/// <summary>
/// AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
/// and returns the best alignment found.
/// </summary>
/// <param name="inputSequences">The sequences to align.</param>
/// <returns>List of sequence alignments.</returns>
public IList <IPairwiseSequenceAlignment> AlignSimple(IEnumerable <ISequence> inputSequences)
{
if (inputSequences == null)
{
throw new ArgumentNullException("inputSequences");
}
var listOfSequences = inputSequences.ToList();
if (listOfSequences.Count != 2)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.PairwiseAlignerWrongArgumentCount,
inputSequences.Count());
Trace.Report(message);
throw new ArgumentException(message, "inputSequences");
}
return(AlignSimple(listOfSequences[0], listOfSequences[1]));
}
/// <summary>
/// Method which performs the alignment work.
/// </summary>
/// <param name="sequence1">First sequence</param>
/// <param name="sequence2">Second sequence</param>
/// <param name="useAffineGapModel">True to use affine gap model (separate open vs. extension cost)</param>
/// <returns></returns>
private IList <IPairwiseSequenceAlignment> DoAlign(ISequence sequence1, ISequence sequence2, bool useAffineGapModel)
{
usingAffineGapModel = useAffineGapModel;
if (sequence1 == null)
{
throw new ArgumentNullException("sequence1");
}
if (sequence2 == null)
{
throw new ArgumentNullException("sequence2");
}
if (!Alphabets.CheckIsFromSameBase(sequence1.Alphabet, sequence2.Alphabet))
{
Trace.Report(Properties.Resource.InputAlphabetsMismatch);
throw new ArgumentException(Properties.Resource.InputAlphabetsMismatch);
}
if (SimilarityMatrix == null)
{
Trace.Report(Properties.Resource.SimilarityMatrixCannotBeNull);
throw new ArgumentException(Properties.Resource.SimilarityMatrixCannotBeNull);
}
if (!SimilarityMatrix.ValidateSequence(sequence1))
{
Trace.Report(Properties.Resource.FirstInputSequenceMismatchSimilarityMatrix);
throw new ArgumentException(Properties.Resource.FirstInputSequenceMismatchSimilarityMatrix);
}
if (!SimilarityMatrix.ValidateSequence(sequence2))
{
Trace.Report(Properties.Resource.SecondInputSequenceMismatchSimilarityMatrix);
throw new ArgumentException(Properties.Resource.SecondInputSequenceMismatchSimilarityMatrix);
}
if (GapOpenCost > GapExtensionCost)
{
Trace.Report(Properties.Resource.GapOpenGreaterThanGapExtension);
throw new ArgumentException(Properties.Resource.GapOpenGreaterThanGapExtension);
}
_sequence1 = sequence1;
_sequence2 = sequence2;
_gap = Alphabets.CheckIsFromSameBase(Alphabets.Protein, sequence1.Alphabet) ? Alphabets.Protein.Gap : Alphabets.DNA.Gap;
ReferenceSequence = GetByteArrayFromSequence(_sequence1);
QuerySequence = GetByteArrayFromSequence(_sequence2);
// Assign consensus resolver if it was not assigned already.
IAlphabet alphabet = sequence1.Alphabet;
if (ConsensusResolver == null)
{
ConsensusResolver = new SimpleConsensusResolver(alphabet.HasAmbiguity ? alphabet : Alphabets.AmbiguousAlphabetMap[sequence1.Alphabet]);
}
else
{
ConsensusResolver.SequenceAlphabet = alphabet.HasAmbiguity ? alphabet : Alphabets.AmbiguousAlphabetMap[sequence1.Alphabet];
}
return(new List <IPairwiseSequenceAlignment> {
Process()
});
}
