X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=1b95afbacbfb1e9e2129b74529985f2154eb3472;hb=aebfa57bbc491dfa8c231704a385ed14f6a5e8ae;hp=0bc84cec72da137deb817f3fd1068d78b9920678;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 0bc84ce..1b95afb 100644
--- 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 
@@ -37,10 +37,8 @@ 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;
@@ -352,7 +350,7 @@ 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);
 
@@ -653,22 +651,23 @@ 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)
-                    {
-                    r.drawRNA(vp.getConfig());
-                    String name = r.getName();
-                    if (name.equals(""))
-                    {
-                      name = path.substring(path
-                              .lastIndexOf(File.separatorChar) + 1);
-                    }
-                    if (mdls.size()>1)
+                    int mn = 1;
+                    Collection<RNA> mdls = fr.orsay.lri.varna.factories.RNAFactory
+                            .loadSecStr(path);
+                    for (RNA r : mdls)
                     {
-                      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);
                     }
                   }
                 }
@@ -810,7 +809,12 @@ 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)
@@ -949,4 +953,4 @@ 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
+ */