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.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.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.datatable
info.bioinfweb.treegraph.gui.dialogs.elementformats
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, 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) 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.
boolean	ContrastManager.ensureContrast(Document document, TextLabel 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, TextLabel[] labels) Checks the text color of the specified labels regarding to their contrast to the background color of the document.
private boolean	ContrastManager.ensureLabelContrast(Document document, TextLabel label) Internal method which does not set state = State.UNDEFINED.
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, NodeDataAdapter internalAdapter)
Document	AbstractDocumentReader.read(java.io.File file, NodeDataAdapter internalAdapter)
Document	DocumentReader.read(java.io.File file, NodeDataAdapter internalAdapter, TreeSelector selector, boolean translateInternalNodes)
Document	AbstractDocumentReader.read(java.io.File file, NodeDataAdapter internalAdapter, 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, NodeDataAdapter internalAdapter)
Document	AbstractDocumentReader.read(java.io.InputStream stream, NodeDataAdapter internalAdapter)
Document	DocumentReader.read(java.io.InputStream stream, NodeDataAdapter internalAdapter, 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, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter)
void	AbstractDocumentWriter.write(Document document, java.io.File file, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter)
void	DocumentWriter.write(Document document, java.io.OutputStream stream)
void	DocumentWriter.write(Document document, java.io.OutputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter)

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, NodeDataAdapter internalAdapter, TreeSelector selector, boolean translateInternals)
Document	NewickReader.read(java.io.InputStream stream, NodeDataAdapter internalAdapter, 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, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter)

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, NodeDataAdapter internalAdapter, TreeSelector selector, boolean translateInternalNodes)
Document	NexusReader.read(java.io.InputStream stream, NodeDataAdapter internalAdapter, 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, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter)

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, NodeDataAdapter internalAdapter, 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, NodeDataAdapter internalAdapter, TreeSelector selector, boolean translateInternalNodes)
Document	XTGReader.read(java.io.InputStream stream, NodeDataAdapter internalAdapter, 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, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter) 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)

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

AddSupportValuesEdit.src

Methods in info.bioinfweb.treegraph.document.undo.edit with parameters of type Document

static AddSupportValuesEdit

AddSupportValuesEdit.createInstance(Document document, Document src, NodeDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, java.lang.String idPrefix) 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.edit with parameters of type Document

AddSupportValuesEdit(Document document, Document src, NodeDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, java.lang.String idPrefix)

ApplyNameTableEdit(Document document, NodeDataAdapter adapter, java.util.List<java.lang.String> oldNames, java.util.List<java.lang.String> newNames, boolean ignoreWhitespaces, boolean caseSensitive, boolean parseNumericValues)

AssignLabelIDsEdit(Document document)

BranchLengthEdit(Document document, Branch branch, double newLength)

ChangeLabelIDEdit(Document document, java.lang.String newID, Label[] labels)

CollapseNodeEdit(Document document, Node node, boolean showWarnings)

CutEdit(Document document, ConcretePaintableElement[] elements)

DeleteEdit(Document document, ConcretePaintableElement[] elements, boolean showWarnings)

DeleteSubelementsEdit(Document document, Node root, boolean showWarnings)

EditNodeBranchDataEdit(Document document, Node newRoot)

InsertLabelEdit(Document document, Label label, Labels owner)

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)

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 anchor, Legend legend)

PasteRootEdit(Document document, Node root)

PasteSiblingEdit(Document document, Node firstSibling, Node newSibling)

PasteSubtreeEdit(Document document, Node parent, Node root)

RemoveLabelEdit(Document document, Label label, Labels owner)

RemoveLegendEdit(Document document, Legend legend)

RemoveSubtreeEdit(Document document, Node parent, Node root, int index, boolean showWarnings)

ReplaceInNodeDataEdit(Document document, NodeDataAdapter adapter, ReplaceInNodeDataEdit.InsertPosition position, java.lang.String oldText, java.lang.String newText, boolean caseSensitive, boolean wordsOnly)

RerootEdit(Document document, Branch rootingPoint)

RescaleNodeDataEdit(Document document, NodeDataAdapter adapter, double factor, double addend)

SeparateBranchEdit(Document document, Branch branch)

TextElementEdit(Document document, TextElement element, TextElementData newData)

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

BranchWidthsFromNodeDataEdit(Document document, NodeDataAdapter adapter, double min, double max, boolean changeUndefined)

ColorsFromNodeDataEdit(Document document, NodeDataAdapter adapter, java.awt.Color min, java.awt.Color max, boolean changeUndefined)

GlobalFormatsEdit(Document document, GlobalFormats newFormats)

NodeDataFormatEdit(Document document)

OperatorsEdit(Document document, PaintableElement[] applyElements, FormatOperator[] operators)

ReanchorLegendEdit(Document document, Legend legend, java.lang.String newAnchor1, java.lang.String newAnchor2)

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)
abstract void	DocumentAction.setEnabled(Document document, TreeSelection selection)

