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 9af68d0..011d8ba 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -6,14 +6,20 @@ import jalview.io.FileParse;
 import jalview.io.ScoreMatrixFile;
 
 import java.io.IOException;
+import java.util.LinkedHashMap;
 import java.util.Map;
-import java.util.TreeMap;
 
 /**
  * A class that can register and serve instances of ScoreModelI
  */
 public class ScoreModels
 {
+  private final ScoreMatrix BLOSUM62;
+
+  private final ScoreMatrix PAM250;
+
+  private final ScoreMatrix DNA;
+
   private static ScoreModels instance = new ScoreModels();
 
   private Map<String, ScoreModelI> models;
@@ -29,6 +35,7 @@ public class ScoreModels
    * <ul>
    * <li>BLOSUM62</li>
    * <li>PAM250</li>
+   * <li>SeqSpace (identity matrix)</li>
    * <li>DNA</li>
    * <li>Sequence Feature Similarity</li>
    * <li>Percentage Identity</li>
@@ -37,23 +44,27 @@ public class ScoreModels
   private ScoreModels()
   {
     /*
-     * using TreeMap keeps models ordered alphabetically by name
+     * using LinkedHashMap keeps models ordered as added
      */
-    models = new TreeMap<String, ScoreModelI>(String.CASE_INSENSITIVE_ORDER);
-    loadScoreMatrix("scoreModel/blosum62.scm");
-    loadScoreMatrix("scoreModel/pam250.scm");
-    loadScoreMatrix("scoreModel/dna.scm");
-    registerScoreModel(new FeatureScoreModel());
-    registerScoreModel(new PIDScoreModel());
+    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());
+    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
     {
@@ -63,18 +74,18 @@ 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;
   }
 
   /**
    * Answers an iterable set of the registered score models. Currently these are
-   * ordered by name (not case sensitive).
+   * returned in the order in which they were registered.
    * 
    * @return
    */
@@ -97,4 +108,26 @@ public class ScoreModels
     }
     models.put(sm.getName(), sm);
   }
+
+  /**
+   * Returns the default peptide or nucleotide score model, currently BLOSUM62
+   * or DNA
+   * 
+   * @param forPeptide
+   * @return
+   */
+  public ScoreMatrix getDefaultModel(boolean forPeptide)
+  {
+    return forPeptide ? BLOSUM62 : DNA;
+  }
+
+  public ScoreMatrix getBlosum62()
+  {
+    return BLOSUM62;
+  }
+
+  public ScoreMatrix getPam250()
+  {
+    return PAM250;
+  }
 }