/// <summary>
/// Creates a new instance of SmithWatermanImplementation
/// </summary>
/// <param name="sequenceTomatch">Sequence to match</param>
/// <param name="targetSequence">Sequence to match against.</param>
public SmithWatermanImplementation(
SequenceMetadata sequenceTomatch,
SequenceMetadata targetSequence,
AlignmentScoreProviderBase scoreProvider,
int gapOpenPenality) :
base(sequenceTomatch, targetSequence, scoreProvider, gapOpenPenality)
{
this.IntializeSubstitutionMatrix();
}
/// <summary>
/// Creates a new instance alignment algorithm.
/// </summary>
public AlignmentImplementationBase(
SequenceMetadata sequenceTomatch,
SequenceMetadata targetSequence,
AlignmentScoreProviderBase scoreProvider, int gapOpenPenality)
{
if (sequenceTomatch == null)
{
throw new ArgumentNullException("sequenceTomatch");
}
if (targetSequence == null)
{
throw new ArgumentNullException("targetSequence");
}
if (scoreProvider == null)
{
throw new ArgumentNullException("scoreProvider");
}
this.TargetSequence = targetSequence;
this.SequenceToMatch = sequenceTomatch;
this.ScoreProvider = scoreProvider;
this.GapOpenPenality = gapOpenPenality;
}