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TreeGraph 2
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I

icon - Variable in class info.bioinfweb.treegraph.document.format.IconLabelFormats
 
icon - Variable in class info.bioinfweb.treegraph.document.format.operate.IconOperator
 
icon - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorCellRenderer
 
ICON_COLOR - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel
 
ICON_DOMENSION - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorIcon
 
iconComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
iconFilled - Variable in class info.bioinfweb.treegraph.document.format.IconLabelFormats
 
iconFilled - Variable in class info.bioinfweb.treegraph.document.format.operate.IconFilledOperator
 
iconFilledCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
iconFilledMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
IconFilledOperator - Class in info.bioinfweb.treegraph.document.format.operate
 
IconFilledOperator(boolean) - Constructor for class info.bioinfweb.treegraph.document.format.operate.IconFilledOperator
 
IconHeightAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
 
IconHeightAdapter(String) - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.IconHeightAdapter
 
iconHeightInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
IconLabel - Class in info.bioinfweb.treegraph.document
 
IconLabel(Labels) - Constructor for class info.bioinfweb.treegraph.document.IconLabel
 
IconLabelFormats - Class in info.bioinfweb.treegraph.document.format
 
IconLabelFormats(Label, boolean, int, int) - Constructor for class info.bioinfweb.treegraph.document.format.IconLabelFormats
 
IconLabelFormats(Label) - Constructor for class info.bioinfweb.treegraph.document.format.IconLabelFormats
 
iconMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
IconOperator - Class in info.bioinfweb.treegraph.document.format.operate
 
IconOperator(String) - Constructor for class info.bioinfweb.treegraph.document.format.operate.IconOperator
 
iconPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
IconPieChartLabelPanel - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats
Panel of the ElementFormatsDialog used to edit the icon label color.
IconPieChartLabelPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
This is the default constructor
iconPreviewPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
IconPreviewPanel - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats
Panel used to display a preview of the formatted icon in the IconPieChartLabelPanel of the ElementFormatsDialog.
IconPreviewPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel
 
IconWidthAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
 
IconWidthAdapter(String) - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.IconWidthAdapter
 
iconWidthInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
id - Variable in class info.bioinfweb.treegraph.document.Label
 
id - Variable in class info.bioinfweb.treegraph.document.nodebranchdata.AbstractIDElementAdapter
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.CrossIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.EllipseIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.HexagonIcon
 
id() - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.OctagonIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RectangleIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RoundRectangleIcon
 
ID - Static variable in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TitedCrossIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TitedHexagonIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TriangleIcon
 
id() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.UnknownIcon
Returns null.
id - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorListEntry
 
id - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.AbstractLabelAdapter
 
ID_PREFIX - Static variable in interface info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLConstants
 
idComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
 
idComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewGraphicalLabelsDialog
 
idComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
 
IDElementAdapter - Interface in info.bioinfweb.treegraph.document.nodebranchdata
This interface should be implemented by all node data adapters that store an ID.
idExists(Node, String) - Static method in class info.bioinfweb.treegraph.document.IDManager
 
IDFunction - Class in info.bioinfweb.treegraph.document.undo.edit.calculatecolumn
 
IDFunction() - Constructor for class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction
 
idIsValid(String) - Static method in class info.bioinfweb.treegraph.document.Label
 
idIterator() - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
 
idLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
 
idList - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
 
idList - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
 
idListScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
 
IDManager - Class in info.bioinfweb.treegraph.document
 
IDManager() - Constructor for class info.bioinfweb.treegraph.document.IDManager
 
idNamePanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
 
idNameTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
 
idPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
 
idPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewGraphicalLabelsDialog
 
idPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
 
idPattern - Static variable in class info.bioinfweb.treegraph.document.Label
 
ids - Variable in class info.bioinfweb.treegraph.document.undo.format.AutoPositionLabelsEdit
 
ignoreWhitespaces - Variable in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
 
IMAGE_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.CmdProcessor
 
ImageGenerator - Class in info.bioinfweb.treegraph.cmd
 
ImageGenerator() - Constructor for class info.bioinfweb.treegraph.cmd.ImageGenerator
 
importButtonGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
 
importData(NodeBranchDataAdapter[], String[][]) - Method in class info.bioinfweb.treegraph.document.undo.file.ImportTableEdit
 
importPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
 
importPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
 
ImportTableAction - Class in info.bioinfweb.treegraph.gui.actions.file
 
ImportTableAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction
 
importTableDialog - Variable in class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction
 
