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()

• 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 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)