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## Uses of Class
info.bioinfweb.treegraph.document.Document

Packages that use Document
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.format | Contains classes that store format information of the different document elements.
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.newick |
info.bioinfweb.treegraph.document.io.nexus |
info.bioinfweb.treegraph.document.io.phyloxml |
info.bioinfweb.treegraph.document.io.tgf |
info.bioinfweb.treegraph.document.io.xtg |
info.bioinfweb.treegraph.document.undo | Contains all document edits to manipulate the TreeGraph 2 data structure.
info.bioinfweb.treegraph.document.undo.edit |
info.bioinfweb.treegraph.document.undo.file |
info.bioinfweb.treegraph.document.undo.format |
info.bioinfweb.treegraph.graphics.export |
info.bioinfweb.treegraph.graphics.positionpaint |
info.bioinfweb.treegraph.gui.actions | Contains the actions classes used in the TreeGraph 2 GUI.
info.bioinfweb.treegraph.gui.actions.edit |
info.bioinfweb.treegraph.gui.actions.file |
info.bioinfweb.treegraph.gui.actions.format |
info.bioinfweb.treegraph.gui.actions.select |
info.bioinfweb.treegraph.gui.actions.view |
info.bioinfweb.treegraph.gui.actions.window |
info.bioinfweb.treegraph.gui.dialogs | Contains dialogs of the TreeGraph 2 GUI.
info.bioinfweb.treegraph.gui.dialogs.elementformats |
info.bioinfweb.treegraph.gui.dialogs.io.exporttographic |
info.bioinfweb.treegraph.gui.mainframe | Contains all classes directly related to the main frame.
info.bioinfweb.treegraph.gui.treeframe | Contains all classes that make up a document window.

Uses of Document in info.bioinfweb.treegraph.document

Methods in info.bioinfweb.treegraph.document with parameters of type Document
`boolean` | `ContrastManager.ensureContrast(Document document, Label label)` Checks the text color of the specified label regarding to its contrast to the background color of the document.
`boolean` | `ContrastManager.ensureContrast(Document document, Label[] labels)` Checks the text color of the specified labels regarding to their contrast to the background color of the document.
`boolean` | `ContrastManager.ensureContrast(Document document, Legend legend)` Checks the text color of the specified legend regarding to its contrast to the background color of the document.
`boolean` | `ContrastManager.ensureContrast(Document document, Node root, Legend[] legends)` Checks the colors of all elements in the subtree under `root` (including `root` and its afferent branch) regarding to their contrast to the background color of the document.
`private boolean` | `ContrastManager.ensureLabelContrast(Document document, Label label)` Internal method which does not set `state = State.UNDEFINED`.
`private boolean` | `ContrastManager.ensureLegendContrast(Document document, Legend legend)`
`private boolean` | `ContrastManager.ensureSubtreeContrast(Document document, Node root)` Rekursive method which contains the actual implementation.

Uses of Document in info.bioinfweb.treegraph.document.format

Methods in info.bioinfweb.treegraph.document.format with parameters of type Document
`static Node` | `FormatUtils.createNode(Document document)` Creates a node with an afferent branch to be inserted in the specified document.
`static java.awt.Color` | `FormatUtils.getLineColor(Document document)` Returns the default line color or its inversion depending in the backgound color of the specified document.
`static java.awt.Color` | `FormatUtils.getTextColor(Document document)` Returns the default text color or its inversion depending in the backgound color of the specified document.

Uses of Document in info.bioinfweb.treegraph.document.io

Fields in info.bioinfweb.treegraph.document.io declared as Document
`protected Document` | `AbstractDocumentWriter.document`
`protected Document` | `AbstractDocumentReader.document`

Methods in info.bioinfweb.treegraph.document.io that return Document
`Document` | `DocumentReader.read(java.io.File file)`
`Document` | `AbstractDocumentReader.read(java.io.File file)`
`Document` | `DocumentReader.read(java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter)`
`Document` | `AbstractDocumentReader.read(java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter)`
`Document` | `DocumentReader.read(java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)`
`Document` | `AbstractDocumentReader.read(java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)` If you want to implement file specific functionalities you should override this method.
`Document` | `DocumentReader.read(java.io.InputStream stream)`
`Document` | `AbstractDocumentReader.read(java.io.InputStream stream)`
`Document` | `DocumentReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter)`
`Document` | `AbstractDocumentReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter)`
`Document` | `DocumentReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)`

