- models = new TreeMap<String, ScoreModelI>(String.CASE_INSENSITIVE_ORDER);
- loadScoreMatrix("/scoreModel/blosum62.scm");
- loadScoreMatrix("/scoreModel/pam250.scm");
- loadScoreMatrix("/scoreModel/dna.scm");
- registerScoreModel(new FeatureScoreModel());
- registerScoreModel(new PIDScoreModel());
+ models = new LinkedHashMap<String, ScoreModelI>();
+ BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
+ PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
+ loadScoreMatrix("scoreModel/seqspace.scm");
+ // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in?
+ // registerScoreModel(new IdentityScoreModel());
+ DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new FeatureDistanceModel());
+ registerScoreModel(new PIDDistanceModel());