JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / jalview / gui / AppVarnaBinding.java

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 366dc06..787ed53 100644 (file)
--- 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.
  * 
@@ -72,7 +72,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
 
   private ReorderableJList _sideList = null;
 
-  private static String errorOpt = "error";
+  private final static String errorOpt = "error";
 
   @SuppressWarnings("unused")
   private boolean _error;
@@ -100,7 +100,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
    */
   private void init()
   {
-    DefaultListModel<FullBackup> dlm = new DefaultListModel<FullBackup>();
+    DefaultListModel<FullBackup> dlm = new DefaultListModel<>();
 
     int marginTools = 40;
 
@@ -122,6 +122,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
     _sideList.setPreferredSize(new Dimension(100, 0));
     _sideList.addListSelectionListener(new ListSelectionListener()
     {
+      @Override
       public void valueChanged(ListSelectionEvent evt)
       {
         changeSelectedStructure_actionPerformed(evt);
@@ -281,15 +282,16 @@ 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
                     }
                   }
                 }
@@ -315,7 +317,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
   {
     private DefaultListModel<FullBackup> _rnalist;
 
-    private List<RNA> _rnas = new ArrayList<RNA>();
+    private List<RNA> _rnas = new ArrayList<>();
 
     JList _l;
 
@@ -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 +547,7 @@ 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);
   }