X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=e5196cc9a8759f55e83d8b1562a59e6f2a7c8f1e;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=829fc3ef6b2f767525fce4da345d36af8a2c04d7;hpb=dfc78969cad82b5150f5a4f554bc9030b5946bbe;p=jalview.git

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 829fc3e..e5196cc 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
                     }
                   }
                 }
@@ -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());
     }
   }
 }