From 2b8762992df7c9ee1a92c31ca7714e1418f15236 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 14 Oct 2008 10:11:39 +0000
Subject: [PATCH] changes for writing out uniquename
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9003 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index 3ca06a356..632f32e78 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.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/PublicDBDocumentEntry.java,v 1.17 2008-09-16 14:42:12 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java,v 1.18 2008-10-14 10:11:39 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -41,7 +41,7 @@ import java.util.Vector;
* entry.
*
* @author Kim Rutherford
- * @version $Id: PublicDBDocumentEntry.java,v 1.17 2008-09-16 14:42:12 tjc Exp $
+ * @version $Id: PublicDBDocumentEntry.java,v 1.18 2008-10-14 10:11:39 tjc Exp $
**/
public class PublicDBDocumentEntry extends SimpleDocumentEntry
@@ -209,6 +209,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
if(transcript != null && GeneUtils.isNonCodingTranscripts(transcript.getKey()))
return null;
+ qualifiers.removeQualifierByName("ID");
// add transcript & protein qualifiers to CDS
try
{
@@ -287,6 +288,10 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
{
Qualifier newQualifier = (Qualifier) newQualifiers.get(i);
+ if( newQualifier.getName().equals("ID") &&
+ ((String)newQualifier.getValues().get(0)).indexOf(':') > -1 )
+ continue;
+
if(newQualifier.getName().equals("orthologous_to"))
{
final StringVector newValues = newQualifier.getValues();
--
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