org.forester.evoinference.parsimony
Class DolloParsimony

java.lang.Object
  org.forester.evoinference.parsimony.DolloParsimony

public class DolloParsimony
extends java.lang.Object

Method Summary

static DolloParsimony	createInstance()
void	execute(Phylogeny p, CharacterStateMatrix<CharacterStateMatrix.BinaryStates> external_node_states_matrix)
int	getCost()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	getInternalStatesMatrix()
int	getTotalGains()
int	getTotalLosses()
int	getTotalUnchanged()
void	setReturnGainLossMatrix(boolean return_gain_loss)
void	setReturnInternalStates(boolean return_internal_states)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

execute

public void execute(Phylogeny p,
                    CharacterStateMatrix<CharacterStateMatrix.BinaryStates> external_node_states_matrix)

getCost

public int getCost()

getGainLossMatrix

public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix()

getInternalStatesMatrix

public CharacterStateMatrix<CharacterStateMatrix.BinaryStates> getInternalStatesMatrix()

getTotalGains

public int getTotalGains()

getTotalLosses

public int getTotalLosses()

getTotalUnchanged

public int getTotalUnchanged()

setReturnGainLossMatrix

public void setReturnGainLossMatrix(boolean return_gain_loss)

setReturnInternalStates

public void setReturnInternalStates(boolean return_internal_states)

createInstance

public static DolloParsimony createInstance()