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 25af7d1..787ed53 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -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;
 
@@ -113,7 +113,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
     _sideList.addMouseListener(new MouseAdapter()
     {
       @Override
-      public void mouseClicked(MouseEvent e) {
+      public void mouseClicked(MouseEvent e)
+      {
         AppVarnaBinding.this.mouseClicked(e);
       }
     });
@@ -121,6 +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);
@@ -150,7 +152,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
     _listPanel.add(j, BorderLayout.NORTH);
     _listPanel.add(listScroller, BorderLayout.CENTER);
 
-    new DropTarget(vp, new DropTargetAdapter() {
+    new DropTarget(vp, new DropTargetAdapter()
+    {
       @Override
       public void drop(DropTargetDropEvent dtde)
       {
@@ -198,8 +201,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
 
   public String[][] getParameterInfo()
   {
-    String[][] info =
-    {
+    String[][] info = {
         // Parameter Name Kind of Value Description,
         { "sequenceDBN", "String", "A raw RNA sequence" },
         { "structureDBN", "String",
@@ -280,14 +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);
+                      _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
                     }
                   }
                 }
@@ -313,7 +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;
 
@@ -372,9 +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(); }
        */
@@ -382,7 +386,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return null;
   }
@@ -482,7 +486,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
        * restore the previous display
        */
       vp.showRNA(sel.rna, sel.config);
-      
+
       return filePath;
     } catch (IOException e)
     {
@@ -500,7 +504,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
    * 
    * @param evt
    */
-  protected void changeSelectedStructure_actionPerformed(ListSelectionEvent evt)
+  protected void changeSelectedStructure_actionPerformed(
+          ListSelectionEvent evt)
   {
     if (!evt.getValueIsAdjusting())
     {
@@ -542,7 +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);
   }