Methods in info.bioinfweb.treegraph.document.io with parameters of type Document
`void` | `DocumentWriter.write(Document document, java.io.File file)`
`void` | `AbstractDocumentWriter.write(Document document, java.io.File file)`
`void` | `DocumentWriter.write(Document document, java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)`
`void` | `AbstractDocumentWriter.write(Document document, java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)`
`void` | `DocumentWriter.write(Document document, java.io.OutputStream stream)`
`void` | `DocumentWriter.write(Document document, java.io.OutputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)`

Uses of Document in info.bioinfweb.treegraph.document.io.newick

Methods in info.bioinfweb.treegraph.document.io.newick that return Document
`Document` | `NewickReader.read(java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternals)`
`Document` | `NewickReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternals)`

Methods in info.bioinfweb.treegraph.document.io.newick with parameters of type Document
`void` | `NewickWriter.write(Document document, java.io.OutputStream stream)`
`void` | `NewickWriter.write(Document document, java.io.OutputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)`

Uses of Document in info.bioinfweb.treegraph.document.io.nexus

Methods in info.bioinfweb.treegraph.document.io.nexus that return Document
`Document` | `NexusReader.read(java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthAdapter, TreeSelector selector, boolean translateInternalNodes)`
`Document` | `NexusReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthAdapter, TreeSelector selector, boolean translateInternalNodes)`

Methods in info.bioinfweb.treegraph.document.io.nexus with parameters of type Document
`void` | `NexusWriter.write(Document document, java.io.OutputStream stream)`
`void` | `NexusWriter.write(Document document, java.io.OutputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)`

Uses of Document in info.bioinfweb.treegraph.document.io.phyloxml

Methods in info.bioinfweb.treegraph.document.io.phyloxml that return Document
`Document` | `PhyloXMLReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)`

Uses of Document in info.bioinfweb.treegraph.document.io.tgf

Methods in info.bioinfweb.treegraph.document.io.tgf that return Document
`Document` | `TGFReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)`

Uses of Document in info.bioinfweb.treegraph.document.io.xtg

Methods in info.bioinfweb.treegraph.document.io.xtg that return Document
`Document` | `XTGReader.read(java.io.File file, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)`
`Document` | `XTGReader.read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)`

Methods in info.bioinfweb.treegraph.document.io.xtg with parameters of type Document
`void` | `XTGWriter.write(Document document, java.io.OutputStream stream)`
`void` | `XTGWriter.write(Document document, java.io.OutputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)` A call of this method is identical with calling `XTGWriter.write(info.bioinfweb.treegraph.document.Document, java.io.OutputStream)` becuase the tgx format supports writing any number of labels by default and there is no need to replace internal node names by label values.

Uses of Document in info.bioinfweb.treegraph.document.undo

Fields in info.bioinfweb.treegraph.document.undo declared as Document
`protected Document` | `DocumentEdit.document`

Constructors in info.bioinfweb.treegraph.document.undo with parameters of type Document
`ComplexDocumentEdit(Document document)`
`DocumentEdit(Document document)`
`NodeBranchDataEdit(Document document, NodeBranchDataAdapter adapter)`
`SaveLegendsEdit(Document document)`

Uses of Document in info.bioinfweb.treegraph.document.undo.edit

Fields in info.bioinfweb.treegraph.document.undo.edit declared as Document
`private Document` | `LegendPaster.document`

