org.forester.phylogenyinference
Class DolloParsimony

java.lang.Object
  extended by org.forester.phylogenyinference.DolloParsimony

public class DolloParsimony
extends 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()