Uses of Class
cs195z.support.ZCharacter

Packages that use ZCharacter

cs195z.phylogeny
cs195z.support

Uses of ZCharacter in cs195z.phylogeny

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

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 ZCharacter in cs195z.support

Methods in cs195z.support that return ZCharacter

ZCharacter[]	PSpeciesNode.getSequence() Gives the ordered sequence of characters at this position
static ZCharacter	ZCharacter.valueOf(String name) Returns the enum constant of this type with the specified name.
static ZCharacter[]	ZCharacter.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

HashMap<ZCharacter,Integer>

PDataSet.getStateIndices()

Methods in cs195z.support with parameters of type ZCharacter

void	PSpeciesNode.addCharacter(ZCharacter z) Adds a character to the back of the stored sequence.
void	PSpeciesNode.addToCost(ZCharacter z, int cost) Increases the cost for a character by the value of "cost".
int	PSpeciesNode.getCost(ZCharacter z) Gives the stored cost for this character in the cost array.
double	PSpeciesNode.getLikelihood(ZCharacter z) Retrieves a likelihood probability for a character.
void	PSpeciesNode.setCharacter(int index, ZCharacter z) Can be used to replace a character at a certain array position.
void	PSpeciesNode.setCost(ZCharacter z, int cost) Stores a cost value for the character.
void	PSpeciesNode.setLikelihood(ZCharacter z, double d) Store a likelihood probability for a character.
void	PSpeciesNode.setSequence(ZCharacter[] z) Sets an entire sequence of characters at once.

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

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.