Package org.forester.msa

Class MsaMethods

java.lang.Object
org.forester.msa.MsaMethods
public final class MsaMethods extends Object

  • Method Details

    • clone

      public Object clone()
      Overrides:
      clone in class Object

    • deleteGapColumns

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

    • getIgnoredSequenceIds

      public ArrayList<String> getIgnoredSequenceIds()

    • calcNumberOfGapsStats

      public static final DescriptiveStatistics calcNumberOfGapsStats(Msa msa)

    • calcNumberOfGapsInMsa

      public static final int[] calcNumberOfGapsInMsa(Msa msa)

    • calcNumberOfGaps

      public static final int calcNumberOfGaps(MolecularSequence seq)

    • calcBasicGapinessStatistics

      public static DescriptiveStatistics calcBasicGapinessStatistics(Msa msa)

    • 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 SortedMap<Character,Integer> calculateResidueDestributionPerColumn(Msa msa, int column)

    • createInstance

      public static MsaMethods createInstance()

    • removeSequence

      public static final Msa removeSequence(Msa msa, String to_remove_id)

    • removeSequences

      public static final Msa removeSequences(Msa msa, List<String> to_remove_ids)

    • removeSequencesByMinimalLength

      public static Msa removeSequencesByMinimalLength(Msa msa, int min_effective_length)

    • removeSequencesByRow

      public static final Msa removeSequencesByRow(Msa msa, List<Integer> to_remove_rows)