X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=74308564ca8fd5cfaa97403e67f73133e3945d1d;hb=5571d7868cad5493b52c9fc421c88c025e7c2d35;hp=8ab1e61d959ad30dfc8c1edc111957c44e9f2e90;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 8ab1e61..7430856 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -281,15 +281,16 @@ public class AppVarnaBinding extends JalviewVarnaBinding
                       String name = r.getName();
                       if (name.equals(""))
                       {
-                        name = path.substring(path
-                                .lastIndexOf(File.separatorChar) + 1);
+                        name = path.substring(
+                                path.lastIndexOf(File.separatorChar) + 1);
                       }
                       if (mdls.size() > 1)
                       {
                         name += " (Model " + mn++ + ")";
                       }
                       _rnaList.add(varnaPanel.getConfig().clone(), r, name,
-                              true);
+                              true); 
+                      // BH 2018 SwingJS clone of varnaPanel or its config will be the object itself, not a clone
                     }
                   }
                 }
@@ -384,7 +385,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return null;
   }
@@ -545,7 +546,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
    */
   public void addStructure(RNA rna)
   {
-    VARNAConfig config = vp.getConfig().clone();
+    VARNAConfig config = vp.getConfig().clone(); // BH 2018 this will NOT be a clone in SwingJS
     addStructure(rna, config);
   }