JAL-2499 JAL-2403 push 'configure for view' inside ScoreModels, defer

[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 494d09f..7146383 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,6 +1,8 @@
 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;
@@ -90,9 +92,33 @@ 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);
+    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)