JAL-3390 respect 'hidden chains' on redisplay after superposition

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index e7aac1c..e7f879c 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -929,9 +929,11 @@ public abstract class AAStructureBindingModel
       /*
        * Show all as backbone before doing superposition(s)
        * (residues used for matching will be shown as ribbon)
+       * while remembering to hide any chains unselected for display
        */
       // todo better way to ensure synchronous than setting getReply true!!
       executeCommands(commandGenerator.showBackbone(), true, null);
+      hideHiddenChains();
 
       /*
        * superpose each (other) structure to the reference in turn
@@ -1300,10 +1302,21 @@ public abstract class AAStructureBindingModel
     StructureCommandI cmd = getCommandGenerator().showStructures(model);
     executeCommand(cmd, false);
 
-    /*
-     * and hide any chains selected _not_ to be shown 
-     * (whether mapped to sequence in the alignment or not)
-     */
+    hideHiddenChains();
+
+    if (refocus)
+    {
+      focusView();
+    }
+  }
+
+  /**
+   * Hides any chains selected _not_ to be shown 
+   * (whether mapped to sequence in the alignment or not)
+   */
+  protected void hideHiddenChains()
+  {
+    StructureCommandI cmd;
     for (String pdbChain : chainsToHide)
     {
       String modelNo = getModelIdForFile(getFileForChain(pdbChain));
@@ -1314,11 +1327,6 @@ public abstract class AAStructureBindingModel
         executeCommand(cmd, false);
       }
     }
-
-    if (refocus)
-    {
-      focusView();
-    }
   }
 
   /**