package jalview.analysis.scoremodels;
import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.api.analysis.SimilarityScoreModelI;
import jalview.datamodel.AlignmentView;
import jalview.math.Matrix;
* </ul>
*/
@Override
- public MatrixI findSimilarities(AlignmentView seqstrings)
+ public MatrixI findSimilarities(AlignmentView seqstrings,
+ SimilarityParamsI options)
{
char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X') : ' ';
String[] seqs = seqstrings.getSequenceStrings(gapChar);
- return findSimilarities(seqs);
+ return findSimilarities(seqs, options);
}
/**
* @param seqs
* @return
*/
- protected MatrixI findSimilarities(String[] seqs)
+ protected MatrixI findSimilarities(String[] seqs,
+ SimilarityParamsI options)
{
+ // todo use options in calculation
double[][] values = new double[seqs.length][];
for (int row = 0; row < seqs.length; row++)
{