Class SimpleSequencePair<S extends Sequence<C>,​C extends Compound>

    • Constructor Detail

      • SimpleSequencePair

        public SimpleSequencePair​(AlignedSequence<S,​C> query,
                                  AlignedSequence<S,​C> target)
        Creates a pair profile for the given already aligned sequences.
        Parameters:
        query - the first sequence of the pair
        target - the second sequence of the pair
        Throws:
        java.lang.IllegalArgumentException - if sequences differ in size
      • SimpleSequencePair

        public SimpleSequencePair​(S query,
                                  S target,
                                  java.util.List<AlignedSequence.Step> sx,
                                  java.util.List<AlignedSequence.Step> sy)
        Creates a pair profile for the given sequences with a global alignment.
        Parameters:
        query - the first sequence of the pair
        target - the second sequence of the pair
        sx - lists whether the query sequence aligns a Compound or gap at each index of the alignment
        sy - lists whether the target sequence aligns a Compound or gap at each index of the alignment
        Throws:
        java.lang.IllegalArgumentException - if alignments differ in size or given sequences do not fit in alignments
      • SimpleSequencePair

        public SimpleSequencePair​(S query,
                                  S target,
                                  java.util.List<AlignedSequence.Step> sx,
                                  int xb,
                                  int xa,
                                  java.util.List<AlignedSequence.Step> sy,
                                  int yb,
                                  int ya)
        Creates a pair profile for the given sequences with a local alignment.
        Parameters:
        query - the first sequence of the pair
        target - the second sequence of the pair
        sx - lists whether the query sequence aligns a Compound or gap at each index of the alignment
        xb - number of Compounds skipped in the query sequence before the aligned region
        xa - number of Compounds skipped in the query sequence after the aligned region
        sy - lists whether the target sequence aligns a Compound or gap at each index of the alignment
        yb - number of Compounds skipped in the target sequence before the aligned region
        ya - number of Compounds skipped in the target sequence after the aligned region
        Throws:
        java.lang.IllegalArgumentException - if alignments differ in size or given sequences do not fit in alignments