X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=95e114e22901954119cc9c6a104b8e1681147651;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=011d8baf161f84af5099d1405c05f6e2c6cdb441;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 011d8ba..95e114e 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,5 +1,26 @@
+/*
+ * 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.io.DataSourceType;
 import jalview.io.FileParse;
@@ -20,12 +41,24 @@ public class ScoreModels
 
   private final ScoreMatrix DNA;
 
-  private static ScoreModels instance = new ScoreModels();
+  private final ScoreMatrix FOLDSEEK3DI;
+
+  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;
   }
 
@@ -35,10 +68,9 @@ public class ScoreModels
    * <ul>
    * <li>BLOSUM62</li>
    * <li>PAM250</li>
-   * <li>SeqSpace (identity matrix)</li>
+   * <li>PID</li>
    * <li>DNA</li>
    * <li>Sequence Feature Similarity</li>
-   * <li>Percentage Identity</li>
    * </ul>
    */
   private ScoreModels()
@@ -46,15 +78,13 @@ public class ScoreModels
     /*
      * using LinkedHashMap keeps models ordered as added
      */
-    models = new LinkedHashMap<String, ScoreModelI>();
+    models = new LinkedHashMap<>();
     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");
+    FOLDSEEK3DI = loadScoreMatrix("scoreModel/foldseek_mat3di.scm");
+    registerScoreModel(new PIDModel());
     registerScoreModel(new FeatureDistanceModel());
-    registerScoreModel(new PIDDistanceModel());
   }
 
   /**
@@ -71,14 +101,15 @@ public class ScoreModels
       /*
        * delegate parsing to ScoreMatrixFile
        */
-      FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+      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());
+      jalview.bin.Console.errPrintln(
+              "Error reading " + resourcePath + ": " + e.getMessage());
     }
     return null;
   }
@@ -94,9 +125,20 @@ public class ScoreModels
     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)
@@ -104,12 +146,21 @@ 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
    * 
@@ -130,4 +181,9 @@ public class ScoreModels
   {
     return PAM250;
   }
+  public ScoreMatrix getFOLDSEEK3DI()
+  {
+    return FOLDSEEK3DI;
+  }
+  
 }