ImportTableDialog - Class in info.bioinfweb.treegraph.gui.dialogs.io
 
ImportTableDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
 
ImportTableEdit - Class in info.bioinfweb.treegraph.document.undo.file
 
ImportTableEdit(Document, String[][], NodeBranchDataAdapter[]) - Constructor for class info.bioinfweb.treegraph.document.undo.file.ImportTableEdit
 
includeHiddenCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
 
includeInternalNodeNames() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
 
includeLeafs - Variable in class info.bioinfweb.treegraph.document.undo.edit.CopyColumnEdit
 
includeLeafsCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
 
incRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
 
increaseGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
 
increaseMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
 
increasing - Variable in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
 
index - Variable in class info.bioinfweb.treegraph.document.undo.edit.CollapseNodeEdit
 
index - Variable in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveSubtreeEdit
 
index - Variable in class info.bioinfweb.treegraph.document.undo.edit.SeparateBranchEdit
 
INDEX_END_SYMBOL - Static variable in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
 
INDEX_START_SYMBOL - Static variable in class info.bioinfweb.treegraph.document.io.newick.CommentDataReader
 
indexOf(Label) - Method in class info.bioinfweb.treegraph.document.LabelLine
 
indexOf(Legend) - Method in class info.bioinfweb.treegraph.document.Legends
 
info.bioinfweb.treegraph - package info.bioinfweb.treegraph
All classes of the TreeGraph 2 application are contained in this package or one of its subpackeges.
info.bioinfweb.treegraph.cmd - package info.bioinfweb.treegraph.cmd
Contains classes that process the command line arguments for TreeGraph 2.
info.bioinfweb.treegraph.document - package info.bioinfweb.treegraph.document
Contains the classes that represent the data structure of TreeGraph 2 (document elements and formats) as well as all edit operations in the undo-package to manipulate the data structure and classes to read and write a document from and to different formats (io- subpackage).
info.bioinfweb.treegraph.document.clipboard - package info.bioinfweb.treegraph.document.clipboard
Classes in this package implement the clipboard of TreeGraph 2 used to copy document elements (subtrees, labels, legends, ...) between and inside tree documents.
info.bioinfweb.treegraph.document.format - package info.bioinfweb.treegraph.document.format
Contains classes that store format information of the different document elements.
info.bioinfweb.treegraph.document.format.adapters.color - package info.bioinfweb.treegraph.document.format.adapters.color
 
info.bioinfweb.treegraph.document.format.adapters.distance - package info.bioinfweb.treegraph.document.format.adapters.distance
 
info.bioinfweb.treegraph.document.format.operate - package info.bioinfweb.treegraph.document.format.operate
Format operators are used to change single formats of document elements.
info.bioinfweb.treegraph.document.io - package info.bioinfweb.treegraph.document.io
Contains classes necessary to read and write the data structure of a TreeGraph 2 document from and to different formats.
info.bioinfweb.treegraph.document.io.log - package info.bioinfweb.treegraph.document.io.log
Classes related to logging messages of document readers are contained in this package.
info.bioinfweb.treegraph.document.io.newick - package info.bioinfweb.treegraph.document.io.newick
Contains classes implementing the import from and export to the Newick format.
info.bioinfweb.treegraph.document.io.nexus - package info.bioinfweb.treegraph.document.io.nexus
Contains classes implementing the import from and export to the Nexus format.
info.bioinfweb.treegraph.document.io.phyloxml - package info.bioinfweb.treegraph.document.io.phyloxml
Contains classes implementing the import from the phyloXML format.
info.bioinfweb.treegraph.document.io.tgf - package info.bioinfweb.treegraph.document.io.tgf
The classes in this package were planned to allow the import of TGF files into TreeGraph 2.
info.bioinfweb.treegraph.document.io.xtg - package info.bioinfweb.treegraph.document.io.xtg
Contains classes implementing reading and writing of TreeGraph 2 documents.
info.bioinfweb.treegraph.document.nodebranchdata - package info.bioinfweb.treegraph.document.nodebranchdata
Contains classes that implement the access to different data fields of the document elements over the common interface NodeBranchDataAdapter.
info.bioinfweb.treegraph.document.position - package info.bioinfweb.treegraph.document.position
Contains classes used by the positioners and painters (see package info.bioinfweb.treegraph.graphics.positionpaint) to store information about the positions where the document elements will be painted.
info.bioinfweb.treegraph.document.undo - package info.bioinfweb.treegraph.document.undo
Contains all document edits to manipulate the TreeGraph 2 data structure.
info.bioinfweb.treegraph.document.undo.edit - package info.bioinfweb.treegraph.document.undo.edit
 
info.bioinfweb.treegraph.document.undo.edit.calculatecolumn - package info.bioinfweb.treegraph.document.undo.edit.calculatecolumn
 