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	UndoAction.setEnabled(Document document, TreeSelection selection)
void	SeparateBranchAction.setEnabled(Document document, TreeSelection selection)
void	SearchTextAction.setEnabled(Document document, TreeSelection selection)
void	RerootAction.setEnabled(Document document, TreeSelection selection)
void	ReplaceInNodeDataAction.setEnabled(Document document, TreeSelection selection)
void	RedoAction.setEnabled(Document document, TreeSelection selection)
void	PasteAction.setEnabled(Document document, TreeSelection selection)
void	NewTextLabelAction.setEnabled(Document document, TreeSelection selection)
void	NewNodeAction.setEnabled(Document document, TreeSelection selection)
void	NewLegendAction.setEnabled(Document document, TreeSelection selection)
void	MoveSubtreeUpAction.setEnabled(Document document, TreeSelection selection)
void	MoveSubtreeDownAction.setEnabled(Document document, TreeSelection selection)
void	LadderizeAction.setEnabled(Document document, TreeSelection selection)
void	EditTextElementAction.setEnabled(Document document, TreeSelection selection)
void	EditBranchNodeDataAction.setEnabled(Document document, TreeSelection selection)
void	EditBranchLengthAction.setEnabled(Document document, TreeSelection selection)
void	DeleteSubelementsAction.setEnabled(Document document, TreeSelection selection)
void	DeleteElementAction.setEnabled(Document document, TreeSelection selection)
void	CopyElementAction.setEnabled(Document document, TreeSelection selection)
void	CopyAllLabelsAction.setEnabled(Document document, TreeSelection selection)
void	CollapseNodeAction.setEnabled(Document document, TreeSelection selection)
void	ChangeLabelIDAction.setEnabled(Document document, TreeSelection selection)
void	AssignLabelIDsAction.setEnabled(Document document, TreeSelection selection)
void	ApplyNameTableAction.setEnabled(Document document, TreeSelection selection)

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)
void	SaveAction.setEnabled(Document document, TreeSelection selection)
void	OpenAction.setEnabled(Document document, TreeSelection selection)
void	NewDocumentAction.setEnabled(Document document, TreeSelection selection)
void	ExportToNewickNexusAction.setEnabled(Document document, TreeSelection selection)
void	ExportToGraphicAction.setEnabled(Document document, TreeSelection selection)
void	ExitAction.setEnabled(Document document, TreeSelection selection)
void	CloseAction.setEnabled(Document document, TreeSelection selection)
void	AddSupportValuesAction.setEnabled(Document document, TreeSelection selection)

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)
void	ShowHideScaleBarAction.setEnabled(Document document, TreeSelection selection)
void	ReanchorLegendAction.setEnabled(Document document, TreeSelection selection)
void	EditGlobalFormatsAction.setEnabled(Document document, TreeSelection selection)
void	EditElementFormatsAction.setEnabled(Document document, TreeSelection selection)
void	ColorsFromNodeDataAction.setEnabled(Document document, TreeSelection selection)
void	BranchWidthsFromNodeDataAction.setEnabled(Document document, TreeSelection selection)

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)
void	SelectTypeInDocumentAction.setEnabled(Document document, TreeSelection selection)
void	SelectSubtreeAction.setEnabled(Document document, TreeSelection selection)
void	SelectLegendsWithPosIndexAction.setEnabled(Document document, TreeSelection selection)
void	SelectLegendsAction.setEnabled(Document document, TreeSelection selection)
void	SelectLeafsInSubtreeAction.setEnabled(Document document, TreeSelection selection)
void	SelectLeafsInDocumentAction.setEnabled(Document document, TreeSelection selection)
void	SelectLabelsWithIDAction.setEnabled(Document document, TreeSelection selection)
void	SelectLabelsInSubtreeAction.setEnabled(Document document, TreeSelection selection)
void	SelectAllAction.setEnabled(Document document, TreeSelection selection)

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)
void	ChangePainterIDAction.setEnabled(Document document, TreeSelection selection)

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)
void	NextDocumentAction.setEnabled(Document document, TreeSelection selection)

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

Fields in info.bioinfweb.treegraph.gui.dialogs declared as Document

private Document	RenameIDDialog.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	RenameIDDialog.execute(Document document)
boolean	EditDialog.execute(Document document, TreeSelection selection)
protected void	EditDialog.setDocument(Document document)
void	LabelIDComboBox.setIDs(Document document)

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

Fields in info.bioinfweb.treegraph.gui.dialogs.datatable declared as Document

private Document

NodeDataTableModel.document

Methods in info.bioinfweb.treegraph.gui.dialogs.datatable that return Document

Document

NodeDataTableModel.getDocument()

Methods in info.bioinfweb.treegraph.gui.dialogs.datatable with parameters of type Document

private void

DataTableDialog.assignDocument(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.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

Methods in info.bioinfweb.treegraph.gui.treeframe that return Document

Document	TreeViewPanel.getDocument() Returns the currently associated document.
Document	TreeInternalFrame.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.

Constructors in info.bioinfweb.treegraph.gui.treeframe with parameters of type 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.