Uses of Class
cs195z.support.PSpeciesNode

Packages that use PSpeciesNode

cs195z.phylogeny
cs195z.support

Uses of PSpeciesNode in cs195z.phylogeny

Method parameters in cs195z.phylogeny with type arguments of type PSpeciesNode

void	PStudentTreeAlgorithms.felsenstein(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree, HashMap<ZCharacter,Integer> stateIndices, double[][] transitionProb, int sequenceLength)
void	PStudentTreeAlgorithms.sankoff(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree, HashMap<ZCharacter,Integer> stateIndices, int[][] costMatrix, int sequenceLength)

Uses of PSpeciesNode in cs195z.support

Methods in cs195z.support that return types with arguments of type PSpeciesNode

net.datastructures.LinkedBinaryTree<PSpeciesNode>

PDataSet.getTree()

Method parameters in cs195z.support with type arguments of type PSpeciesNode

static org.forester.phylogeny.Phylogeny	PTreeVisualizer.convertTree(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree) Converts an nds4 LinkedBinaryTree into an org.forester.phylogeny.Phylogeny
void	PTreeAlgorithms.felsenstein(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree, HashMap<ZCharacter,Integer> stateIndices, double[][] transitionProb, int sequenceLength) Implements the Felsenstein max likelihood algorithm and makes changes to the PSpeciesNodes.
void	PTreeAlgorithms.sankoff(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree, HashMap<ZCharacter,Integer> stateIndices, int[][] costMatrix, int sequenceLength) Implements the Sankoff algorithm and makes changes to the PSpeciesNodes.
static void	PTreeVisualizer.treeHelper(net.datastructures.LinkedBinaryTree<PSpeciesNode> t, net.datastructures.Position<PSpeciesNode> n, org.forester.phylogeny.PhylogenyNode parent) Helper method for the preorder traversal recursion of convertTree()
static void	PTreeVisualizer.treeHelper(net.datastructures.LinkedBinaryTree<PSpeciesNode> t, net.datastructures.Position<PSpeciesNode> n, org.forester.phylogeny.PhylogenyNode parent) Helper method for the preorder traversal recursion of convertTree()