X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=82ce8359874e9964066a88f7d468c3544eaf4c2c;hb=9a05eeccaf18e0c82cd183f0b84a8be42bf181c7;hp=8197688f7c9dd6ab6f6f19b4f3774c61f321a7cb;hpb=ecb2c593fb296f6908deb65492835fac476b2378;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8197688..82ce835 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -161,8 +161,8 @@ public class PopupMenu extends JPopupMenu
    * @param links
    * @param groupLinks
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
-          Vector groupLinks)
+  public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links,
+          final Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -253,40 +253,40 @@ public class PopupMenu extends JPopupMenu
         }
       }
       else
-      {	  
-        //JAN structureMenu.remove(viewStructureMenu);
+      {	
+    	  if(ap.av.alignment.isNucleotide()==false){
+    		  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);
-	  
-      //}
-     
+      if(ap.av.alignment.isNucleotide()==true){
+    	  AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    	  String rnastruc=new String();
+    	  for(int i=0; i<aa.length;i++){
+    		  if(aa[i]._rnasecstr != null){
+    			  rnastruc=aa[i].getRNAStruc();
+    			  break;
+    		  }
+    	  }
+    	  
+    	  SequenceGroup a = aa[0].groupRef;
+
+    	  //TODO: make rnastrucF a bit more nice
+    	  final String rnastrucF=rnastruc;
+    	  menuItem = new JMenuItem();
+    	  menuItem.setText("RNA structure");
+    	  menuItem.addActionListener(new java.awt.event.ActionListener()
+    	  {
+    		  public void actionPerformed(ActionEvent e)
+    		  {
+    			  System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
+    			  //TODO: VARNA does'nt print gaps in the sequence
+    			  new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName(),ap);
+    		  }
+		  	});	  
+		  	viewStructureMenu.add(menuItem);
+      	}
 
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()