/// <summary>
/// Pairwise alignment of two sequences using an affine gap penalty. The various algorithms in derived classes (NeedlemanWunsch,
/// SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with an affine gap penalty.
/// </summary>
/// <param name="localSimilarityMatrix">Scoring matrix.</param>
/// <param name="gapOpenPenalty">Gap open penalty (by convention, use a negative number for this.).</param>
/// <param name="gapExtensionPenalty">Gap extension penalty (by convention, use a negative number for this.).</param>
/// <param name="inputA">First input sequence.</param>
/// <param name="inputB">Second input sequence.</param>
/// <returns>A list of sequence alignments.</returns>
public IList <IPairwiseSequenceAlignment> Align(
SimilarityMatrix localSimilarityMatrix,
int gapOpenPenalty,
int gapExtensionPenalty,
ISequence inputA,
ISequence inputB)
{
// Initialize and perform validations for alignment
// In addition, initialize gap extension penalty.
SimpleAlignPrimer(localSimilarityMatrix, gapOpenPenalty, inputA, inputB);
GapExtensionCost = gapExtensionPenalty;
DynamicProgrammingPairwiseAlignerJob alignerJob = this.CreateAffineAlignmentJob(inputA, inputB);
IList <IPairwiseSequenceAlignment> result = alignerJob.Align();
foreach (IPairwiseSequenceAlignment alignment in result)
{
foreach (PairwiseAlignedSequence sequence in alignment.AlignedSequences)
{
AddSimpleConsensusToResult(sequence);
}
}
return(result);
}
/// <summary>
/// Pairwise alignment of two sequences using a linear gap penalty. The various algorithms in derived classes (NeedlemanWunsch,
/// SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with a linear gap penalty.
/// </summary>
/// <param name="localSimilarityMatrix">Scoring matrix.</param>
/// <param name="gapPenalty">Gap penalty (by convention, use a negative number for this.).</param>
/// <param name="inputA">First input sequence.</param>
/// <param name="inputB">Second input sequence.</param>
/// <returns>A list of sequence alignments.</returns>
public IList <IPairwiseSequenceAlignment> AlignSimple(SimilarityMatrix localSimilarityMatrix, int gapPenalty, ISequence inputA, ISequence inputB)
{
// Initialize and perform validations for simple alignment
SimpleAlignPrimer(localSimilarityMatrix, gapPenalty, inputA, inputB);
DynamicProgrammingPairwiseAlignerJob alignerJob = this.CreateSimpleAlignmentJob(inputA, inputB);
IList <IPairwiseSequenceAlignment> result = alignerJob.Align();
foreach (IPairwiseSequenceAlignment alignment in result)
{
foreach (PairwiseAlignedSequence sequence in alignment.AlignedSequences)
{
AddSimpleConsensusToResult(sequence);
}
}
return(result);
}
