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 07840fc..011d8ba 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -14,17 +14,14 @@ import java.util.Map;
  */
 public class ScoreModels
 {
-  /*
-   * constants for built-in score model names
-   * NB! these have to match names in loaded score matrix files
-   */
-  public static final String BLOSUM62 = "BLOSUM62";
+  private final ScoreMatrix BLOSUM62;
 
-  public static final String PAM250 = "PAM250";
+  private final ScoreMatrix PAM250;
 
-  public static final String DNA = "DNA";
+  private final ScoreMatrix DNA;
 
   private static ScoreModels instance = new ScoreModels();
+
   private Map<String, ScoreModelI> models;
 
   public static ScoreModels getInstance()
@@ -50,21 +47,24 @@ public class ScoreModels
      * using LinkedHashMap keeps models ordered as added
      */
     models = new LinkedHashMap<String, ScoreModelI>();
-    loadScoreMatrix("scoreModel/blosum62.scm");
-    loadScoreMatrix("scoreModel/pam250.scm");
+    BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
+    PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
     loadScoreMatrix("scoreModel/seqspace.scm");
-    loadScoreMatrix("scoreModel/dna.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());
   }
 
   /**
-   * Try to load a score matrix from the given resource file, and if successful,
-   * register it. Answers true if successful, else false.
+   * Tries to load a score matrix from the given resource file, and if
+   * successful, registers it.
    * 
    * @param string
+   * @return
    */
-  boolean loadScoreMatrix(String resourcePath)
+  ScoreMatrix loadScoreMatrix(String resourcePath)
   {
     try
     {
@@ -74,13 +74,13 @@ public class ScoreModels
       FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
       ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
       registerScoreModel(sm);
-      return true;
+      return sm;
     } catch (IOException e)
     {
       System.err.println("Error reading " + resourcePath + ": "
               + e.getMessage());
     }
-    return false;
+    return null;
   }
 
   /**
@@ -116,9 +116,18 @@ public class ScoreModels
    * @param forPeptide
    * @return
    */
-  public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+  public ScoreMatrix getDefaultModel(boolean forPeptide)
+  {
+    return forPeptide ? BLOSUM62 : DNA;
+  }
+
+  public ScoreMatrix getBlosum62()
+  {
+    return BLOSUM62;
+  }
+
+  public ScoreMatrix getPam250()
   {
-    return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
-            : forName("DNA"));
+    return PAM250;
   }
 }