Constructors in info.bioinfweb.treegraph.document.undo.edit with parameters of type Document
`BranchLengthEdit(Document document, Branch branch, double newLength)`
`CalculateColumnEdit(Document document, NodeBranchDataAdapter targetAdapter, java.lang.String expression)`
`ChangeLabelIDEdit(Document document, java.lang.String newID, Label[] labels)`
`CollapseNodeEdit(Document document, Node node, boolean showWarnings)`
`CopyColumnEdit(Document document, NodeBranchDataAdapter source, NodeBranchDataAdapter dest, boolean includeLeafs)`
`CutEdit(Document document, ConcretePaintableElement[] elements)`
`DeleteColumnEdit(Document document, NodeBranchDataAdapter adapter)`
`DeleteEdit(Document document, ConcretePaintableElement[] elements, boolean showWarnings)`
`DeleteOutsideIntervalEdit(Document document, NodeBranchDataAdapter adapter, double lowerBorder, double upperBorder)`
`DeleteSubelementsEdit(Document document, Node root, boolean showWarnings)`
`EditNodeBranchDataEdit(Document document, Node newRoot)`
`InsertLabelEdit(Document document, Label label, Labels owner)`
`InsertLabelsEdit(Document document, Label label, Branch[] branches)`
`InsertLegendEdit(Document document, Legend legend, Node anchor0, Node anchor1)`
`InsertRemoveLabelEdit(Document document, Label label, Labels owner)`
`InsertRemoveLegendEdit(Document document, Legend legend, Node anchor0, Node anchor1)`
`InsertRemoveSubtreeEdit(Document document, Node parent, Node root, int index)`
`InsertSiblingEdit(Document document, Node firstSibling, Node newSibling)`
`InsertSubtreeEdit(Document document, Node parent, Node root, int index)`
`LadderizeEdit(Document document, Node root, boolean down)`
`LegendPaster(Document document, Legend[] legends)`
`MoveSubtreeEdit(Document document, Node root, boolean down)`
`PasteAllLabelsEdit(Document document, Branch branch, Label[] labelList)`
`PasteLabelEdit(Document document, Branch branch, Label label)`
`PasteLegendEdit(Document document, Node anchor1, Node anchor2, Legend legend)`
`PasteRootEdit(Document document, Node root, Legend[] legends)`
`PasteSiblingEdit(Document document, Node firstSibling, Node newSibling, Legend[] legends)`
`PasteSubtreeEdit(Document document, Node parent, Node root, Legend[] legends)`
`RemoveLabelEdit(Document document, Label label, Labels owner)`
`RemoveLegendEdit(Document document, Legend legend)`
`RemoveSubtreeEdit(Document document, Node parent, Node root, int index, boolean showWarnings)`
`RenameDataIDEdit(Document document, java.lang.String[] newIDs, java.lang.String[] oldIDs)`
`ReplaceInNodeDataEdit(Document document, NodeBranchDataAdapter adapter, ReplaceInNodeDataEdit.InsertPosition position, java.lang.String oldText, java.lang.String newText, boolean caseSensitive, boolean wordsOnly)`
`RerootEdit(Document document, Branch rootingPoint)`
`RescaleNodeDataEdit(Document document, NodeBranchDataAdapter adapter, double factor, double addend)`
`SeparateBranchEdit(Document document, Branch branch)`
`SetColumnTypeEdit(Document document, TextElementDataAdapter adapter, boolean decimal)`
`TextElementEdit(Document document, TextElement element, TextElementData newData)`

Uses of Document in info.bioinfweb.treegraph.document.undo.file

Fields in info.bioinfweb.treegraph.document.undo.file declared as Document
`private Document` | `AddSupportValuesEdit.src`

Methods in info.bioinfweb.treegraph.document.undo.file with parameters of type Document
`static AddSupportValuesEdit` | `AddSupportValuesEdit.createInstance(Document document, Document src, TextElementDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, java.lang.String idPrefix, boolean importNodeNames, boolean processRooted)` Returns a new instance of `AddSupportValuesEdit` or `null` if the given source document contains internal node names that are not decimal.

Constructors in info.bioinfweb.treegraph.document.undo.file with parameters of type Document
`AddSupportValuesEdit(Document document, Document src, TextElementDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, java.lang.String idPrefix, NodeBranchDataAdapter sourceAdapter, boolean processRooted)`
`ApplyNameTableEdit(Document document, NodeBranchDataAdapter adapter, java.util.List<java.lang.String> oldNames, java.util.List<java.lang.String> newNames, boolean ignoreWhitespaces, boolean caseSensitive, boolean parseNumericValues)`
`ImportTableEdit(Document document, java.lang.String[][] data, NodeBranchDataAdapter[] adapters)`

Uses of Document in info.bioinfweb.treegraph.document.undo.format

Methods in info.bioinfweb.treegraph.document.undo.format with parameters of type Document
`static ShowRootedEdit` | `ShowRootedEdit.createInstance(Document document, boolean showRooted)`
`static ShowHideScaleBarEdit` | `ShowHideScaleBarEdit.createInstance(Document document, boolean showScaleBar)`

