A C D F G I M P R S T V Z

S

sankoff(LinkedBinaryTree<PSpeciesNode>, HashMap<ZCharacter, Integer>, int[][], int) - Method in class cs195z.phylogeny.PStudentTreeAlgorithms

sankoff(LinkedBinaryTree<PSpeciesNode>, HashMap<ZCharacter, Integer>, int[][], int) - Method in interface cs195z.support.PTreeAlgorithms

Implements the Sankoff algorithm and makes changes to the PSpeciesNodes.

setCharacter(int, ZCharacter) - Method in class cs195z.support.PSpeciesNode

Can be used to replace a character at a certain array position.

setCost(ZCharacter, int) - Method in class cs195z.support.PSpeciesNode

Stores a cost value for the character.

setLikelihood(ZCharacter, double) - Method in class cs195z.support.PSpeciesNode

Store a likelihood probability for a character.

setName(E) - Method in class cs195z.support.CElement

Stores the serializable object that "names" the element.

setName(String) - Method in class cs195z.support.PSpeciesNode

setSequence(ZCharacter[]) - Method in class cs195z.support.PSpeciesNode

Sets an entire sequence of characters at once.

setTreeLevel(int) - Method in class cs195z.support.PSpeciesNode

Stores the tree level.

step() - Method in class cs195z.cluster.CStudentCAST

step() - Method in class cs195z.cluster.CStudentKMeans

step() - Method in interface cs195z.support.CAlgorithm

Performs the main iteration of the algorithm.