Uses of Class
phylosort.TreeNode

Packages that use TreeNode

phylosort	PhyloSort core package.
phylosort.ui	Command line and graphical user interface.

Uses of TreeNode in phylosort

Methods in phylosort that return TreeNode

static TreeNode	TreeNodeUtil.copy(TreeNode root, TreeNode exclude) Returns a copy of a TreeNode
static TreeNode	TreeNode.find(TreeNode tree, java.lang.String label) Finds a node with a specific label
static TreeNode	TreeNodeUtil.findOutgroup(TreeNode node, java.util.List<java.util.Set<java.lang.String>> taxa) Finds a leaf node with a taxon not included within a list of taxa
static TreeNode	TreeNodeUtil.findOutgroup(TreeNode node, java.util.Set<java.lang.String> taxa) Finds a leaf node with a taxon not included within a list of taxa
static TreeNode	TreeNodeUtil.getMonophyleticNode(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa) Checks whether a tree has a common branch holding groups of taxa
static TreeNode	TreeNodeUtil.getMonophyleticNode(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa, boolean exclusive) Checks whether a tree has a common branch holding groups of taxa
TreeNode	TreeNode.getNode(int id) Retrieve a node using its id
TreeNode	TreeNode.getParent() Returns the parent of the node
TreeNode	TreeNode.getRoot() Returns the root of the tree of a node
static TreeNode	TreeNodeUtil.load(java.io.File file) Loads a tree from a text file
static TreeNode	NewickParser.parse(java.lang.String str) Parses a tree string into a TreeNode
static TreeNode	NewickParser.parse(java.lang.String _str, TreeNode parent) Parses a tree string into a TreeNode
static TreeNode	TreeNodeUtil.reroot(TreeNode outgroup) Reroots a tree based on an outgroup node.

Methods in phylosort that return types with arguments of type TreeNode

static java.util.Collection<TreeNode>	TreeNodeUtil.getAllMonophyleticNodes(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa) Checks whether a tree has a common branch holding groups of taxa
static java.util.Collection<TreeNode>	TreeNodeUtil.getAllMonophyleticNodes(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa, boolean exclusive) Checks whether a tree has a common branch holding groups of taxa
java.lang.Iterable<TreeNode>	TreeNode.getChildren() Returns an iterator to the children
java.util.List<TreeNode>	TreeNode.getLeaves() Returns all leaves under this node
static java.util.Collection<TreeNode>	TreeNodeUtil.getNodesByTaxa(TreeNode tree, java.util.Set<java.lang.String> taxa) Returns all OTU nodes with labels matching the set of taxa
static java.util.Collection<TreeNode>	TreeNodeUtil.getNodesByTaxa(TreeNode node, java.util.Set<java.lang.String> taxa, boolean equal) Returns all OTU nodes with labels matching the set of taxa
java.lang.Iterable<TreeNode>	TreeNode.getSortedChildren() Returns an iterorator to the sorted children
java.lang.Iterable<TreeNode>	TreeNode.iterator() Returns depth first search Iterable

Methods in phylosort with parameters of type TreeNode

void	TreeCluster.add(java.io.File file, TreeNode tree) Adds a tree to cluster
void	TreeNode.addChild(TreeNode child) Adds a child to the tree
static boolean	TreeNodeUtil.belongs(TreeNode node, java.util.Set<java.lang.String> taxa) Checks whether the set of all OTUs is a subset of taxa
int	TreeNodeComparator.compare(TreeNode t1, TreeNode t2) Compares between two subtrees based on their branch lengths.
boolean	TreeCluster.contains(TreeNode tree) Returns true if cluster contains at least one taxon from a tree
boolean	TreeCluster.contains(TreeNode tree, int minimumOverlap) Returns true if cluster contains at least one taxon from a tree
static boolean	TreeNodeUtil.contains(TreeNode node, java.util.Set<java.lang.String> taxa) Checks whether each group of taxa is represented at least by one OTU
static TreeNode	TreeNodeUtil.copy(TreeNode root, TreeNode exclude) Returns a copy of a TreeNode
static TreeNode	TreeNode.find(TreeNode tree, java.lang.String label) Finds a node with a specific label
static TreeNode	TreeNodeUtil.findOutgroup(TreeNode node, java.util.List<java.util.Set<java.lang.String>> taxa) Finds a leaf node with a taxon not included within a list of taxa
static TreeNode	TreeNodeUtil.findOutgroup(TreeNode node, java.util.Set<java.lang.String> taxa) Finds a leaf node with a taxon not included within a list of taxa
static java.util.Collection<TreeNode>	TreeNodeUtil.getAllMonophyleticNodes(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa) Checks whether a tree has a common branch holding groups of taxa
static java.util.Collection<TreeNode>	TreeNodeUtil.getAllMonophyleticNodes(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa, boolean exclusive) Checks whether a tree has a common branch holding groups of taxa
static float	TreeNodeUtil.getAverageNumberOfCopies(TreeNode root) Returns the average number of copies per species
static TreeNode	TreeNodeUtil.getMonophyleticNode(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa) Checks whether a tree has a common branch holding groups of taxa
static TreeNode	TreeNodeUtil.getMonophyleticNode(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa, boolean exclusive) Checks whether a tree has a common branch holding groups of taxa
static java.util.Collection<TreeNode>	TreeNodeUtil.getNodesByTaxa(TreeNode tree, java.util.Set<java.lang.String> taxa) Returns all OTU nodes with labels matching the set of taxa
static java.util.Collection<TreeNode>	TreeNodeUtil.getNodesByTaxa(TreeNode node, java.util.Set<java.lang.String> taxa, boolean equal) Returns all OTU nodes with labels matching the set of taxa
static java.util.Set<java.lang.String>	TreeNodeUtil.getTaxa(TreeNode node) Returns a Set of String of taxa in a TreeNode
static int	TreeNodeUtil.hasMonophyly(TreeNode node, java.util.Set<java.lang.String> extended, java.util.List<java.util.Set<java.lang.String>> sets, java.util.Set<java.lang.Integer> excluded) Returns node id if the node is valid, otherwise returns -1
static TreeNode	NewickParser.parse(java.lang.String _str, TreeNode parent) Parses a tree string into a TreeNode
void	TreeNode.removeChild(TreeNode child) Removes a child
static TreeNode	TreeNodeUtil.reroot(TreeNode outgroup) Reroots a tree based on an outgroup node.
void	TreeNode.setParent(TreeNode parent) Sets the parent of the node

Method parameters in phylosort with type arguments of type TreeNode

static int

TreeNodeUtil.lca(java.lang.Iterable<TreeNode> nodes) Returns the lowest common ancestor (LCA) for a list of nodes

Uses of TreeNode in phylosort.ui

Methods in phylosort.ui with parameters of type TreeNode

void	TreeWindow.populateTree(TreeNode data) Populates DefaultMutableTreeNode from TreeNode