Hi Chris, and thanks for your post.
One of our developers have suggested the following, hope it helps:
Match and Mismatch scores are properties of similarity matrices and not aligners. It is used only with DiagonalSimilarityMatrix. Other similarity matrices have their own standard and well defined scores(which
are called as BLOSUM50 etc…)
So if one has to use custom scores, he can always go ahead and use a DSM which has a constructor which takes Match and Mismatch scores and assign this SM
to any aligner.
public DiagonalSimilarityMatrix(int matchValue,
Please let us know if this resolves your question.
The MBF Team