/// <summary>
/// Get the alignment using pair wise
/// </summary>
/// <param name="seq1">Sequence 1</param>
/// <param name="seq2">Sequence 2</param>
/// <returns>A list of sequence alignments.</returns>
private IList <IPairwiseSequenceAlignment> RunPairWise(ISequence seq1, ISequence seq2)
{
IList <IPairwiseSequenceAlignment> sequenceAlignment = null;
if (PairWiseAlgorithm == null)
{
PairWiseAlgorithm = new NeedlemanWunschAligner();
}
PairWiseAlgorithm.SimilarityMatrix = SimilarityMatrix;
PairWiseAlgorithm.GapOpenCost = GapOpenCost;
PairWiseAlgorithm.ConsensusResolver = this.ConsensusResolver;
if (UseGapExtensionCost)
{
PairWiseAlgorithm.GapExtensionCost = GapExtensionCost;
sequenceAlignment = PairWiseAlgorithm.Align(seq1, seq2);
}
else
{
sequenceAlignment = PairWiseAlgorithm.AlignSimple(seq1, seq2);
}
// MUMmer does not support other aligners. Throw exception.
//throw new NotSupportedException(Properties.Resource.MUMmerIncompatibleAligner);
return(sequenceAlignment);
}
/// <summary>
/// Initializes a new instance of the MUMmer class.
/// Constructor for all the pairwise aligner
/// (NeedlemanWunsch, SmithWaterman, Overlap).
/// Sets default similarity matrix and gap penalty.
/// Users will typically reset these using parameters
/// specific to their particular sequences
/// and needs.
/// </summary>
protected MUMmer()
{
// Set default similarity matrix and gap penalty.
// User will typically choose their own parameters, these
// defaults are reasonable for many cases.
// Default is set to 20
LengthOfMUM = 20;
SimilarityMatrix = null;
GapOpenCost = -13; // 5, -4 diagonal matrix for Dna
// default affine gap is -1
GapExtensionCost = -8;
// Set the default alignment algorithm to NeedlemanWunsch
PairWiseAlgorithm = new NeedlemanWunschAligner();
}