Merge branch 'features/JAL-2393customMatrices' into develop

[jalview.git] / src / jalview / analysis / scoremodels / ScoreModels.java

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
new file mode 100644 (file)
index 0000000..7146383
--- /dev/null
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -0,0 +1,155 @@
+package jalview.analysis.scoremodels;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.ScoreMatrixFile;
+
+import java.io.IOException;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+/**
+ * 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;
+
+  public static ScoreModels getInstance()
+  {
+    return instance;
+  }
+
+  /**
+   * Private constructor to enforce use of singleton. Registers Jalview's
+   * "built-in" score models:
+   * <ul>
+   * <li>BLOSUM62</li>
+   * <li>PAM250</li>
+   * <li>PID</li>
+   * <li>DNA</li>
+   * <li>Sequence Feature Similarity</li>
+   * </ul>
+   */
+  private ScoreModels()
+  {
+    /*
+     * using LinkedHashMap keeps models ordered as added
+     */
+    models = new LinkedHashMap<String, ScoreModelI>();
+    BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
+    PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
+    registerScoreModel(new PIDModel());
+    DNA = loadScoreMatrix("scoreModel/dna.scm");
+    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)
+    {
+      System.err.println("Error reading " + resourcePath + ": "
+              + e.getMessage());
+    }
+    return null;
+  }
+
+  /**
+   * 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.values();
+  }
+
+  /**
+   * 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)
+  {
+    ScoreModelI model = models.get(name);
+    if (model instanceof ViewBasedAnalysisI)
+    {
+      try
+      {
+        model = model.getClass().newInstance();
+        ((ViewBasedAnalysisI) model).configureFromAlignmentView(avp);
+      } catch (IllegalAccessException | InstantiationException e)
+      {
+        System.err.println("Error creating score model " + name + ": "
+                + e.getMessage());
+        return null;
+      }
+    }
+    return model;
+  }
+
+  public void registerScoreModel(ScoreModelI sm)
+  {
+    ScoreModelI 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;
+  }
+}