X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=043e6fbbcfd3471a6b00876f4a9dde30519d60d7;hb=f46c404585087d8937c48504bfcff716440d5186;hp=4fa639686dd69e5530f70efb9f0eabc28776f801;hpb=1750b2f1dcdb6e7de41d0ef7beda88dc3400afba;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 4fa6396..043e6fb 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,19 +1,28 @@
 package jalview.analysis.scoremodels;
 
-import jalview.api.analysis.ScoreModelI;
-import jalview.schemes.ResidueProperties;
+import jalview.api.analysis.DistanceModelI;
+import jalview.io.DataSourceType;
+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;
+  private Map<String, DistanceModelI> models;
 
   public static ScoreModels getInstance()
   {
@@ -26,6 +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>
@@ -34,35 +44,100 @@ 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);
-    registerScoreModel(new ScoreMatrix("BLOSUM62",
-            ResidueProperties.BLOSUM62, 0));
-    registerScoreModel(new ScoreMatrix("PAM250", ResidueProperties.PAM250,
-            0));
-    registerScoreModel(new ScoreMatrix("DNA", ResidueProperties.DNA, 1));
-    registerScoreModel(new FeatureScoreModel());
-    registerScoreModel(new PIDScoreModel());
+    models = new LinkedHashMap<String, DistanceModelI>();
+    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());
   }
 
-  public Iterable<String> getModelNames()
+  /**
+   * Tries to load a score matrix from the given resource file, and if
+   * successful, registers it.
+   * 
+   * @param string
+   * @return
+   */
+  ScoreMatrix loadScoreMatrix(String resourcePath)
   {
-    return models.keySet();
+    try
+    {
+      /*
+       * delegate parsing to ScoreMatrixFile
+       */
+      FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+      ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
+      registerScoreModel(sm);
+      return sm;
+    } catch (IOException e)
+    {
+      System.err.println("Error reading " + resourcePath + ": "
+              + e.getMessage());
+    }
+    return null;
   }
 
-  public ScoreModelI forName(String s)
+  /**
+   * 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()
+  {
+    return models.values();
+  }
+
+  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());
     }
     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;
+  }
 }