move isSelenocysteine() to GFFUtils

uk/ac/sanger/artemis/io/GFFStreamFeature.java

@@ -1319,67 +1319,4 @@ public class GFFStreamFeature extends SimpleDocumentFeature
     }
     return false;
   }
-  
-  /**
-   * Test if this is feature is marked as having a stop codon
-   * redefined as selenocysteine
-   * @param f
-   * @return
-   */
-  public static boolean isSelenocysteine(Feature f)
-  {
-    if(!(f instanceof GFFStreamFeature))
-      return false;
-    try
-    {
-      ChadoCanonicalGene gffGene = ((GFFStreamFeature)f).getChadoGene();
-      if(gffGene == null)
-        return false;
-      String transcript = gffGene.getTranscriptFromName(
-          GeneUtils.getUniqueName(f));
-      if(transcript == null)
-        return false;
-      Feature pep = gffGene.getProteinOfTranscript(transcript);
-      if(pep == null)
-        return false;
-      if(pep.getQualifierByName("stop_codon_redefined_as_selenocysteine") != null)
-        return true;
-    }
-    catch (Exception e){}
-
-    return false;
-  }
-  
-  public static void main(String args[])
-  {
-    Key key = new Key("region");
-    try
-    {
-      final EntryInformation entry_information =
-        SimpleEntryInformation.getDefaultEntryInformation ();
-      GFFDocumentEntry entry = new GFFDocumentEntry(entry_information);
-
-      Location location = new Location("1003..1222");
-      QualifierVector qualifiers = new QualifierVector();
-      GFFStreamFeature f = new GFFStreamFeature(key, location, qualifiers);
-      entry.add(f);
-      
-      java.io.File aFile = new java.io.File("x");
-      java.io.FileWriter writer = new java.io.FileWriter(aFile);
-      f.writeToStream(writer);
-      writer.close();
-    }
-    catch (LocationParseException e)
-    {
-      e.printStackTrace();
-    }
-    catch (IOException e)
-    {
-      e.printStackTrace();
-    }
-    catch (EntryInformationException e)
-    {
-      e.printStackTrace();
-    }
-  }
 }