-
- String sm = nucleotides ? "DNA" : "BLOSUM62";
- ScoreMatrix smtrx = ResidueProperties.getScoreMatrix(sm);
+ ScoreMatrix smtrx = null;
+ String sm=s_m;
+ if (sm!=null)
+ {
+ smtrx = ResidueProperties.getScoreMatrix(sm);
+ }
+ if (smtrx==null)
+ {
+ // either we were given a non-existent score matrix or a scoremodel that isn't based on a pairwise symbol score matrix
+ smtrx = ResidueProperties.getScoreMatrix(sm=(nucleotides ? "DNA" : "BLOSUM62"));
+ }