X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=5cfe72ab7725f48bd04ed94dcff52982e4d629aa;hb=d1e20f6a5654ea6baf378afa3277b4e751c69a96;hp=521bb3eb9c8414561a1ec101e22b03a9f37a15d3;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 521bb3e..5cfe72a 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -281,8 +281,8 @@ 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)
                       {
@@ -290,6 +290,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
                       }
                       _rnaList.add(varnaPanel.getConfig().clone(), r, name,
                               true);
+                      // BH 2018 SwingJS clone of varnaPanel or its config will
+                      // be the object itself, not a clone
                     }
                   }
                 }
@@ -374,9 +376,9 @@ public class AppVarnaBinding extends JalviewVarnaBinding
 
       _sideList.ensureIndexIsVisible(index);
       /*
-       * TODO Object newName = JOptionPane.showInputDialog( this,
+       * TODO Object newName = JvOptionPane.showInputDialog( this,
        * "Specify a new name for this RNA", "Rename RNA",
-       * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
+       * JvOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
        * (newName!=null) { item.name = newName.toString();
        * this._sideList.repaint(); }
        */
@@ -384,7 +386,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return null;
   }
@@ -545,7 +547,8 @@ 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);
   }