-
- String sm=nucleotides ? "DNA" : "BLOSUM62";
- ScoreMatrix smtrx=ResidueProperties.getScoreMatrix(sm);
- details.append("PCA calculation using "+sm+" sequence similarity matrix\n========\n\n");
-
+ 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"));
+ }
+ details.append("PCA calculation using " + sm
+ + " sequence similarity matrix\n========\n\n");