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

  • Type Parameters:
    S - each Sequence of the alignment pair is of type S
    C - each element of an AlignedSequence is a Compound of type C
    All Implemented Interfaces:
    Aligner<S,​C>, MatrixAligner<S,​C>, PairwiseSequenceAligner<S,​C>, PairwiseSequenceScorer<S,​C>, Scorer
    Direct Known Subclasses:
    GuanUberbacher, NeedlemanWunsch

    public class AnchoredPairwiseSequenceAligner<S extends Sequence<C>,​C extends Compound>
    extends AbstractPairwiseSequenceAligner<S,​C>
    This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors. This class performs such global sequence comparisons efficiently by dynamic programming with a space requirement reduced from quadratic (a multiple of query sequence length times target sequence length) to only linear (a multiple of query sequence length). The counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
    Mark Chapman, Daniel Cameron