public int GetCompressionScore(Profile<TSeq, TItem> sequence1, AlignmentCell<TItem>[] p1, AlignmentCell<TItem>[] p2, Profile<TSeq, TItem> sequence2, AlignmentCell<TItem>[] q)
{
throw new NotImplementedException();
}
public int GetTranspositionScore(Profile<TSeq, TItem> sequence1, AlignmentCell<TItem>[] p1, AlignmentCell<TItem>[] p2, Profile<TSeq, TItem> sequence2, AlignmentCell<TItem>[] q1, AlignmentCell<TItem>[] q2)
{
throw new NotImplementedException();
}
public int GetSubstitutionScore(Profile<TSeq, TItem> sequence1, AlignmentCell<TItem>[] p, Profile<TSeq, TItem> sequence2, AlignmentCell<TItem>[] q)
{
int sum = 0;
for (int i = 0; i < sequence1.Alignment.SequenceCount; i++)
{
for (int j = 0; j < sequence2.Alignment.SequenceCount; j++)
{
if (!p[i].IsNull && !q[j].IsNull)
{
sum += (int) (_scorer.GetSubstitutionScore(sequence1.Alignment.Sequences[i], p[i][0], sequence2.Alignment.Sequences[j], q[j][0])
* sequence1.Weights[i] * sequence2.Weights[j]);
}
}
}
return sum / (sequence1.Alignment.SequenceCount * sequence2.Alignment.SequenceCount);
}