Constructors in info.bioinfweb.treegraph.document.undo.format with parameters of type Document
`AutoPositionLabelsEdit(Document document, Branch[] branches)`
`ColorsByNodeBranchDataEdit(Document document, NodeBranchDataAdapter sourceAdapter, java.awt.Color min, java.awt.Color max, boolean changeUndefined, boolean inheritToTerminals, ColorAdapter[] targetAdapters)`
`DistanceValuesByNodeBranchDataEdit(Document document, NodeBranchDataAdapter sourceAdapter, float min, float max, boolean changeUndefined, boolean inheritToTerminals, DistanceAdapter[] targetAdapters)`
`GlobalFormatsEdit(Document document, GlobalFormats newFormats)`
`NodeBranchDataFormatEdit(Document document)`
`OperatorsEdit(Document document, PaintableElement[] applyElements, FormatOperator[] operators)`
`ReanchorLegendEdit(Document document, Legend legend, java.lang.String newAnchor1, java.lang.String newAnchor2)`
`ScaleBranchLengthsEdit(Document document, float length)`
`ScaleDistanceValuesEdit(Document document, Node root, float factor, DistanceAdapter[] targetAdapters)`
`ShowHideScaleBarEdit(Document document, GlobalFormats newFormats)`
`ShowRootedEdit(Document document, GlobalFormats newFormats)`

Uses of Document in info.bioinfweb.treegraph.graphics.export

Methods in info.bioinfweb.treegraph.graphics.export with parameters of type Document
`void` | `GraphicWriter.write(Document document, TreePainter painter, GraphicWriterHints hints, java.io.File file)`
`void` | `AbstractGraphicWriter.write(Document document, TreePainter painter, GraphicWriterHints hints, java.io.File file)`
`void` | `SVGTranscodeWriter.write(Document document, TreePainter painter, GraphicWriterHints hints, java.io.OutputStream stream)` Writes the given document to the given stream in the graphic format provided by the transcoder-class specified in the constructor.
`void` | `GraphicWriter.write(Document document, TreePainter painter, GraphicWriterHints hints, java.io.OutputStream stream)`
`void` | `FreeHEPWriter.write(Document document, TreePainter painter, GraphicWriterHints hints, java.io.OutputStream stream)`

Uses of Document in info.bioinfweb.treegraph.graphics.positionpaint

Fields in info.bioinfweb.treegraph.graphics.positionpaint declared as Document
`protected Document` | `RectangularCladogramPositioner.document`
`private Document` | `RectangularCladogramPainter.document`

Methods in info.bioinfweb.treegraph.graphics.positionpaint with parameters of type Document
`ConcretePaintableElement` | `TreePositioner.elementToPosition(Document document, float x, float y, float margin)` Return the SelectableElement of the tree in which the given coordinates are located.
`ConcretePaintableElement` | `RectangularCladogramPositioner.elementToPosition(Document document, float x, float y, float margin)` Determines the element to a position defined by x- and y-coordinates (e.g. to select an element by mouse).
`void` | `TreePainter.paintTree(java.awt.Graphics2D g, Document document, TreeSelection selection, int x, int y, float pixelsPerMm, boolean transparent)`
`void` | `RectangularCladogramPainter.paintTree(java.awt.Graphics2D g, Document document, TreeSelection selection, int x, int y, float pixelsPerMillimeter, boolean transparent)`
`void` | `TreePositioner.positionAll(Document document, float rescalingFactorX)`
`void` | `RectangularCladogramPositioner.positionAll(Document document, float rescalingFactorX)`

Uses of Document in info.bioinfweb.treegraph.gui.actions

Methods in info.bioinfweb.treegraph.gui.actions with parameters of type Document
`private void` | `ActionManagement.setActionStatusBySelection(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`abstract void` | `DocumentAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`

Uses of Document in info.bioinfweb.treegraph.gui.actions.edit

Methods in info.bioinfweb.treegraph.gui.actions.edit with parameters of type Document
`static boolean` | `NewNodeAction.insertSubtree(Document document, Node parent, Node root)` Inserts a new subelement as the last subelement of the given parent.
`static boolean` | `NewNodeAction.insertSubtree(Document document, Node parent, Node root, int index)` Inserts a new subelement at the given position.
`void` | `UndoRedoToAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `UndoAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SetColumnTypeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SeparateBranchAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SearchTextAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `RerootAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ReplaceInNodeDataAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `RenameDataIDAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `RedoAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `PasteAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `NewTextLabelAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `NewNodeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `NewLegendAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `NewIconLabelsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `MoveSubtreeUpAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `MoveSubtreeDownAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `LadderizeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `EditTextElementAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `EditBranchLengthAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `DeleteSubelementsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `DeleteOutsideIntervalAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `DeleteElementAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `DeleteColumnAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `CopyElementAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `CopyColumnAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `CopyAllLabelsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `CollapseNodeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ChangeLabelIDAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `CalculateColumnAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`

Uses of Document in info.bioinfweb.treegraph.gui.actions.file

Methods in info.bioinfweb.treegraph.gui.actions.file with parameters of type Document
`void` | `SaveAsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SaveAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `OpenAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `NewDocumentAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ImportTableAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ExportToPDFAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ExportToNewickNexusAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ExportToGraphicAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ExportTableAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ExitAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `CloseAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ApplyNameTableAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `AddSupportValuesAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`

