info.bioinfweb.treegraph.document.io.ReadWriteFactory
 
firstInstance - Static variable in class info.bioinfweb.treegraph.document.PieColorManager
 
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.loadlogger.LoadLoggerDialog
 
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
Panel of the ElementFormatsDialog used to edit the font color.
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
Panel of the ElementFormatsDialog used to edit the font formats (not including the font color).
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
Returns the file format guessed from the file extension.
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.PieChartLabel
 
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
 
formatsPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
 
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
 
FULL_SCHEMA_LOCATION - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
 
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