From 49f7baf461f2145484d808c44bd915077cdf9d1b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 16 Sep 2008 14:42:12 +0000
Subject: [PATCH] add ignore obsolete flag and remove CDS on non-coding
transcript
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8851 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/io/PublicDBDocumentEntry.java | 29 +++++++++++++++++--
1 file changed, 26 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index 933188b0a..3ca06a356 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 1.16 2008-07-16 10:12:44 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java,v 1.17 2008-09-16 14:42:12 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 1.16 2008-07-16 10:12:44 tjc Exp $
+ * @version $Id: PublicDBDocumentEntry.java,v 1.17 2008-09-16 14:42:12 tjc Exp $
**/
public class PublicDBDocumentEntry extends SimpleDocumentEntry
@@ -57,6 +57,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
// database qualifiers to ignore when converting to embl
private static Object[] DATABASE_QUALIFIERS_TO_REMOVE;
+ public static boolean IGNORE_OBSOLETE_FEATURES = true;
/**
* Create a new PublicDBDocumentEntry object associated with the given
@@ -157,6 +158,18 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
Key key = feature.getKey();
QualifierVector qualifiers = feature.getQualifiers().copy();
+ // ignore if obsolete
+ if(IGNORE_OBSOLETE_FEATURES)
+ {
+ Qualifier isObsoleteQualifier = qualifiers.getQualifierByName("isObsolete");
+ if(isObsoleteQualifier != null)
+ {
+ String value = (String)isObsoleteQualifier.getValues().get(0);
+ if(Boolean.parseBoolean(value))
+ return null;
+ }
+ }
+
key = map(key, qualifiers);
if(getEntryInformation().isValidQualifier((String) DATABASE_QUALIFIERS_TO_REMOVE[0]))
{
@@ -189,12 +202,22 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
final String name = GeneUtils.getUniqueName(feature);
final String transcriptName = chadoGene.getTranscriptFromName(name);
- // add protein qualifiers to CDS
+ StringVector sv = new StringVector();
+ sv.add(transcriptName);
+ final Feature transcript = chadoGene.containsTranscript(sv);
+
+ if(transcript != null && GeneUtils.isNonCodingTranscripts(transcript.getKey()))
+ return null;
+
+ // add transcript & protein qualifiers to CDS
try
{
final Feature protein = chadoGene.getProteinOfTranscript(transcriptName);
if(protein != null)
combineQualifiers(qualifiers, protein.getQualifiers().copy());
+
+ if(transcript != null)
+ combineQualifiers(qualifiers, transcript.getQualifiers().copy());
}
catch(NullPointerException npe){}
--
GitLab