info.bioinfweb.treegraph.document.undo.file - package info.bioinfweb.treegraph.document.undo.file
 
info.bioinfweb.treegraph.document.undo.file.addsupportvalues - package info.bioinfweb.treegraph.document.undo.file.addsupportvalues
 
info.bioinfweb.treegraph.document.undo.format - package info.bioinfweb.treegraph.document.undo.format
 
info.bioinfweb.treegraph.graphics.export - package info.bioinfweb.treegraph.graphics.export
The classes in this package implement the export of a tree document to the different supported graphic formats.
info.bioinfweb.treegraph.graphics.export.emf - package info.bioinfweb.treegraph.graphics.export.emf
The classes of this package implement exporting trees to a Windows Enhanced Metafile (EMF).
info.bioinfweb.treegraph.graphics.export.jpeg - package info.bioinfweb.treegraph.graphics.export.jpeg
The classes of this package implement exporting trees to the JPEG File Interchange Format.
info.bioinfweb.treegraph.graphics.export.pdf - package info.bioinfweb.treegraph.graphics.export.pdf
The classes of this package implement exporting trees to the Portable Document Format (PDF).
info.bioinfweb.treegraph.graphics.export.png - package info.bioinfweb.treegraph.graphics.export.png
The classes of this package implement exporting trees as Portable network graphics (PNG).
info.bioinfweb.treegraph.graphics.export.svg - package info.bioinfweb.treegraph.graphics.export.svg
The classes of this package implement exporting trees as Scalable vector graphics (SVG).
info.bioinfweb.treegraph.graphics.export.tiff - package info.bioinfweb.treegraph.graphics.export.tiff
The classes of this package implement exporting trees to the Tagged Image File Format (TIFF).
info.bioinfweb.treegraph.graphics.positionpaint - package info.bioinfweb.treegraph.graphics.positionpaint
The classes in this package implement the output of an TreeGraph 2 document with Graphics2D.
info.bioinfweb.treegraph.graphics.positionpaint.labelicons - package info.bioinfweb.treegraph.graphics.positionpaint.labelicons
 
info.bioinfweb.treegraph.gui - package info.bioinfweb.treegraph.gui
Contains the TreeGraph 2 GUI.
info.bioinfweb.treegraph.gui.actions - package info.bioinfweb.treegraph.gui.actions
Contains the actions classes used in the TreeGraph 2 GUI.
info.bioinfweb.treegraph.gui.actions.edit - package info.bioinfweb.treegraph.gui.actions.edit
 
info.bioinfweb.treegraph.gui.actions.file - package info.bioinfweb.treegraph.gui.actions.file
 
info.bioinfweb.treegraph.gui.actions.format - package info.bioinfweb.treegraph.gui.actions.format
 
info.bioinfweb.treegraph.gui.actions.help - package info.bioinfweb.treegraph.gui.actions.help
 
info.bioinfweb.treegraph.gui.actions.select - package info.bioinfweb.treegraph.gui.actions.select
 
info.bioinfweb.treegraph.gui.actions.view - package info.bioinfweb.treegraph.gui.actions.view
 
info.bioinfweb.treegraph.gui.actions.window - package info.bioinfweb.treegraph.gui.actions.window
 
info.bioinfweb.treegraph.gui.dialogs - package info.bioinfweb.treegraph.gui.dialogs
Contains dialogs of the TreeGraph 2 GUI.
info.bioinfweb.treegraph.gui.dialogs.editelement - package info.bioinfweb.treegraph.gui.dialogs.editelement
 
info.bioinfweb.treegraph.gui.dialogs.elementformats - package info.bioinfweb.treegraph.gui.dialogs.elementformats
 
info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor - package info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor
 
info.bioinfweb.treegraph.gui.dialogs.io - package info.bioinfweb.treegraph.gui.dialogs.io
 
info.bioinfweb.treegraph.gui.dialogs.io.exporttographic - package info.bioinfweb.treegraph.gui.dialogs.io.exporttographic
 
info.bioinfweb.treegraph.gui.dialogs.io.loadlogger - package info.bioinfweb.treegraph.gui.dialogs.io.loadlogger
 
info.bioinfweb.treegraph.gui.dialogs.nodebranchdata - package info.bioinfweb.treegraph.gui.dialogs.nodebranchdata
 
info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput - package info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput
 
info.bioinfweb.treegraph.gui.dialogs.specialformats - package info.bioinfweb.treegraph.gui.dialogs.specialformats
 
info.bioinfweb.treegraph.gui.mainframe - package info.bioinfweb.treegraph.gui.mainframe
Contains all classes directly related to the main frame.
info.bioinfweb.treegraph.gui.mainframe.tools - package info.bioinfweb.treegraph.gui.mainframe.tools
 
