From ac2d0fc14b8f7e8a37f45a784d3e637b35f98e81 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 13 Apr 2007 07:50:15 +0000
Subject: [PATCH] combine pseudogene features e.g. psuedogenic_exon
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5900 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/GFFDocumentEntry.java | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
index 537ebd0b1..05d71f4ae 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);
--
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