JAL-2418 add GPL to main sources

[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 7146383..7262fb8 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,8 +1,27 @@
+/*
+ * 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.api.analysis.ViewBasedAnalysisI;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.ScoreMatrixFile;
@@ -69,14 +88,15 @@ 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());
+      System.err.println(
+              "Error reading " + resourcePath + ": " + e.getMessage());
     }
     return null;
   }
@@ -105,20 +125,7 @@ public class ScoreModels
   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;
+    return model == null ? null : model.getInstance(avp);
   }
 
   public void registerScoreModel(ScoreModelI sm)