JAL-2416 scoreMatrices removed from ResidueProperties

[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 f1990c0..07840fc 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,20 +1,30 @@
 package jalview.analysis.scoremodels;
 
 import jalview.api.analysis.ScoreModelI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.ScoreMatrixFile;
 
 import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
+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 static ScoreModels instance = new 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";
+
+  public static final String PAM250 = "PAM250";
+
+  public static final String DNA = "DNA";
 
+  private static ScoreModels instance = new ScoreModels();
   private Map<String, ScoreModelI> models;
 
   public static ScoreModels getInstance()
@@ -28,6 +38,7 @@ 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>
@@ -36,62 +47,45 @@ 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");
+    models = new LinkedHashMap<String, ScoreModelI>();
+    loadScoreMatrix("scoreModel/blosum62.scm");
+    loadScoreMatrix("scoreModel/pam250.scm");
+    loadScoreMatrix("scoreModel/seqspace.scm");
+    loadScoreMatrix("scoreModel/dna.scm");
     registerScoreModel(new FeatureScoreModel());
     registerScoreModel(new PIDScoreModel());
   }
 
   /**
    * Try to load a score matrix from the given resource file, and if successful,
-   * register it. Answers true if successful, else false. Any errors are
-   * reported on syserr but not thrown.
+   * register it. Answers true if successful, else false.
    * 
    * @param string
    */
   boolean loadScoreMatrix(String resourcePath)
   {
-    URL url = this.getClass().getResource(resourcePath);
-    if (url == null)
-    {
-      System.err.println("Failed to locate " + resourcePath);
-      return false;
-    }
-    boolean success = false;
-    InputStream is = null;
     try
     {
-      is = url.openStream();
-      ScoreMatrix sm = ScoreMatrix.parse(is);
-      if (sm != null)
-      {
-        registerScoreModel(sm);
-        success = true;
-      }
+      /*
+       * delegate parsing to ScoreMatrixFile
+       */
+      FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+      ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
+      registerScoreModel(sm);
+      return true;
     } catch (IOException e)
     {
-    } finally
-    {
-      if (is != null)
-      {
-        try
-        {
-          is.close();
-        } catch (IOException e)
-        {
-        }
-      }
+      System.err.println("Error reading " + resourcePath + ": "
+              + e.getMessage());
     }
-    return success;
+    return false;
   }
 
   /**
    * 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
    */
@@ -114,4 +108,17 @@ public class ScoreModels
     }
     models.put(sm.getName(), sm);
   }
+
+  /**
+   * Returns the default peptide or nucleotide score model, currently BLOSUM62
+   * or DNA
+   * 
+   * @param forPeptide
+   * @return
+   */
+  public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+  {
+    return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
+            : forName("DNA"));
+  }
 }