info.bioinfweb.treegraph.gui.treeframe - package info.bioinfweb.treegraph.gui.treeframe
Contains all classes that make up a document window.
info.bioinfweb.treegraph.gui.treeframe.ruler - package info.bioinfweb.treegraph.gui.treeframe.ruler
 
inheritToTerminals - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit
 
inheritToTerminals - Variable in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit
 
inheritToTerminalsCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
 
inheritToTerminalsCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
 
init(boolean) - Method in class info.bioinfweb.treegraph.document.Document
 
init() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats
 
INITIAL_CAPACITY - Static variable in class info.bioinfweb.treegraph.document.LabelLine
 
INITIAL_CAPACITY - Static variable in class info.bioinfweb.treegraph.document.Labels
 
initialFile - Variable in class info.bioinfweb.treegraph.cmd.CmdProcessor
 
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditTextElementDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
This method initializes this dialog
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog
 
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.JPEGPrefPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TIFFPrefPanel
 
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TransparentBgPrefPanel
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.loadlogger.LoadLoggerDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel
 
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup
This method initializes this
initialize() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
This method initializes this
initLabel(String, JPanel, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput
 
initLabelFormats() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFReader
 
initSets() - Method in class info.bioinfweb.treegraph.document.Document
 
input - Variable in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup
 
inputListeners - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
 
inputPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog
 
inputs - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog
 
inScaleUnits - Variable in class info.bioinfweb.treegraph.document.format.ScaleValue
 
insert(Label) - Method in class info.bioinfweb.treegraph.document.LabelLine
 
insert(Legend) - Method in class info.bioinfweb.treegraph.document.Legends
Inserts the specified legend to the list and calls l.setLegends(this).
insert() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveLabelEdit
 
insert() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveLegendEdit
 
insert() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveSubtreeEdit
 
insertGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
InsertLabelEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
InsertLabelEdit(Document, Label, Labels) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertLabelEdit
 
InsertLabelsEdit - Class in info.bioinfweb.treegraph.document.undo.edit
Used to insert multiple labels and one or more branches.
InsertLabelsEdit(Document, Label, Branch[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertLabelsEdit
 
InsertLegendEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
InsertLegendEdit(Document, Legend, Node, Node) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertLegendEdit
 
InsertRemoveLabelEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
InsertRemoveLabelEdit(Document, Label, Labels) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveLabelEdit
 
InsertRemoveLegendEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
InsertRemoveLegendEdit(Document, Legend, Node, Node) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveLegendEdit
 
InsertRemoveSubtreeEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
InsertRemoveSubtreeEdit(Document, Node, Node, int) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveSubtreeEdit
 
InsertSiblingEdit - Class in info.bioinfweb.treegraph.document.undo.edit
This edit is executed if a branch is selected and a new node should be inserted.
InsertSiblingEdit(Document, Node, Node) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertSiblingEdit
 
insertSubtree(Document, Node, Node) - Static method in class info.bioinfweb.treegraph.gui.actions.edit.NewNodeAction
Inserts a new subelement as the last subelement of the given parent.
insertSubtree(Document, Node, Node, int) - Static method in class info.bioinfweb.treegraph.gui.actions.edit.NewNodeAction
Inserts a new subelement at the given position.
InsertSubtreeEdit - Class in info.bioinfweb.treegraph.document.undo.edit
 
InsertSubtreeEdit(Document, Node, Node, int) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.InsertSubtreeEdit
 
inSubtreeOf(LeafField, boolean) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
Returns false if this field (or its complement) contains any terminal the specified field does not contain and this field (or its complement) contains at least one terminal less than the specified field.
internalAdapter - Variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
internalFrameListener - Variable in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame
 
internalInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
 
internalLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
 
internalLinesMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
internalNodesPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
 
InternalPieChartLinesOperator - Class in info.bioinfweb.treegraph.document.format.operate
 
InternalPieChartLinesOperator(boolean) - Constructor for class info.bioinfweb.treegraph.document.format.operate.InternalPieChartLinesOperator
 
internalsAreDecimal(Node, NodeBranchDataAdapter) - Static method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit
Tests if all internal nodes in the subtree under root contain decimal values.
InternalsRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
IntervalDialog - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdata
 
IntervalDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
 
intervalPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel
 
intervalPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog
 
InvalidFormatException - Exception in info.bioinfweb.treegraph.document.undo.edit
This exception is throw if a name table file does not have two entries seperated by the specified String in a line.
InvalidFormatException() - Constructor for exception info.bioinfweb.treegraph.document.undo.edit.InvalidFormatException
 
