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 a2b4ee3..8197688 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -253,25 +253,40 @@ public class PopupMenu extends JPopupMenu
         }
       }
       else
-      {
-         //TODO: Something to check if it's an RNA
-         //like: if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S')
-         menuItem = new JMenuItem();
-         menuItem.setText("RNA structure");
-          menuItem.addActionListener(new java.awt.event.ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-               System.out.println("Call Varna");
-               new AppVarna();
-               
-            }
-          });
-          viewStructureMenu.add(menuItem);
-         
+      {          
         //JAN structureMenu.remove(viewStructureMenu);
         // structureMenu.remove(colStructureMenu);
       }
+      
+      //if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S'){
+      //TODO: Something to check if it's an RNA
+         //like: if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S')
+         final SequenceI seqI = seq.getDatasetSequence();
+         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()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+               System.out.println("Call Varna "+seqI.getSequenceAsString()+" "+seqI.getName());
+               new AppVarna(seqI.getSequenceAsString(),rnastruc,seqI.getName());
+               
+        }
+      });        
+      viewStructureMenu.add(menuItem);
+         
+      //}
+     
 
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()