Uses of Document in info.bioinfweb.treegraph.gui.actions.format

Methods in info.bioinfweb.treegraph.gui.actions.format with parameters of type Document
`void` | `ShowRootedAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ShowHideScaleBarAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ScaleDistanceValuesAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ScaleBranchLengthsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ReanchorLegendAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `EditGlobalFormatsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `EditElementFormatsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `DistanceValuesByNodeBranchDataAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ColorsByNodeBranchDataAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `AutoPositionLabelsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`

Uses of Document in info.bioinfweb.treegraph.gui.actions.select

Methods in info.bioinfweb.treegraph.gui.actions.select with parameters of type Document
`void` | `SelectTypeInSubtreeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectTypeInDocumentAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectSubtreeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectLegendsWithPosIndexAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectLegendsInSubtreeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectLegendsAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectLeafsInSubtreeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectLeafsInDocumentAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectLabelsWithIDAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectLabelsInSubtreeAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `SelectAllAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `InvertSelectionAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`

Uses of Document in info.bioinfweb.treegraph.gui.actions.view

Methods in info.bioinfweb.treegraph.gui.actions.view with parameters of type Document
`void` | `SetZoomAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `ChangePainterIDAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`

Uses of Document in info.bioinfweb.treegraph.gui.actions.window

Methods in info.bioinfweb.treegraph.gui.actions.window with parameters of type Document
`void` | `PreviousDocumentAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`
`void` | `NextDocumentAction.setEnabled(Document document, TreeSelection selection, NodeBranchDataAdapter tableAdapter)`

Uses of Document in info.bioinfweb.treegraph.gui.dialogs

Fields in info.bioinfweb.treegraph.gui.dialogs declared as Document
`private Document` | `EditDialog.document`

Methods in info.bioinfweb.treegraph.gui.dialogs that return Document
`protected Document` | `EditDialog.getDocument()`

Methods in info.bioinfweb.treegraph.gui.dialogs with parameters of type Document
`boolean` | `EditDialog.execute(Document document, TreeSelection selection, NodeBranchDataAdapter selectedAdapter)`
`protected void` | `EditDialog.setDocument(Document document)`
`void` | `LabelIDComboBox.setIDs(Document document)`

Uses of Document in info.bioinfweb.treegraph.gui.dialogs.elementformats

Methods in info.bioinfweb.treegraph.gui.dialogs.elementformats that return Document
`Document` | `ElementFormatsDialog.getDocument()`

Uses of Document in info.bioinfweb.treegraph.gui.dialogs.io.exporttographic

Methods in info.bioinfweb.treegraph.gui.dialogs.io.exporttographic with parameters of type Document
`boolean` | `ExportToGraphicDialog.execute(Document document, TreeSelection selection, NodeBranchDataAdapter selectedAdapter)` This method throws a Runtime exception if it is called.

Uses of Document in info.bioinfweb.treegraph.gui.mainframe

Methods in info.bioinfweb.treegraph.gui.mainframe with parameters of type Document
`TreeInternalFrame` | `MainFrame.addInternalFrame(Document document)`

Uses of Document in info.bioinfweb.treegraph.gui.treeframe

Fields in info.bioinfweb.treegraph.gui.treeframe declared as Document
`private Document` | `TreeViewPanel.document`
`private Document` | `TreeInternalFrame.document`
`private Document` | `DocumentTableModel.document`

Methods in info.bioinfweb.treegraph.gui.treeframe that return Document
`Document` | `TreeViewPanel.getDocument()` Returns the currently associated document.
`Document` | `TreeInternalFrame.getDocument()`
`Document` | `DocumentTableModel.getDocument()`

Methods in info.bioinfweb.treegraph.gui.treeframe with parameters of type Document
`void` | `TreeViewPanel.setDocument(Document document)` Sets this view to a new model and repaints the element using the data of the new document.
`void` | `DocumentTableModel.setDocument(Document document)` Sets this view to a new model and repaints the element using the data of the new document.

Constructors in info.bioinfweb.treegraph.gui.treeframe with parameters of type Document
`DocumentTableModel(Document document)` Creates a new `DocumentTableModel` which shows the tree contained in document.
`TreeInternalFrame(Document document)` This is the xxx default constructor
`TreeViewPanel(Document document)` Creates a new swing-panel which shows the tree contained in document.

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