X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=ea7b30eea7798d238bcf2ad9b80616e256605fb2;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=494d09f663283ae1dc662b353ad8c61824149f70;hpb=582493a5b56d3e01d901c6da9906685c31a32abb;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 494d09f..ea7b30e 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,5 +1,6 @@
 package jalview.analysis.scoremodels;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.ScoreModelI;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
@@ -67,14 +68,15 @@ 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;
   }
@@ -90,9 +92,20 @@ 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)