org.forester.evoinference.parsimony

Class FitchParsimony<STATE_TYPE>

java.lang.Object

org.forester.evoinference.parsimony.FitchParsimony<STATE_TYPE>

public class FitchParsimony<STATE_TYPE>
extends Object

Constructor Summary

Constructors

Constructor and Description
FitchParsimony()

Method Summary

Modifier and Type	Method and Description
void	execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
void	execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix, boolean verbose)
int	getCost()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	getGainLossMatrix()
CharacterStateMatrix<STATE_TYPE>	getInternalStatesMatrix()
CharacterStateMatrix<List<STATE_TYPE>>	getInternalStatesMatrixPriorToTraceback() Returns a view of the internal states prior to trace-back.
int	getTotalGains()
int	getTotalLosses()
int	getTotalUnchanged()
boolean	isVerbose()
void	setRandomize(boolean randomize)
void	setRandomNumberSeed(long random_number_seed)
void	setReturnGainLossMatrix(boolean return_gain_loss)
void	setReturnInternalStates(boolean return_internal_states)
void	setUseLast(boolean use_last) This sets whether to use the first or last state in the sorted states at the undecided internal nodes.
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Constructor Detail

FitchParsimony

public FitchParsimony()

Method Detail

execute

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

execute

public void execute(Phylogeny p,
                    CharacterStateMatrix<STATE_TYPE> external_node_states_matrix,
                    boolean verbose)

getCost

public int getCost()

getGainLossMatrix

public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix()

getInternalStatesMatrix

public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix()

getInternalStatesMatrixPriorToTraceback

public CharacterStateMatrix<List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback()

Returns a view of the internal states prior to trace-back.

Returns:

getTotalGains

public int getTotalGains()

getTotalLosses

public int getTotalLosses()

getTotalUnchanged

public int getTotalUnchanged()

isVerbose

public boolean isVerbose()

setRandomize

public void setRandomize(boolean randomize)

setRandomNumberSeed

public void setRandomNumberSeed(long random_number_seed)

setReturnGainLossMatrix

public void setReturnGainLossMatrix(boolean return_gain_loss)

setReturnInternalStates

public void setReturnInternalStates(boolean return_internal_states)

setUseLast

public void setUseLast(boolean use_last)

This sets whether to use the first or last state in the sorted states at the undecided internal nodes. For randomized choices set randomize to true (and this to false). Note. It might be advisable to set this to false for BinaryStates if absence at the root is preferred (given the enum BinaryStates sorts in the following order: ABSENT, UNKNOWN, PRESENT).

Parameters:

use_last -

setVerbose

public void setVerbose(boolean verbose)