From f48809e82f26d2460882d3f2a64503fcb83670e5 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 29 Jun 2010 10:07:12 +0000
Subject: [PATCH] fix so that multiple locus_tags are not written out
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14122 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index 50f3ae163..cb1b78444 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
@@ -232,7 +232,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
{
final Feature protein = chadoGene.getProteinOfTranscript(transcriptName);
if(protein != null)
- combineQualifiers(qualifiers, protein.getQualifiers().copy());
+ combineQualifiers(qualifiers, protein.getQualifiers().copy(), false);
if(transcript != null)
ntranscripts = handleTranscripts(qualifiers, transcript, ntranscripts, chadoGene);
@@ -250,7 +250,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
addNewQualifier(qualifiers, newIDQualifier);
geneQualifiers.removeQualifierByName("ID");
}
- combineQualifiers(qualifiers, geneQualifiers);
+ combineQualifiers(qualifiers, geneQualifiers, true);
}
try
@@ -359,15 +359,15 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
* @param newQualifiers
*/
private void combineQualifiers(final QualifierVector qualifiers,
- final QualifierVector newQualifiers)
+ final QualifierVector newQualifiers,
+ final boolean isGene)
{
Qualifier qualifier;
for(int i=0; i<newQualifiers.size(); i++)
{
Qualifier newQualifier = (Qualifier) newQualifiers.get(i);
- if( newQualifier.getName().equals("ID") &&
- ((String)newQualifier.getValues().get(0)).indexOf(':') > -1 )
+ if( newQualifier.getName().equals("ID") && !isGene )
{
continue;
}
@@ -496,7 +496,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
ChadoCanonicalGene chadoGene)
{
QualifierVector transcriptQualifiers = transcript.getQualifiers().copy();
- combineQualifiers(qualifiers, transcriptQualifiers);
+ combineQualifiers(qualifiers, transcriptQualifiers, false);
ntranscripts = chadoGene.getTranscripts().size();
if(ntranscripts > 1)
{
--
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