Merge branch 'JAL-1347' into develop

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

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 87bbae3..61c44c2 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -37,28 +37,20 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.io.File;
-import java.text.DateFormat;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Date;
 import java.util.List;
 
 import javax.swing.DefaultListModel;
 import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
 import javax.swing.JButton;
-import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JList;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
 import javax.swing.JTextField;
 import javax.swing.ListModel;
 import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
@@ -148,19 +140,19 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
   {
     // super("VARNA in Jalview");
     initVarna(seq, struc);
-    System.out.println("here(1)");
+   
   }
 
   public AppVarnaBinding(ArrayList<RNA> rnaList)
   {
-        System.out.println("here(2)");
+
     // super("VARNA in Jalview");
     initVarnaEdit(rnaList);
   }
 
   private void initVarna(String seq, String str)
   {
-         System.out.println("initialisation VARNA (appvarnabinding");
+         
     DefaultListModel dlm = new DefaultListModel();
 
     DefaultListSelectionModel m = new DefaultListSelectionModel();
@@ -193,7 +185,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
     try
     {
-    System.out.println("here");
+    
       vp = new VARNAPanel("0", ".");
       _RNA1.setRNA(seq, str);
       _RNA1.drawRNARadiate(vp.getConfig());
@@ -222,7 +214,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   private void initVarnaEdit(ArrayList<RNA> rnaInList)
   {
-        System.out.println("initialisation VARNA(2) (appvarnabinding");
+       
     DefaultListModel dlm = new DefaultListModel();
 
     int marginTools = 40;
@@ -246,7 +238,8 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
           FullBackup sel = (FullBackup) _sideList.getSelectedValue();
           Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
                   .getSize(), sel.rna.getSize());
-          vp.showRNAInterpolated(sel.rna, sel.config, map);
+          //vp.showRNAInterpolated(sel.rna, sel.config, map);
+          vp.showRNA(sel.rna, sel.config);
           // _seq.setText(sel.rna.getSeq());
           _str.setText(sel.rna.getStructDBN());
         }
@@ -256,12 +249,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
     try
     {
-       System.out.println("here(plop)");
+       
       vp = new VARNAPanel("0", ".");
       for (int i = 0; i < rnaInList.size(); i++)
       {
         rnaInList.get(i).drawRNARadiate(vp.getConfig());
-        System.out.println(i);
+       
       }
     } catch (ExceptionNonEqualLength e)
     {
@@ -351,7 +344,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
     JLabel j = new JLabel("Structures Manager", JLabel.CENTER);
     _listPanel.setLayout(new BorderLayout());
 
-    //_listPanel.add(ops, BorderLayout.SOUTH);
+    // _listPanel.add(ops, BorderLayout.SOUTH);
     _listPanel.add(j, BorderLayout.NORTH);
     _listPanel.add(listScroller, BorderLayout.CENTER);
 
@@ -652,22 +645,23 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
                     _rnaList.add(bck.config, bck.rna, bck.name, true);
                   } catch (ExceptionLoadingFailed e3)
                   {
-                    int mn=1;
-                    Collection<RNA> mdls=fr.orsay.lri.varna.factories.RNAFactory.loadSecStr(path);
-                    for (RNA r:mdls)
+                    int mn = 1;
+                    Collection<RNA> mdls = fr.orsay.lri.varna.factories.RNAFactory
+                            .loadSecStr(path);
+                    for (RNA r : mdls)
                     {
-                    r.drawRNA(vp.getConfig());
-                    String name = r.getName();
-                    if (name.equals(""))
-                    {
-                      name = path.substring(path
-                              .lastIndexOf(File.separatorChar) + 1);
-                    }
-                    if (mdls.size()>1)
-                    {
-                      name += " (Model "+mn+++")";
-                    }
-                    _rnaList.add(vp.getConfig().clone(), r, name, true);
+                      r.drawRNA(vp.getConfig());
+                      String name = r.getName();
+                      if (name.equals(""))
+                      {
+                        name = path.substring(path
+                                .lastIndexOf(File.separatorChar) + 1);
+                      }
+                      if (mdls.size() > 1)
+                      {
+                        name += " (Model " + mn++ + ")";
+                      }
+                      _rnaList.add(vp.getConfig().clone(), r, name, true);
                     }
                   }
                 }
@@ -809,7 +803,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   public void onUINewStructure(VARNAConfig v, RNA r)
   {
-    _rnaList.add(v, r, "", true);
+    // patch to fix infinite loop
+    // The problem is that onUINewStructure is called when user clicks 
+    // check with Yann about whether Jalview should do anything with this event.
+    // e.g. if user has used VARNA's menu to import a structure .. Jalview may need to be told which structure is displayed.
+    
+    // _rnaList.add(v, r, "", true);
   }
 
   public void onWarningEmitted(String s)
@@ -939,6 +938,20 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
     // TODO Auto-generated method stub
 
   }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }
 
 /*
@@ -948,4 +961,4 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
  * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
  * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
  * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
- */
\ No newline at end of file
+ */