From ac5afac89ed48593d2bb52bf5aee1166f2610bf3 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 8 May 2009 08:35:46 +0000
Subject: [PATCH] check for primary dbxref in addLazyQualifiers()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10750 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../components/genebuilder/GeneUtils.java | 61 +++++++++++--------
1 file changed, 37 insertions(+), 24 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
index 57d1d52a9..8c0e37fee 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
@@ -43,6 +43,7 @@ import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import org.gmod.schema.general.DbXRef;
import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureDbXRef;
import org.gmod.schema.sequence.FeaturePub;
@@ -136,6 +137,17 @@ public class GeneUtils
}
// dbxrefs
+ if(feature.getQualifierByName("Dbxref") == null)
+ {
+ DbXRef dbxref = feature.getChadoLazyFeature().getDbXRef();
+ if(dbxref != null)
+ {
+ String value = dbxref.getDb().getName() + ":" +
+ dbxref.getAccession();
+ feature.getQualifiers().setQualifier(new Qualifier("Dbxref", value));
+ }
+ }
+
final Collection featureDbXRefs = feature.getChadoLazyFeature().getFeatureDbXRefs();
final Iterator it2 = featureDbXRefs.iterator();
while(it2.hasNext())
@@ -155,39 +167,40 @@ public class GeneUtils
// feature cvterms (GO, product....)
final Collection featureCvTerms = feature.getChadoLazyFeature().getFeatureCvTerms();
- final Iterator it3 = featureCvTerms.iterator();
-
- while(it3.hasNext())
+ if(featureCvTerms != null)
{
- FeatureCvTerm featureCvTerm = (FeatureCvTerm)it3.next();
- List featureCvTermDbXRefList = null;
-
- if(featureCvTerm.getFeatureCvTermDbXRefs() != null)
- featureCvTermDbXRefList = new Vector(featureCvTerm.getFeatureCvTermDbXRefs());
+ final Iterator it3 = featureCvTerms.iterator();
+ while(it3.hasNext())
+ {
+ FeatureCvTerm featureCvTerm = (FeatureCvTerm)it3.next();
+ List featureCvTermDbXRefList = null;
+
+ if(featureCvTerm.getFeatureCvTermDbXRefs() != null)
+ featureCvTermDbXRefList = new Vector(featureCvTerm.getFeatureCvTermDbXRefs());
- List featureCvTermPubList = null;
+ List featureCvTermPubList = null;
- if(featureCvTerm.getFeatureCvTermPubs() != null)
- featureCvTermPubList = new Vector(featureCvTerm.getFeatureCvTermPubs());
+ if(featureCvTerm.getFeatureCvTermPubs() != null)
+ featureCvTermPubList = new Vector(featureCvTerm.getFeatureCvTermPubs());
- ByteBuffer this_buff = new ByteBuffer();
- DatabaseDocument.appendControlledVocabulary(this_buff, null, featureCvTerm,
+ ByteBuffer this_buff = new ByteBuffer();
+ DatabaseDocument.appendControlledVocabulary(this_buff, null, featureCvTerm,
featureCvTermDbXRefList,featureCvTermPubList, null, false);
- final String qualifierString = new String(this_buff.getBytes());
- int ind = qualifierString.indexOf('=');
- final String name = qualifierString.substring(0, ind);
- final String value = GFFStreamFeature.decode(
+ final String qualifierString = new String(this_buff.getBytes());
+ int ind = qualifierString.indexOf('=');
+ final String name = qualifierString.substring(0, ind);
+ final String value = GFFStreamFeature.decode(
qualifierString.substring(ind+1, qualifierString.length()-1));
- Qualifier qualifier = feature.getQualifiers().getQualifierByName(name);
- if(qualifier == null)
- qualifier = new Qualifier(name, value);
- else
- qualifier.addValue(value);
- feature.getQualifiers().setQualifier(qualifier);
+ Qualifier qualifier = feature.getQualifiers().getQualifierByName(name);
+ if(qualifier == null)
+ qualifier = new Qualifier(name, value);
+ else
+ qualifier.addValue(value);
+ feature.getQualifiers().setQualifier(qualifier);
+ }
}
-
// feature pubs - literature
final Collection featurePubs = feature.getChadoLazyFeature().getFeaturePubs();
--
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