diff --git a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java index 537ebd0b13eb961f8e7328526f7a7f045148ae9d..05d71f4aef4e7da723a516ee31530a2691569397 100644 --- a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java +++ b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.41 2007-03-28 09:16:10 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.42 2007-04-13 07:50:15 tjc Exp $ */ package uk.ac.sanger.artemis.io; @@ -42,7 +42,7 @@ import java.sql.Timestamp; * A DocumentEntry that can read an GFF entry from a Document. * * @author Kim Rutherford - * @version $Id: GFFDocumentEntry.java,v 1.41 2007-03-28 09:16:10 tjc Exp $ + * @version $Id: GFFDocumentEntry.java,v 1.42 2007-04-13 07:50:15 tjc Exp $ **/ public class GFFDocumentEntry extends SimpleDocumentEntry @@ -159,7 +159,7 @@ public class GFFDocumentEntry extends SimpleDocumentEntry this_feature = original_features.featureAt(i); String key = this_feature.getKey().getKeyString(); - if(key.equals("gene")) + if(key.equals("gene") || key.equals("pseudogene")) { String id = (String)this_feature.getQualifierByName("ID").getValues().get(0); ChadoCanonicalGene gene = new ChadoCanonicalGene(); @@ -242,7 +242,8 @@ public class GFFDocumentEntry extends SimpleDocumentEntry gene.add3PrimeUtr(parent, this_feature); else if(key.equals("five_prime_UTR")) gene.add5PrimeUtr(parent, this_feature); - else if(key.equals("exon") || featureRelationship != null) + else if(key.equals("exon") || featureRelationship != null || + key.equals("pseudogenic_exon")) gene.addSplicedFeatures(parent, this_feature); else gene.addOtherFeatures(parent, this_feature);