From dd58d5e578c43c69b57db9d3724c23d556d717ce Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 30 Nov 2006 10:02:14 +0000
Subject: [PATCH] add FeatureCvTermPubs
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5044 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 79 +++++++++++++++++--
1 file changed, 72 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index a14ccbed2..096e06712 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -43,6 +43,7 @@ import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.sequence.FeatureCvTermDbXRef;
+import org.gmod.schema.sequence.FeatureCvTermPub;
import org.gmod.schema.cv.CvTerm;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
@@ -503,6 +504,8 @@ public class DatabaseDocument extends Document
Hashtable featureCvTerms = getFeatureCvTermsByFeature(dao);
Hashtable featureCvTermDbXRefs = getFeatureCvTermDbXRef(dao);
+ Hashtable featureCvTermPubs = getFeatureCvTermPub(dao);
+
List pubDbXRefs= dao.getPubDbXRef();
// create gff byte stream
@@ -522,7 +525,8 @@ public class DatabaseDocument extends Document
chadoToGFF(feat, parentFeature.getUniqueName(),
dbxrefs, synonym, featureCvTerms,
- pubDbXRefs, featureCvTermDbXRefs, id_store, dao,
+ pubDbXRefs, featureCvTermDbXRefs, featureCvTermPubs,
+ id_store, dao,
feat.getFeatureLoc(), this_buff);
if( i%10 == 0 || i == feature_size-1)
@@ -592,7 +596,7 @@ public class DatabaseDocument extends Document
private Hashtable getFeatureCvTermDbXRef(final GmodDAO dao)
{
- List list = dao.getFeatureCvTermDbXRef(null);
+ List list = dao.getFeatureCvTermDbXRefByFeature(null);
if(list == null || list.size() == 0)
return null;
@@ -620,6 +624,36 @@ public class DatabaseDocument extends Document
return featureCvTermDbXRefs;
}
+ private Hashtable getFeatureCvTermPub(final GmodDAO dao)
+ {
+ List list = dao.getFeatureCvTermPubByFeature(null);
+ if(list == null || list.size() == 0)
+ return null;
+
+ Integer featureCvTermId;
+ List value;
+
+ Hashtable featureCvTermPubs = new Hashtable(list.size());
+ for(int i=0; i<list.size(); i++)
+ {
+ FeatureCvTermPub featureCvTermPub =
+ (FeatureCvTermPub)list.get(i);
+
+ featureCvTermId = new Integer(
+ featureCvTermPub.getFeatureCvTerm().getFeatureCvTermId());
+
+ if(featureCvTermPubs.containsKey(featureCvTermId))
+ value = (Vector)featureCvTermPubs.get(featureCvTermId);
+ else
+ value = new Vector();
+
+ value.add(featureCvTermPub);
+ featureCvTermPubs.put(featureCvTermId, value);
+ }
+
+ return featureCvTermPubs;
+ }
+
/**
* Use by the gene editor to retrieve the gene and related
* features
@@ -663,7 +697,7 @@ public class DatabaseDocument extends Document
ByteBuffer buff = new ByteBuffer();
- chadoToGFF(feature, null, null, null, null, null, null, null, dao,
+ chadoToGFF(feature, null, null, null, null, null, null, null, null, dao,
featureloc, buff);
// get children of gene
@@ -683,7 +717,7 @@ public class DatabaseDocument extends Document
FeatureLoc loc = getFeatureLoc(new Vector(
transcript.getFeatureLocsForFeatureId()), src_id);
- chadoToGFF(transcript, feature.getUniqueName(), null, null,
+ chadoToGFF(transcript, feature.getUniqueName(), null, null, null,
null, null, null, id_store, dao, loc, buff);
// get children of transcript - exons and pp
@@ -703,7 +737,7 @@ public class DatabaseDocument extends Document
loc = getFeatureLoc(
new Vector(child.getFeatureLocsForFeatureId()),src_id);
- chadoToGFF(child, transcript.getUniqueName(), null,null,
+ chadoToGFF(child, transcript.getUniqueName(), null,null, null,
null, null, null, id_store, dao, loc, buff);
}
}
@@ -733,6 +767,7 @@ public class DatabaseDocument extends Document
final Hashtable featureCvTerms,
final List pubDbXRefs,
final Hashtable featureCvTermDbXRefs,
+ final Hashtable featureCvTermPubs,
final Hashtable id_store,
final GmodDAO dao,
final FeatureLoc featureloc,
@@ -914,9 +949,11 @@ public class DatabaseDocument extends Document
List featureCvTermDbXRefList =
(List)featureCvTermDbXRefs.get(featureCvTermId);
+
+ List featureCvTermPubList = (List)featureCvTermPubs.get(featureCvTermId);
appendControlledVocabulary(this_buff, dao, feature_cvterm,
- featureCvTermDbXRefList, pubDbXRefs);
+ featureCvTermDbXRefList,featureCvTermPubList, pubDbXRefs);
}
//System.out.println(new String(this_buff.getBytes()));
}
@@ -935,6 +972,7 @@ public class DatabaseDocument extends Document
final GmodDAO dao,
final FeatureCvTerm feature_cvterm,
final List featureCvTermDbXRefs,
+ final List featureCvTermPubs,
final List pubDbXRefs)
{
CvTerm cvterm = getCvTerm( feature_cvterm.getCvTerm().getCvTermId(), dao);
@@ -1029,14 +1067,41 @@ public class DatabaseDocument extends Document
attr_buff.append("term="+feature_cvterm.getCvTerm().getName()+"%3B");
// PMID
+ int nfound_pub = 0;
if(feature_cvterm.getPub().getUniqueName() != null &&
!feature_cvterm.getPub().getUniqueName().equals("NULL"))
{
Pub pub = feature_cvterm.getPub();
attr_buff.append("db_xref="+
- pub.getUniqueName()+ "%3B");
+ pub.getUniqueName());
+ nfound_pub++;
+ }
+
+ 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_pub == 0)
+ attr_buff.append("db_xref=");
+ else if(nfound_pub > 1)
+ attr_buff.append("|");
+
+ attr_buff.append(featureCvTermPub.getPub().getUniqueName());
+ nfound_pub++;
+ }
}
+ if(nfound_pub > 0)
+ attr_buff.append("%3B");
+
if(featureCvTermDbXRefs != null &&
featureCvTermDbXRefs.size() > 0 )
{
--
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