Constructor Detail

• SankoffParsimony

  public SankoffParsimony()

Method Detail

• 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<java.util.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 -