JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

[jalview.git] / src / jalview / analysis / scoremodels / ScoreModels.java

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 2419997..011d8ba 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -18,6 +18,8 @@ public class ScoreModels
 
   private final ScoreMatrix PAM250;
 
+  private final ScoreMatrix DNA;
+
   private static ScoreModels instance = new ScoreModels();
 
   private Map<String, ScoreModelI> models;
@@ -47,10 +49,12 @@ public class ScoreModels
     models = new LinkedHashMap<String, ScoreModelI>();
     BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
     PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
-    loadScoreMatrix("scoreModel/dna.scm");
     loadScoreMatrix("scoreModel/seqspace.scm");
-    registerScoreModel(new FeatureScoreModel());
-    registerScoreModel(new PIDScoreModel());
+    // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in?
+    // registerScoreModel(new IdentityScoreModel());
+    DNA = loadScoreMatrix("scoreModel/dna.scm");
+    registerScoreModel(new FeatureDistanceModel());
+    registerScoreModel(new PIDDistanceModel());
   }
 
   /**
@@ -112,10 +116,9 @@ public class ScoreModels
    * @param forPeptide
    * @return
    */
-  public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+  public ScoreMatrix getDefaultModel(boolean forPeptide)
   {
-    return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
-            : forName("DNA"));
+    return forPeptide ? BLOSUM62 : DNA;
   }
 
   public ScoreMatrix getBlosum62()