Abstract class for implementing a Smith-Waterman pairwise alignment.
Performs a pairwise alignment of two sequences using constant penalties.
Performs a pairwise alignment of two sequences using constant penalties.
The first sequence in the pair.
The second sequence in the pair.
The alignment gap penalty for a residue match.
The alignment gap penalty for a residue mismatch.
The alignment gap penalty for an insertion in the first sequence.
The alignment gap penalty for a deletion in the first sequence.
scoreFn
Abstract class for implementing a Smith-Waterman pairwise alignment.
Contains shell code for everything except for building the pairwise alignment score matrix. This way, a new scoring method (e.g., affine gap, residue specific scores) can be implemented without needing to implement core functionality like trackback, etc.