X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=043e6fbbcfd3471a6b00876f4a9dde30519d60d7;hb=fcb39fa3bc47777bf4e0eb209f765dd254dc3cb9;hp=07840fcff6f5038499ba5734cd0f724d60697f25;hpb=a45b4529c64901e9e4b53b6c74ee804370c91002;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 07840fc..043e6fb 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.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.ScoreMatrixFile;
@@ -14,18 +14,15 @@ 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;
+
+  private Map<String, DistanceModelI> models;
 
   public static ScoreModels getInstance()
   {
@@ -49,22 +46,25 @@ public class ScoreModels
     /*
      * using LinkedHashMap keeps models ordered as added
      */
-    models = new LinkedHashMap<String, ScoreModelI>();
-    loadScoreMatrix("scoreModel/blosum62.scm");
-    loadScoreMatrix("scoreModel/pam250.scm");
+    models = new LinkedHashMap<String, DistanceModelI>();
+    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 +74,23 @@ 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;
+  }
+
+  /**
+   * Registers a pairwise score model
+   * 
+   * @param sm
+   */
+  public void registerScoreModel(PairwiseScoreModelI sm)
+  {
+    registerScoreModel(new PairwiseDistanceModel(sm));
   }
 
   /**
@@ -89,19 +99,19 @@ public class ScoreModels
    * 
    * @return
    */
-  public Iterable<ScoreModelI> getModels()
+  public Iterable<DistanceModelI> getModels()
   {
     return models.values();
   }
 
-  public ScoreModelI forName(String s)
+  public DistanceModelI forName(String s)
   {
     return models.get(s);
   }
 
-  public void registerScoreModel(ScoreModelI sm)
+  public void registerScoreModel(DistanceModelI sm)
   {
-    ScoreModelI sm2 = models.get(sm.getName());
+    DistanceModelI sm2 = models.get(sm.getName());
     if (sm2 != null)
     {
       System.err.println("Warning: replacing score model " + sm2.getName());
@@ -116,9 +126,18 @@ 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;
   }
 }