Class DomainParsimonyCalculator


  • public final class DomainParsimonyCalculator
    extends java.lang.Object
    • Method Detail

      • executeDolloParsimonyOnBinaryDomainCombintionPresence

        public void executeDolloParsimonyOnBinaryDomainCombintionPresence()
      • executeDolloParsimonyOnDomainPresence

        public void executeDolloParsimonyOnDomainPresence()
      • executeDolloParsimonyOnDomainPresence

        public void executeDolloParsimonyOnDomainPresence​(java.util.SortedSet<java.lang.String> positive_filter)
      • executeDolloParsimonyOnSecondaryFeatures

        public void executeDolloParsimonyOnSecondaryFeatures​(java.util.Map<Species,​MappingResults> mapping_results_map)
      • executeFitchParsimonyOnBinaryDomainCombintion

        public void executeFitchParsimonyOnBinaryDomainCombintion​(boolean use_last)
      • executeFitchParsimonyOnBinaryDomainCombintion

        public void executeFitchParsimonyOnBinaryDomainCombintion​(long random_number_seed)
      • executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures

        public void executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures​(boolean use_last)
      • executeFitchParsimonyOnDomainPresence

        public void executeFitchParsimonyOnDomainPresence​(boolean use_last)
      • executeFitchParsimonyOnDomainPresence

        public void executeFitchParsimonyOnDomainPresence​(long random_number_seed)
      • getCost

        public int getCost()
      • getGainLossCountsMatrix

        public CharacterStateMatrix<java.lang.Integer> getGainLossCountsMatrix()
      • getNetGainsOnNode

        public int getNetGainsOnNode​(java.lang.String node_identifier)
      • getSumOfGainsOnNode

        public int getSumOfGainsOnNode​(java.lang.String node_identifier)
      • getSumOfLossesOnNode

        public int getSumOfLossesOnNode​(java.lang.String node_identifier)
      • getSumOfPresentOnNode

        public int getSumOfPresentOnNode​(java.lang.String node_identifier)
      • getTotalGains

        public int getTotalGains()
      • getTotalLosses

        public int getTotalLosses()
      • getTotalUnchanged

        public int getTotalUnchanged()
      • getUnitsGainedOnNode

        public java.util.SortedSet<java.lang.String> getUnitsGainedOnNode​(java.lang.String node_identifier)
      • getUnitsLostOnNode

        public java.util.SortedSet<java.lang.String> getUnitsLostOnNode​(java.lang.String node_identifier)
      • getUnitsOnNode

        public java.util.SortedSet<java.lang.String> getUnitsOnNode​(java.lang.String node_identifier)