X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=494d09f663283ae1dc662b353ad8c61824149f70;hb=4a4a5ad26799d8bd157c210153beaf21045d0402;hp=043e6fbbcfd3471a6b00876f4a9dde30519d60d7;hpb=fcb39fa3bc47777bf4e0eb209f765dd254dc3cb9;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 043e6fb..494d09f 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,6 +1,6 @@
 package jalview.analysis.scoremodels;
 
-import jalview.api.analysis.DistanceModelI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.ScoreMatrixFile;
@@ -22,7 +22,7 @@ public class ScoreModels
 
   private static ScoreModels instance = new ScoreModels();
 
-  private Map<String, DistanceModelI> models;
+  private Map<String, ScoreModelI> models;
 
   public static ScoreModels getInstance()
   {
@@ -35,10 +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()
@@ -46,15 +45,12 @@ public class ScoreModels
     /*
      * using LinkedHashMap keeps models ordered as added
      */
-    models = new LinkedHashMap<String, DistanceModelI>();
+    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());
+    registerScoreModel(new PIDModel());
     DNA = loadScoreMatrix("scoreModel/dna.scm");
     registerScoreModel(new FeatureDistanceModel());
-    registerScoreModel(new PIDDistanceModel());
   }
 
   /**
@@ -84,34 +80,24 @@ public class ScoreModels
   }
 
   /**
-   * Registers a pairwise score model
-   * 
-   * @param sm
-   */
-  public void registerScoreModel(PairwiseScoreModelI sm)
-  {
-    registerScoreModel(new PairwiseDistanceModel(sm));
-  }
-
-  /**
    * Answers an iterable set of the registered score models. Currently these are
    * returned in the order in which they were registered.
    * 
    * @return
    */
-  public Iterable<DistanceModelI> getModels()
+  public Iterable<ScoreModelI> getModels()
   {
     return models.values();
   }
 
-  public DistanceModelI forName(String s)
+  public ScoreModelI forName(String s)
   {
     return models.get(s);
   }
 
-  public void registerScoreModel(DistanceModelI sm)
+  public void registerScoreModel(ScoreModelI sm)
   {
-    DistanceModelI sm2 = models.get(sm.getName());
+    ScoreModelI sm2 = models.get(sm.getName());
     if (sm2 != null)
     {
       System.err.println("Warning: replacing score model " + sm2.getName());