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 043e6fb..011d8ba 100644 (file)
--- 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()
   {
@@ -46,7 +46,7 @@ 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");
@@ -84,34 +84,24 @@ 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());