smithwaterman

Type Members

1. trait SmithWaterman extends Serializable

   

   Abstract class for implementing a Smith-Waterman pairwise alignment.

   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.

2. case class SmithWatermanConstantGapScoring(xSequence: String, ySequence: String, wMatch: Double, wMismatch: Double, wInsert: Double, wDelete: Double) extends SmithWatermanGapScoringFromFn with Product with Serializable

   

   Performs a pairwise alignment of two sequences using constant penalties.

   Performs a pairwise alignment of two sequences using constant penalties.

   xSequence

   The first sequence in the pair.

   ySequence

   The second sequence in the pair.

   wMatch

   The alignment gap penalty for a residue match.

   wMismatch

   The alignment gap penalty for a residue mismatch.

   wInsert

   The alignment gap penalty for an insertion in the first sequence.

   wDelete

   The alignment gap penalty for a deletion in the first sequence.

   See also

   scoreFn