Further structure accessing feature

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index dcf745b..8197688 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -262,7 +262,16 @@ public class PopupMenu extends JPopupMenu
       //TODO: Something to check if it's an RNA
          //like: if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S')
          final SequenceI seqI = seq.getDatasetSequence();
-         //ap.getAlignment().get
+         AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+       
+
+         //for(int i=0; i<aa.length;i++){
+         final String rnastruc=aa[0].getRNAStruc();
+                 if(aa[0]._rnasecstr != null){
+                         System.out.println("Is RNA: "+aa[0].getRNAStruc()+" "+aa.length);
+                         
+                 }             
+         
          menuItem = new JMenuItem();
          menuItem.setText("RNA structure");
       menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -270,11 +279,12 @@ public class PopupMenu extends JPopupMenu
         public void actionPerformed(ActionEvent e)
         {
                System.out.println("Call Varna "+seqI.getSequenceAsString()+" "+seqI.getName());
-               new AppVarna(seqI.getSequenceAsString(),seqI.getName());
+               new AppVarna(seqI.getSequenceAsString(),rnastruc,seqI.getName());
                
         }
-      });
+      });        
       viewStructureMenu.add(menuItem);
+         
       //}