Add support RNAML format

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index c1bbc8d..3e589aa 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -23,6 +23,13 @@ import java.awt.*;
 import java.awt.event.*;
 
 import javax.swing.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 
 import MCview.*;
 import jalview.analysis.*;
@@ -277,8 +284,15 @@ public class PopupMenu extends JPopupMenu
             {
               public void actionPerformed(ActionEvent e)
               {
+                       System.out.println("1:"+structureLine);
+                       System.out.println("2:"+seq);
+                       System.out.println("3:"+seq.getSequenceAsString());
+                       System.out.println("4:"+rnastruc);
+                       System.out.println("5:"+seq.getName());
+                       System.out.println("6:"+ap);
                 new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
                         .getName(), ap);
+                       System.out.println("end");
               }
             });
             viewStructureMenu.add(menuItem);
@@ -304,6 +318,7 @@ public class PopupMenu extends JPopupMenu
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
+                
                   new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
                           .getName(), ap);
                 }
@@ -1004,7 +1019,24 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        pdbFromFile_actionPerformed();
+        try {
+                       pdbFromFile_actionPerformed();
+               } catch (ExceptionFileFormatOrSyntax e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (ParserConfigurationException e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (SAXException e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (ExceptionPermissionDenied e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (ExceptionLoadingFailed e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               }
       }
     });
     enterPDB.setText("Enter PDB Id");
@@ -1847,7 +1879,7 @@ public class PopupMenu extends JPopupMenu
     oal = null;
   }
 
-  public void pdbFromFile_actionPerformed()
+  public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));