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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`.

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