X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=494d09f663283ae1dc662b353ad8c61824149f70;hb=4a4a5ad26799d8bd157c210153beaf21045d0402;hp=2419997633123242e2417e8931c48050f2f4c844;hpb=67428050d76de7946d96d43ba16ee02d439026bd;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 2419997..494d09f 100644
--- 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;
@@ -33,10 +35,9 @@ public class ScoreModels
    * <ul>
    * <li>BLOSUM62</li>
    * <li>PAM250</li>
-   * <li>SeqSpace (identity matrix)</li>
+   * <li>PID</li>
    * <li>DNA</li>
    * <li>Sequence Feature Similarity</li>
-   * <li>Percentage Identity</li>
    * </ul>
    */
   private ScoreModels()
@@ -47,10 +48,9 @@ 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());
+    registerScoreModel(new PIDModel());
+    DNA = loadScoreMatrix("scoreModel/dna.scm");
+    registerScoreModel(new FeatureDistanceModel());
   }
 
   /**
@@ -112,10 +112,9 @@ 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()