From c7db7e64ee23405d07ec7acec082af48066d2648 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 22 Mar 2011 16:23:03 +0000
Subject: [PATCH] add with/from to controlled_curation
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15788 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 50 +++++++++++++++----
1 file changed, 39 insertions(+), 11 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 29dbfbbb3..8586421bb 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -1544,33 +1544,61 @@ public class DatabaseDocument extends Document
attr_buff.append("db_xref="+ pub.getUniqueName());
nfound_dbxref++;
}
-
- if(featureCvTermDbXRefs != null &&
- featureCvTermDbXRefs.size() > 0)
+
+ if(featureCvTermPubs != null &&
+ featureCvTermPubs.size() > 0)
{
+ for(int i=0; i<featureCvTermPubs.size(); i++)
+ {
+ FeatureCvTermPub featureCvTermPub =
+ (FeatureCvTermPub)featureCvTermPubs.get(i);
+
+ if(feature_cvterm.getFeatureCvTermId() !=
+ featureCvTermPub.getFeatureCvTerm().getFeatureCvTermId())
+ continue;
+
+ if(nfound_dbxref == 0)
+ attr_buff.append("db_xref=");
+ else if(nfound_dbxref > 0)
+ attr_buff.append("|");
+
+ attr_buff.append(featureCvTermPub.getPub().getUniqueName());
+ nfound_dbxref++;
+ }
+ }
+ if(nfound_dbxref > 0)
+ attr_buff.append("%3B");
+
+ if(featureCvTermDbXRefs != null &&
+ featureCvTermDbXRefs.size() > 0 )
+ {
+ int nfound = 0;
for(int i=0; i<featureCvTermDbXRefs.size(); i++)
{
FeatureCvTermDbXRef featureCvTermDbXRef =
(FeatureCvTermDbXRef)featureCvTermDbXRefs.get(i);
-
+
if(feature_cvterm.getFeatureCvTermId() !=
featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
+ {
continue;
-
- if(nfound_dbxref == 0)
- attr_buff.append("db_xref=");
- else if(nfound_dbxref > 0)
+ }
+
+ if(nfound == 0)
+ attr_buff.append("with=");
+ else if(nfound > 0)
attr_buff.append("|");
DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
attr_buff.append(fc_dbXRef.getDb().getName()+":");
attr_buff.append(fc_dbXRef.getAccession());
- nfound_dbxref++;
+ nfound++;
}
+
+ if(nfound > 0)
+ attr_buff.append("%3B");
}
- if(nfound_dbxref > 0)
- attr_buff.append("%3B");
List feature_cvtermprops = (List) feature_cvterm.getFeatureCvTermProps();
for(int i = 0; i < feature_cvtermprops.size(); i++)
--
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