X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=d0f21bd19ce796f730647860f79de60afc80c498;hb=6ca8a32d88328b8f2162512f41c657c87e131045;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..d0f21bd 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,22 +1,62 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis.scoremodels;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.ScoreModelI;
-import jalview.schemes.ResidueProperties;
+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 static ScoreModels instance = new ScoreModels();
+  private final ScoreMatrix BLOSUM62;
+
+  private final ScoreMatrix PAM250;
+
+  private final ScoreMatrix DNA;
+
+  private static ScoreModels instance;
 
   private Map<String, ScoreModelI> models;
 
+  /**
+   * Answers the singleton instance of this class, with lazy initialisation
+   * (built-in score models are loaded on the first call to this method)
+   * 
+   * @return
+   */
   public static ScoreModels getInstance()
   {
+    if (instance == null)
+    {
+      instance = new ScoreModels();
+    }
     return instance;
   }
 
@@ -26,34 +66,76 @@ public class ScoreModels
    * <ul>
    * <li>BLOSUM62</li>
    * <li>PAM250</li>
+   * <li>PID</li>
    * <li>DNA</li>
    * <li>Sequence Feature Similarity</li>
-   * <li>Percentage Identity</li>
    * </ul>
    */
   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<>();
+    BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
+    PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
+    DNA = loadScoreMatrix("scoreModel/dna.scm");
+    registerScoreModel(new PIDModel());
+    registerScoreModel(new FeatureDistanceModel());
+  }
+
+  /**
+   * Tries to load a score matrix from the given resource file, and if
+   * successful, registers it.
+   * 
+   * @param string
+   * @return
+   */
+  ScoreMatrix loadScoreMatrix(String resourcePath)
+  {
+    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)
+    {
+      jalview.bin.Console.errPrintln(
+              "Error reading " + resourcePath + ": " + e.getMessage());
+    }
+    return null;
   }
 
-  public Iterable<String> getModelNames()
+  /**
+   * Answers an iterable set of the registered score models. Currently these are
+   * returned in the order in which they were registered.
+   * 
+   * @return
+   */
+  public Iterable<ScoreModelI> getModels()
   {
-    return models.keySet();
+    return models.values();
   }
 
-  public ScoreModelI forName(String s)
+  /**
+   * Returns an instance of a score model for the given name. If the model is of
+   * 'view dependent' type (e.g. feature similarity), instantiates a new
+   * instance configured for the given view. Otherwise returns a cached instance
+   * of the score model.
+   * 
+   * @param name
+   * @param avp
+   * @return
+   */
+  public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
   {
-    return models.get(s);
+    ScoreModelI model = models.get(name);
+    return model == null ? null : model.getInstance(avp);
   }
 
   public void registerScoreModel(ScoreModelI sm)
@@ -61,8 +143,38 @@ public class ScoreModels
     ScoreModelI sm2 = models.get(sm.getName());
     if (sm2 != null)
     {
-      System.err.println("Warning: replacing score model " + sm2.getName());
+      jalview.bin.Console.errPrintln("Warning: replacing score model " + sm2.getName());
     }
     models.put(sm.getName(), sm);
   }
+
+  /**
+   * Resets to just the built-in score models
+   */
+  public void reset()
+  {
+    instance = new ScoreModels();
+  }
+
+  /**
+   * 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;
+  }
 }