give a warning if the reference feature names do not match the contig names in the VCF

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14677 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/variant/VCFview.java

@@ -632,6 +632,14 @@ public class VCFview extends JPanel
           }
         }
       }
+      
+      if(offsetLengths.size() != contigs.length)
+        JOptionPane.showMessageDialog(this, 
+            "There is a problem matching the reference sequences\n"+
+            "to the names in the VCF file. This may mean the labels\n"+
+            "on the reference features do not match those in the in\n"+
+            "the VCF file.", 
+            "Problem Found", JOptionPane.WARNING_MESSAGE);
     }
     return offsetLengths.get(refName);
   }