X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=f1f2d307d4014f0a1424017e5a84a470d0561c6b;hb=05e40b4dd4e216024024fb921d797917d74daa76;hp=289d340260858586e695f5bfd6d036b6f13bcc0e;hpb=0e8ea80cb031f3bb9cf8f979fe138bf68dbc2446;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 289d340..f1f2d30 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;
             }
@@ -1072,7 +1075,10 @@ public abstract class AAStructureBindingModel
    * executed.
    * <p>
    * If a reply is wanted, the execution is done synchronously (waits),
-   * otherwise it is done in a separate thread (doesn't wait).
+   * otherwise it is done in a separate thread (doesn't wait). WARNING: if you
+   * are sending commands that need to execute before later calls to
+   * executeCommand (e.g. mouseovers, which clean up after previous ones) then
+   * set getReply true to ensure that commands are not executed out of order.
    * 
    * @param getReply
    * @param msg
@@ -1216,8 +1222,7 @@ 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
@@ -1230,9 +1235,7 @@ public abstract class AAStructureBindingModel
     {
       return null;
     }
-    return ap.getAlignViewport().isShowSequenceFeatures()
-            ? ap.getFeatureRenderer()
-            : null;
+    return ap.getFeatureRenderer();
   }
 
   protected void setStructureCommands(StructureCommandsI cmd)