package smithwaterman
Type Members
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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.
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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