X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=748381f1743e30a1a27f3577c8f723bf3e3197aa;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=16dd96cbd92e579aa1d5c9f779b015b6990764e7;hpb=aad3cb1e3d4250bebbf709624e3e15530a377df0;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 16dd96c..748381f 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,6 +20,8 @@
  */
 package jalview.structures.models;
 
+import java.util.Locale;
+
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
@@ -67,7 +69,7 @@ import jalview.util.MessageManager;
 
 /**
  * 
- * A base class to hold common function for protein structure model binding.
+ * A base class to hold common function for 3D structure model binding.
  * Initial version created by refactoring JMol and Chimera binding models, but
  * other structure viewers could in principle be accommodated in future.
  * 
@@ -582,6 +584,7 @@ public abstract class AAStructureBindingModel
       }
     }
   }
+  
 
   @Override
   public abstract void highlightAtoms(List<AtomSpec> atoms);
@@ -930,7 +933,7 @@ public abstract class AAStructureBindingModel
           for (String reply : replies)
           {
             // return this error (Chimera only) to the user
-            if (reply.toLowerCase().contains("unequal numbers of atoms"))
+            if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
             {
               error += "; " + reply;
             }
@@ -1096,7 +1099,10 @@ public abstract class AAStructureBindingModel
         for (StructureCommandI cmd : cmds)
         {
           List<String> replies = executeCommand(cmd, true);
-          response.addAll(replies);
+          if (replies != null)
+          {
+            response.addAll(replies);
+          }
         }
         return response;
       } finally
@@ -1213,8 +1219,7 @@ public abstract class AAStructureBindingModel
   }
 
   /**
-   * Returns the FeatureRenderer for the given alignment view, or null if
-   * feature display is turned off in the view.
+   * Returns the FeatureRenderer for the given alignment view
    * 
    * @param avp
    * @return
@@ -1227,9 +1232,7 @@ public abstract class AAStructureBindingModel
     {
       return null;
     }
-    return ap.getAlignViewport().isShowSequenceFeatures()
-            ? ap.getFeatureRenderer()
-            : null;
+    return ap.getFeatureRenderer();
   }
 
   protected void setStructureCommands(StructureCommandsI cmd)