InvalidFormatException(String, Throwable) - Constructor for exception info.bioinfweb.treegraph.document.undo.edit.InvalidFormatException
 
InvalidFormatException(String) - Constructor for exception info.bioinfweb.treegraph.document.undo.edit.InvalidFormatException
 
InvalidFormatException(Throwable) - Constructor for exception info.bioinfweb.treegraph.document.undo.edit.InvalidFormatException
 
InvalidTargetException - Exception in info.bioinfweb.treegraph.document.format.operate
 
InvalidTargetException() - Constructor for exception info.bioinfweb.treegraph.document.format.operate.InvalidTargetException
 
InvalidTargetException(String, Throwable) - Constructor for exception info.bioinfweb.treegraph.document.format.operate.InvalidTargetException
 
InvalidTargetException(String) - Constructor for exception info.bioinfweb.treegraph.document.format.operate.InvalidTargetException
 
InvalidTargetException(Throwable) - Constructor for exception info.bioinfweb.treegraph.document.format.operate.InvalidTargetException
 
InvertSelectionAction - Class in info.bioinfweb.treegraph.gui.actions.select
 
InvertSelectionAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.select.InvertSelectionAction
 
isAbove() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats
 
isAbove() - Method in class info.bioinfweb.treegraph.document.Label
Tests if this label is located in the upper label block.
isCellEditable(int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
 
isCharAfterLength(char) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
 
isChild(int) - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.LeafField
 
isChildOf(Node) - Method in class info.bioinfweb.treegraph.document.Node
Tests if the specified node is an ancestor of this node.
isConstantWidth() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats
 
isDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
 
isDecimal(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
 
isDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
 
isDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
 
isDecimal() - Method in class info.bioinfweb.treegraph.document.TextElementData
Return whether this object contains a decimal value.
isEmpty() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard
 
isEmpty() - Method in class info.bioinfweb.treegraph.document.HiddenDataMap
 
isEmpty() - Method in class info.bioinfweb.treegraph.document.Labels
Tests if any labels are present
isEmpty() - Method in class info.bioinfweb.treegraph.document.Legends
 
isEmpty(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
 
isEmpty(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
 
isEmpty(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
 
isEmpty(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
 
isEmpty() - Method in class info.bioinfweb.treegraph.document.TextElementData
Return whether this object is empty.
isEmpty() - Method in class info.bioinfweb.treegraph.document.Tree
Tests if there are tree elements present.
isEmpty() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
 
isEmpty() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
 
isEvaluating - Variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
 
isEvaluatingDecimal - Variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
 
isFirst() - Method in class info.bioinfweb.treegraph.document.Node
 
isFreeName(String) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringWriter
 
isFreeNameChar(char) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
 
isFreeNameFirstChar(char) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
 
isIncreasing() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
 
isInScaleUnits() - Method in class info.bioinfweb.treegraph.document.format.ScaleValue
 
isLadderizeDown() - Method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
 
isLast() - Method in class info.bioinfweb.treegraph.document.Node
 
isLeaf() - Method in class info.bioinfweb.treegraph.document.Node
Tests if this Node is at the deepest level of the tree (has no subnodes).
isNewColumn() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.AbstractIDElementAdapter
 
isNewColumn() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
 
isNewColumn() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NewHiddenBranchDataAdapter
 
isNewColumn() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NewHiddenNodeDataAdapter
 
isNewColumn() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NewTextLabelAdapter
 
isNewColumn() - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
 
isNewColumn() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
 
isNewColumn() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
 
isOnlySubelement() - Method in class info.bioinfweb.treegraph.document.Node
Tests if this element is the only Node under the parent node.
isPainter(TreePainter) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory
 
isPainter(TreePainter) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory
 
isPainter(TreePainter) - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory
 
isPositioner(TreePositioner) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory
 
isPositioner(TreePositioner) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory
 
isPositioner(TreePositioner) - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory
 
isSet - Variable in class info.bioinfweb.treegraph.document.format.operate.TextStyleOperator
 
isSignificant() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit
 
isStartLeft() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats
 
isString(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter
 
isString(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter
 
isString(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter
 
isString(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter
 
isString() - Method in class info.bioinfweb.treegraph.document.TextElementData
Return whether this object contains a string value.
isSubedit - Variable in class info.bioinfweb.treegraph.document.undo.DocumentEdit
 
ITALIC - Static variable in interface info.bioinfweb.treegraph.document.format.TextFormats
 
italicCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
 
italicMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel
 
items - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel
 
iterator() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection
 
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