Class FitchParsimony<STATE_TYPE>


  • public class FitchParsimony<STATE_TYPE>
    extends java.lang.Object
    • Constructor Detail

      • FitchParsimony

        public FitchParsimony()
    • Method Detail

      • getCost

        public int getCost()
      • 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()
      • 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)