Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index d191212..ad91c20 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -46,20 +46,14 @@ 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;
 
@@ -149,16 +143,19 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
   {
     // super("VARNA in Jalview");
     initVarna(seq, struc);
+   
   }
 
   public AppVarnaBinding(ArrayList<RNA> rnaList)
   {
+
     // super("VARNA in Jalview");
     initVarnaEdit(rnaList);
   }
 
   private void initVarna(String seq, String str)
   {
+         
     DefaultListModel dlm = new DefaultListModel();
 
     DefaultListSelectionModel m = new DefaultListSelectionModel();
@@ -191,6 +188,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
     try
     {
+    
       vp = new VARNAPanel("0", ".");
       _RNA1.setRNA(seq, str);
       _RNA1.drawRNARadiate(vp.getConfig());
@@ -219,6 +217,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   private void initVarnaEdit(ArrayList<RNA> rnaInList)
   {
+       
     DefaultListModel dlm = new DefaultListModel();
 
     int marginTools = 40;
@@ -242,7 +241,8 @@ 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());
         }
@@ -252,10 +252,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
     try
     {
+       
       vp = new VARNAPanel("0", ".");
       for (int i = 0; i < rnaInList.size(); i++)
       {
         rnaInList.get(i).drawRNARadiate(vp.getConfig());
+       
       }
     } catch (ExceptionNonEqualLength e)
     {
@@ -804,7 +806,12 @@ 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)
@@ -934,6 +941,20 @@ 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
+    
+  }
 }
 
 /*