last version stay many bugs ..

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index f6c1379..0e83c6e 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -30,6 +30,7 @@ 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 fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 
 import MCview.*;
 import jalview.analysis.*;
@@ -293,10 +294,12 @@ public class PopupMenu extends JPopupMenu
                 
                        //System.out.println("3:"+seq.getSequenceAsString());
                        System.out.println("3:strucseq"+rnastruc);
-                       System.out.println("4:struc"+seq.getRNA());
+                       //System.out.println("4:struc"+seq.getRNA());
                        System.out.println("5:name"+seq.getName());
                        System.out.println("6:ap"+ap);
-                new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+                       new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
+                            .getName(), ap);
+                       //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
                        System.out.println("end");
               }
             });
@@ -324,8 +327,9 @@ public class PopupMenu extends JPopupMenu
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
                 
-                  new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(), 
-                                 seq.getName(), ap);
+                  //new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+                  new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
+                          .getName(), ap);
                 }
               });
               viewStructureMenu.add(menuItem);
@@ -1049,6 +1053,9 @@ public class PopupMenu extends JPopupMenu
                } catch (InterruptedException e1) {
                        // TODO Auto-generated catch block
                        e1.printStackTrace();
+               } catch (ExceptionUnmatchedClosingParentheses e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
                }
       }
     });
@@ -1908,7 +1915,7 @@ public class PopupMenu extends JPopupMenu
     oal = null;
   }
 
-  public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));