Package org.forester.evoinference.parsimony

Class SankoffParsimony<STATE_TYPE>

java.lang.Object
org.forester.evoinference.parsimony.SankoffParsimony<STATE_TYPE>
Type Parameters:
STATE_TYPE -
public class SankoffParsimony<STATE_TYPE> extends Object
IN PROGRESS! DO NOT USE!

  • Constructor Details

    • SankoffParsimony

      public SankoffParsimony()

  • Method Details

    • 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 -