/// <summary>
/// When implemented in a derived class, performs the execution of the activity.
/// </summary>
/// <returns>
/// The result of the activity’s execution.
/// </returns>
/// <param name="context">The execution context under which the activity executes.</param>
protected override ISequenceAlignment Execute(CodeActivityContext context)
{
string alignerName = (AlignerName ?? DefaultAligner).ToLowerInvariant();
var aligner = SequenceAligners.All.FirstOrDefault(sa => sa.Name.ToLowerInvariant() == alignerName);
if (aligner == null)
{
throw new ArgumentException("Could not find aligner: " + alignerName);
}
aligner.GapOpenCost = GapOpenCost;
aligner.GapExtensionCost = GapExtensionCost;
var smName = SimilarityMatrix ?? DefaultMatrix;
SimilarityMatrix.StandardSimilarityMatrix sm;
if (Enum.TryParse(smName, true, out sm))
{
aligner.SimilarityMatrix = new SimilarityMatrix(sm);
}
ISequenceAlignment result;
if (GapOpenCost == GapExtensionCost || GapExtensionCost == 0)
{
result = aligner.AlignSimple(new[] { FirstSequence.Get(context), SecondSequence.Get(context) }).First();
}
else
{
result = aligner.Align(new[] { FirstSequence.Get(context), SecondSequence.Get(context) }).First();
}
IPairwiseSequenceAlignment pwAlignment = result as IPairwiseSequenceAlignment;
if (pwAlignment != null)
{
if (pwAlignment.PairwiseAlignedSequences.Count > 0)
{
FirstResult.Set(context, pwAlignment.PairwiseAlignedSequences[0].FirstSequence);
SecondResult.Set(context, pwAlignment.PairwiseAlignedSequences[0].SecondSequence);
Consensus.Set(context, pwAlignment.PairwiseAlignedSequences[0].Consensus);
}
}
return(result);
}
// same algorithm as above
/// <exception cref="NotComputedException"></exception>
public FirstResult Sequence(IEnumerable <Symbol> syms)
{
_ = Algo.Nullable ?? throw new NotComputedException(nameof(Algo.Nullable));
var result = new FirstResult();
foreach (var Bi in syms)
{
if (Bi.Type == Symbol.Types.Terminal)
{
result.Add(Bi);
break;
}
else
{
result.UnionWith(this[Bi]);
}
if (!Algo.Nullable[Bi])
{
break;
}
}
return(result);
}
public void ClickFirstResult() => FirstResult.Click();
