Class MsaMethods


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

      • clone

        public java.lang.Object clone()
        Overrides:
        clone in class java.lang.Object
      • deleteGapColumns

        public final Msa deleteGapColumns​(double max_allowed_gap_ratio,
                                          int min_allowed_length,
                                          Msa msa)
      • getIgnoredSequenceIds

        public java.util.ArrayList<java.lang.String> getIgnoredSequenceIds()
      • calcNumberOfGapsInMsa

        public static final int[] calcNumberOfGapsInMsa​(Msa msa)
      • calcNumberOfGaps

        public static final int calcNumberOfGaps​(MolecularSequence seq)
      • calcGapRatio

        public static double calcGapRatio​(Msa msa)
      • calcGapSumPerColumn

        public static int calcGapSumPerColumn​(Msa msa,
                                              int col)
      • calcNormalizedShannonsEntropy

        public static final double calcNormalizedShannonsEntropy​(int k,
                                                                 Msa msa)
      • calcNormalizedShannonsEntropy

        public static final double calcNormalizedShannonsEntropy​(int k,
                                                                 Msa msa,
                                                                 int col)
      • calculateEffectiveLengthStatistics

        public static final DescriptiveStatistics calculateEffectiveLengthStatistics​(Msa msa)
      • calculateIdentityRatio

        public static final DescriptiveStatistics calculateIdentityRatio​(int from,
                                                                         int to,
                                                                         Msa msa)
      • calculateIdentityRatio

        public static final double calculateIdentityRatio​(Msa msa,
                                                          int column)
      • calculateResidueDestributionPerColumn

        public static java.util.SortedMap<java.lang.Character,​java.lang.Integer> calculateResidueDestributionPerColumn​(Msa msa,
                                                                                                                             int column)
      • createInstance

        public static MsaMethods createInstance()
      • removeSequence

        public static final Msa removeSequence​(Msa msa,
                                               java.lang.String to_remove_id)
      • removeSequences

        public static final Msa removeSequences​(Msa msa,
                                                java.util.List<java.lang.String> to_remove_ids)
      • removeSequencesByMinimalLength

        public static Msa removeSequencesByMinimalLength​(Msa msa,
                                                         int min_effective_length)
      • removeSequencesByRow

        public static final Msa removeSequencesByRow​(Msa msa,
                                                     java.util.List<java.lang.Integer> to_remove_rows)