/// <summary>
/// Performs Stage 1, 2, and 3 as described in class description.
/// </summary>
/// <param name="inputSequences">Input sequences</param>
/// <returns>Alignment results</returns>
public IList <Alignment.ISequenceAlignment> Align(IEnumerable <ISequence> inputSequences)
{
// Reset all our data in case this same instance is used multiple times.
_alignedSequences = _alignedSequencesA = _alignedSequencesB = _alignedSequencesC = null;
_alignmentScore = _alignmentScoreA = _alignmentScoreB = _alignmentScoreC = float.MinValue;
// Get our list of sequences.
List <ISequence> sequences = inputSequences.ToList();
if (sequences.Count == 0)
{
throw new ArgumentException("Empty input sequences");
}
// Assign the gap open/extension cost if it hasn't been assigned.
if (GapOpenCost == 0)
{
GapOpenCost = -4;
}
if (GapExtensionCost == 0)
{
GapExtensionCost = -1;
}
Performance.Start();
// Assign the alphabet
SetAlphabet(sequences, SimilarityMatrix, true);
MsaUtils.SetProfileItemSets(_alphabet);
Performance.Snapshot("Start Aligning");
// Work...
DoAlignment(sequences);
// just for the purpose of integrating PW and MSA with the same output
var alignment = new Alignment.SequenceAlignment();
IAlignedSequence aSequence = new AlignedSequence();
foreach (var alignedSequence in AlignedSequences)
{
aSequence.Sequences.Add(alignedSequence);
}
foreach (var inputSequence in sequences)
{
alignment.Sequences.Add(inputSequence);
}
alignment.AlignedSequences.Add(aSequence);
return(new List <Alignment.ISequenceAlignment>()
{
alignment
});
}
/// <summary>
/// Performs Stage 1, 2, and 3 as described in class description.
/// </summary>
/// <param name="inputSequences">Input sequences</param>
/// <returns>Alignment results</returns>
public IList<Alignment.ISequenceAlignment> Align(IEnumerable<ISequence> inputSequences)
{
// Reset all our data in case this same instance is used multiple times.
this.AlignedSequences = this.AlignedSequencesA = this.AlignedSequencesB = this.AlignedSequencesC = null;
this.AlignmentScore = this.AlignmentScoreA = this.AlignmentScoreB = this.AlignmentScoreC = float.MinValue;
// Get our list of sequences.
List<ISequence> sequences = inputSequences.ToList();
if (sequences.Count == 0)
{
throw new ArgumentException("Empty input sequences");
}
// Assign the gap open/extension cost if it hasn't been assigned.
if (GapOpenCost == 0)
GapOpenCost = -4;
if (GapExtensionCost == 0)
GapExtensionCost = -1;
StartLog();
// Assign the alphabet
SetAlphabet(sequences, SimilarityMatrix, true);
MsaUtils.SetProfileItemSets(this.alphabet);
ReportLog("Start Aligning");
// Work...
DoAlignment(sequences);
// just for the purpose of integrating PW and MSA with the same output
var alignment = new Alignment.SequenceAlignment();
IAlignedSequence aSequence = new AlignedSequence();
foreach (var alignedSequence in AlignedSequences)
aSequence.Sequences.Add(alignedSequence);
foreach (var inputSequence in sequences)
alignment.Sequences.Add(inputSequence);
alignment.AlignedSequences.Add(aSequence);
return new List<Alignment.ISequenceAlignment>() {alignment};
}
