Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...

[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 ea7b30e..d0f21bd 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -21,12 +41,22 @@ public class ScoreModels
 
   private final ScoreMatrix DNA;
 
-  private static ScoreModels instance = new ScoreModels();
+  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;
   }
 
@@ -46,11 +76,11 @@ 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");
-    registerScoreModel(new PIDModel());
     DNA = loadScoreMatrix("scoreModel/dna.scm");
+    registerScoreModel(new PIDModel());
     registerScoreModel(new FeatureDistanceModel());
   }
 
@@ -75,7 +105,7 @@ public class ScoreModels
       return sm;
     } catch (IOException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error reading " + resourcePath + ": " + e.getMessage());
     }
     return null;
@@ -113,12 +143,20 @@ 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
    *