From eb4c971f200959664cb2b609ce912c9abc6f436a Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 1 Apr 2008 10:14:04 +0000
Subject: [PATCH] fix to write embl from database
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@7254 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/io/PublicDBDocumentEntry.java | 29 ++++++++++++-------
1 file changed, 19 insertions(+), 10 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index dcd7a10b7..afa5d71b5 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 1.6 2008-01-24 15:45:37 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java,v 1.7 2008-04-01 10:14:04 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -36,7 +36,7 @@ import java.io.IOException;
* entry.
*
* @author Kim Rutherford
- * @version $Id: PublicDBDocumentEntry.java,v 1.6 2008-01-24 15:45:37 tjc Exp $
+ * @version $Id: PublicDBDocumentEntry.java,v 1.7 2008-04-01 10:14:04 tjc Exp $
**/
public class PublicDBDocumentEntry extends SimpleDocumentEntry
@@ -146,16 +146,20 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
Key key = feature.getKey();
QualifierVector qualifiers = feature.getQualifiers().copy();
- if(key.getKeyString().equals("transcript"))
- key = new Key("mRNA");
- if(key.getKeyString().equals("mRNA"))
+ if(key.getKeyString().equals(DatabaseDocument.EXONMODEL))
{
- // add protein qualifiers to transcript
- final String transcriptName = GeneUtils.getUniqueName(feature);
- final Feature protein =
- ((GFFStreamFeature)feature).getChadoGene().getProteinOfTranscript(transcriptName);
+ ChadoCanonicalGene chadoGene = ((GFFStreamFeature)feature).getChadoGene();
+
+ final String name = GeneUtils.getUniqueName(feature);
+ final String transcriptName = chadoGene.getTranscriptFromName(name);
+
+ // add protein qualifiers to CDS
+ final Feature protein = chadoGene.getProteinOfTranscript(transcriptName);
if(protein != null)
qualifiers.addAll(protein.getQualifiers().copy());
+
+ // add gene qualifiers to CDS
+ qualifiers.addAll(chadoGene.getGene().getQualifiers().copy());
}
try
@@ -185,7 +189,12 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
key = new Key("5'UTR");
else if(key.getKeyString().equals("three_prime_UTR"))
key = new Key("3'UTR");
- else if(key.getKeyString().equals("polypepide"))
+ else if(key.getKeyString().equals("polypeptide"))
+ return null;
+ else if(key.getKeyString().equals("gene"))
+ return null;
+ else if(key.getKeyString().equals("transcript") ||
+ key.getKeyString().equals("mRNA"))
return null;
else if(key.getKeyString().startsWith("pseudo"))
{
--
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