Uses of Class
edu.upenn.crimson.Tree

Packages that use Tree

edu.upenn.crimson
edu.upenn.crimson.gui
edu.upenn.crimson.io

Uses of Tree in edu.upenn.crimson

Methods in edu.upenn.crimson that return Tree

Tree	TreeTableModel.getRow(int row) Returns the Tree that represents the specified row in the table.
Tree	Tree.getSubtree(Species subroot) Returns the subtree given the specified root.
static Tree	ObjectHandles.getTree(java.lang.String id) Returns the Tree object for the given ID.
Tree	Tree.manualSampleByID(java.util.ArrayList oldLeaves) This will return a subtree that contains the specified leaves.
Tree	Tree.randomSample(int num) This will randomly sample the tree, returning a subtree that contains 'num' leaves.
Tree	Tree.uniformSampleByLevel(int level, int num) Returns the random, uniform sampling of species from each subtree demarkated by the level value.
Tree	Tree.uniformSampleByTempDepth(double tempDepth, int num) Returns the random, uniform sampling of species from each subtree demarkated by the temporal depth value.
Tree	Tree.weightedSampleByLevel(int level, int num) Returns the random, weighted sampling of species from each subtree demarkated by the level value.
Tree	Tree.weightedSampleByTempDepth(double tempDepth, int num) Returns the random, weighted sampling of species from each subtree demarkated by the temporal depth value.

Methods in edu.upenn.crimson with parameters of type Tree

void	TreeTableModel.addRow(Tree tree) Append a new row to the end of the table.
void	TreeTableModel.addRowAt(Tree tree, int row) Add new row to table.
static void	ObjectHandles.addTree(Tree tree) This will add the tree to the relevant lists.
Species	Species.copy(Tree tree) This will return a copy of the current species WITHOUT the parent, children, or level.

Constructors in edu.upenn.crimson with parameters of type Tree

Partition(java.lang.String id, Tree tree)

Partition(java.lang.String id, Tree tree, Model model, int length, java.lang.String notes)

Species(int id, Tree tree)

Species(java.lang.String id, double stemLength, int level, Tree tree)

Species(java.lang.String id, Tree tree)

Uses of Tree in edu.upenn.crimson.gui

Fields in edu.upenn.crimson.gui declared as Tree

(package private) Tree	TreeManager.NotesPanel.npTree
(package private) Tree	QueryEditor.ViewDistributePanel.thisTree
private Tree	TreeManager.PanelFrame.tree Reference to the Tree selected.
private Tree	QueryEditor.tree

Methods in edu.upenn.crimson.gui with parameters of type Tree

static boolean

TreeUtils.isTreeBuilt(Tree tree)

Constructors in edu.upenn.crimson.gui with parameters of type Tree

QueryEditor.ViewDistributePanel(Tree tree, int threshType)

TreeManager.NotesPanel(Tree tree)

TreeManager.NotesPanel(Tree tree, Partition partition)

Uses of Tree in edu.upenn.crimson.io

Methods in edu.upenn.crimson.io that return Tree

static Tree	NexusFile.append(java.lang.String filename, java.lang.String treeID, java.lang.String partitionID) Appends a Nexus file into the current database.
static Tree	NexusFile.load(java.lang.String filename, java.lang.String treeID, java.lang.String partitionID) Loads a Nexus file.
static Tree	NexusFile.loadNewick(java.lang.String filename) Loads a tree structure from a Nexus file into memory.
static Tree	NexusFile.parseNewick(Tree tree) This might be faster if we use char[] instead of String for "newick".
static Tree	NexusFile.parseNewick(Tree tree, java.lang.String newick) This might be faster if we use char[] instead of String for "newick".
static Tree	Queries.run(java.lang.String queryID, java.lang.String filename, boolean incSequence, boolean incCrimson, int incTree, boolean incNotes) This will perform a tree query, generating a NEXUS file.
static Tree	Queries.runPhylip(java.lang.String queryID, java.lang.String filename, int incTree) This will perform a tree query, generating a phylip formatted file.

Methods in edu.upenn.crimson.io with parameters of type Tree

static Tree	NexusFile.parseNewick(Tree tree) This might be faster if we use char[] instead of String for "newick".
static Tree	NexusFile.parseNewick(Tree tree, java.lang.String newick) This might be faster if we use char[] instead of String for "newick".