}
@Override
- public MatrixI findSimilarities(AlignmentView seqData)
+ public MatrixI findSimilarities(AlignmentView seqData,
+ SimilarityParamsI options)
{
- // TODO reuse code in ScoreMatrix instead somehow
String[] seqs = seqData.getSequenceStrings(' ');
- return findSimilarities(seqs, SimilarityParams.Jalview);
+ return findSimilarities(seqs, options);
}
/**
protected MatrixI findSimilarities(String[] seqs,
SimilarityParamsI options)
{
+ // TODO reuse code in ScoreMatrix instead somehow
double[][] values = new double[seqs.length][];
for (int row = 0; row < seqs.length; row++)
{