X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=e5196cc9a8759f55e83d8b1562a59e6f2a7c8f1e;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=366dc06d5b992a8118dc16f8e1860d25d9462533;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 366dc06..e5196cc 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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);
   }
 
@@ -571,7 +574,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
     } catch (ExceptionNAViewAlgorithm e)
     {
       // only throwable for draw mode = 3 NAView
-      System.err.println("Error drawing RNA: " + e.getMessage());
+      jalview.bin.Console
+              .errPrintln("Error drawing RNA: " + e.getMessage());
     }
   }
 }