X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=654136ac0cf498007a6bdc4ef9ef5e743ee78975;hb=9c007fa50a82b3ae0f987e6454ae17c941b63563;hp=011d8baf161f84af5099d1405c05f6e2c6cdb441;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 011d8ba..654136a 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,5 +1,6 @@
 package jalview.analysis.scoremodels;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.ScoreModelI;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
@@ -35,10 +36,9 @@ 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()
@@ -49,12 +49,9 @@ public class ScoreModels
     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());
   }
 
   /**
@@ -94,9 +91,20 @@ public class ScoreModels
     return models.values();
   }
 
-  public ScoreModelI forName(String s)
+  /**
+   * Returns an instance of a score model for the given name. If the model is of
+   * 'view dependent' type (e.g. feature similarity), instantiates a new
+   * instance configured for the given view. Otherwise returns a cached instance
+   * of the score model.
+   * 
+   * @param name
+   * @param avp
+   * @return
+   */
+  public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
   {
-    return models.get(s);
+    ScoreModelI model = models.get(name);
+    return model == null ? null : model.getInstance(avp);
   }
 
   public void registerScoreModel(ScoreModelI sm)