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Uses of Class
info.bioinfweb.treegraph.document.Tree

Packages that use Tree

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	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.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	Contains classes implementing the import from and export to the Newick format.
info.bioinfweb.treegraph.document.io.nexus	Contains classes implementing the import from and export to the Nexus format.
info.bioinfweb.treegraph.document.io.phyloxml	Contains classes implementing the import from the phyloXML format.
info.bioinfweb.treegraph.document.undo.format
info.bioinfweb.treegraph.gui.actions.edit
info.bioinfweb.treegraph.gui.dialogs.io
info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput
info.bioinfweb.treegraph.gui.dialogs.specialformats

Uses of Tree in info.bioinfweb.treegraph.document

Fields in info.bioinfweb.treegraph.document declared as Tree

private Tree	Legends.tree
private Tree	Document.tree

Methods in info.bioinfweb.treegraph.document that return Tree

Tree	Legends.getTree()
Tree	Document.getTree()

Methods in info.bioinfweb.treegraph.document with parameters of type Tree

static Legend[]	TreeSerializer.getLegendsInSubtree(Tree tree, Node root) Returns an array of all legends which are completely anchored inside the subtree under root.
static void	IDManager.renameID(String oldName, String newName, Tree tree) Renames a data ID in the specified tree and updates possible links to this ID in pie chart labels.
void	Document.setTree(Tree tree)

Constructors in info.bioinfweb.treegraph.document with parameters of type Tree

Legends(Tree tree)

Uses of Tree in info.bioinfweb.treegraph.document.clipboard

Methods in info.bioinfweb.treegraph.document.clipboard with parameters of type Tree

void	TreeClipboard.copySubtree(Tree tree, Node root)

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

Methods in info.bioinfweb.treegraph.document.io with parameters of type Tree

int	TreeSelector.select(String[] names, Tree[] trees)
int	DefaultTreeSelector.select(String[] names, Tree[] trees)

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

Methods in info.bioinfweb.treegraph.document.io.newick that return Tree

Tree	NewickStringReader.read(String newick)
static Tree[]	NewickStringReader.read(String[] newick, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)
Tree	NewickStringReader.read(String newick, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter)
Tree	NewickStringReader.read(String newick, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)
private Tree	NewickStringReader.readTree()

Methods in info.bioinfweb.treegraph.document.io.newick with parameters of type Tree

void	BranchLengthsScaler.setAverageScale(Tree tree, double averageLength, float smallIntervalLength) Sets the branch lengths scale of a tree so that the contained branched have the specified average length.
void	BranchLengthsScaler.setDefaultAverageScale(Tree tree) Sets the branch lengths scale of a tree so that the contained branched have BranchFormats.DEFAULT_MIN_LENGTH as their average length.
static String	NewickStringWriter.write(Tree tree, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)

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

Methods in info.bioinfweb.treegraph.document.io.nexus that return Tree

Tree[]

NexusDocument.createTrees(NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, boolean translateInternals) Creates a Tree object from each stored Newick string.

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

Fields in info.bioinfweb.treegraph.document.io.phyloxml with type parameters of type Tree

private Vector<Tree>

PhyloXMLReader.phylogenies

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

Methods in info.bioinfweb.treegraph.document.undo.format with parameters of type Tree

static float

ScaleBranchLengthsEdit.calculateScaleByLength(Tree tree, float pathLength) Returns the branch length scale necessary for the specified tree so that the longest path to a leaf of this tree has the specified length.

Constructors in info.bioinfweb.treegraph.document.undo.format with parameters of type Tree

DistanceValuesBackup(Tree tree, Node root, DistanceAdapter[] targetAdapters)

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

Methods in info.bioinfweb.treegraph.gui.actions.edit with parameters of type Tree

private void

SearchTextAction.searchScaleBar(Tree tree)

Uses of Tree in info.bioinfweb.treegraph.gui.dialogs.io

Fields in info.bioinfweb.treegraph.gui.dialogs.io declared as Tree

private Tree[]

TreeSelectionDialog.trees

Methods in info.bioinfweb.treegraph.gui.dialogs.io with parameters of type Tree

private void	AssignImportColumnsDialog.createInputs(int count, Tree tree)
NodeBranchDataAdapter[]	AssignImportColumnsDialog.execute(int count, Tree tree)
int	TreeSelectionDialog.select(String[] names, Tree[] trees)

Uses of Tree in info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput

Methods in info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput with parameters of type Tree

void	NodeDataComboBoxModel.setAdapters(Tree tree) Equvilent to a call of setAdapters(tree, true, false, false).
void	NodeBranchDataInput.setAdapters(Tree tree) Refeshs the selectable node data adapters.
void	NodeDataComboBoxModel.setAdapters(Tree tree, boolean nodeNamesSelectable, boolean branchLengthSelectable, boolean decimalOnly, boolean newIDSelectable)
void	NodeBranchDataInput.setAdapters(Tree tree, boolean nodeNamesSelectable, boolean branchLengthSelectable, boolean decimalOnly, boolean newIDSelectable) Refreshes the selectable node data adapters.

Uses of Tree in info.bioinfweb.treegraph.gui.dialogs.specialformats

Methods in info.bioinfweb.treegraph.gui.dialogs.specialformats with parameters of type Tree

void	DistanceAdapterListModel.setAdapters(Tree tree, boolean includeLegendFormats) Creates all distance adapters valid for the whole tree.
void	DistanceAdapterListModel.setAdapters(Tree tree, Node root, boolean includeLegendFormats) Creates all distance adapters valid for the subtree under root.