org.forester.phylogenyinference
Class FitchParsimony<STATE_TYPE>
java.lang.Object
org.forester.phylogenyinference.FitchParsimony<STATE_TYPE>
public class FitchParsimony<STATE_TYPE>
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FitchParsimony
public FitchParsimony()
execute
public void execute(Phylogeny p,
CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
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()
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
-