From d19c3f1bc3b1734775ff616ca29320d14d8b6026 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 1 Sep 2009 11:19:10 +0000
Subject: [PATCH] changes to handle ortho/paralogs that do not have a match
feature but just have a feature_relationship link
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11678 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/chado/ArtemisUtils.java | 16 ++++-
.../chado/ChadoTransactionManager.java | 63 ++++++++++++++++---
.../chado/ClusterLazyQualifierValue.java | 4 +-
3 files changed, 72 insertions(+), 11 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/ArtemisUtils.java b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
index 82e76f486..8fb15c642 100644
--- a/uk/ac/sanger/artemis/chado/ArtemisUtils.java
+++ b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
@@ -518,7 +518,8 @@ public class ArtemisUtils
* @return
*/
protected static Feature getMatchFeatureWithFeatureRelations(final String uniqueName,
- final String qualifierName, String qualifierString, final GFFStreamFeature feature)
+ final String qualifierName, String qualifierString, final GFFStreamFeature feature,
+ final boolean isDelete)
{
final int queryFeatureId;
@@ -559,7 +560,18 @@ public class ArtemisUtils
String matchName = getString(qualifierStrings, "match_name");
String clusterName = getString(qualifierStrings, "cluster_name");
if(!matchName.equals(""))
- matchFeature.setUniqueName(matchName.substring(11));
+ {
+ // there is no match feature just a direct feature_relationship link
+ if(link.equals(matchName.substring(11)))
+ {
+ if(isDelete)
+ return null;
+ else
+ matchFeature.setUniqueName("ORTHO_PARA_" + uniqueName + "_" + link);
+ }
+ else
+ matchFeature.setUniqueName(matchName.substring(11));
+ }
else if(!clusterName.equals(""))
matchFeature.setUniqueName(clusterName.substring(13));
else
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 4f5617230..d168e2082 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -98,7 +98,7 @@ public class ChadoTransactionManager
org.apache.log4j.Logger.getLogger(ChadoTransactionManager.class);
public static boolean addSegments = true;
- private Vector sql = new Vector();
+ private Vector<ChadoTransaction> sql = new Vector<ChadoTransaction>();
/** GFF3 predefined tags, i.e. not feature_prop's */
private static String reserved_tags[] =
@@ -1644,13 +1644,21 @@ public class ChadoTransactionManager
org.gmod.schema.sequence.Feature matchFeature =
ArtemisUtils.getMatchFeatureWithFeatureRelations(uniquename, qualifierName,
- qualifierString, feature);
+ qualifierString, feature, true);
- tsn = new ChadoTransaction(ChadoTransaction.DELETE,
- matchFeature,
- null, (GFFStreamFeature)null, feature.getKey().getKeyString(),
- qualifierName.toUpperCase()+ ": ID="+uniquename+" "+qualifierString);
- sql.add(tsn);
+ if(matchFeature == null)
+ {
+ logger4j.debug("NO MATCH FEATURE FOUND. DELETE FEATURE_RELATIONSHIP");
+ deleteFeatureRelationShip(qualifierName, qualifierString, uniquename, feature);
+ }
+ else
+ {
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ matchFeature,
+ null, (GFFStreamFeature)null, feature.getKey().getKeyString(),
+ qualifierName.toUpperCase()+ ": ID="+uniquename+" "+qualifierString);
+ sql.add(tsn);
+ }
}
else
logger4j.warn("Ignoring reserved tag missing : "+qualifierName);
@@ -1839,7 +1847,7 @@ public class ChadoTransactionManager
org.gmod.schema.sequence.Feature matchFeature =
ArtemisUtils.getMatchFeatureWithFeatureRelations(uniquename, qualifierName,
- qualifierString, feature);
+ qualifierString, feature, false);
if(isDuplicate)
{
@@ -2373,6 +2381,45 @@ public class ChadoTransactionManager
return feature_cvterm;
}
+ private void deleteFeatureRelationShip(final String qualifierName,
+ final String qualifierString,
+ final String uniquename,
+ final GFFStreamFeature feature)
+ {
+ FeatureRelationship fr = new FeatureRelationship();
+
+ // orthologous_to or paralogous_to should be retrieved from sequence ontology !!
+ CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(qualifierName, "sequence");
+
+ org.gmod.schema.sequence.Feature objectFeature = new org.gmod.schema.sequence.Feature();
+ objectFeature.setUniqueName(uniquename);
+
+ int index1 = qualifierString.indexOf("link=")+5;
+ int index2 = qualifierString.indexOf("type=");
+ String link = qualifierString.substring(index1, index2).trim();
+ org.gmod.schema.sequence.Feature subjectFeature = new org.gmod.schema.sequence.Feature();
+ subjectFeature.setUniqueName(link);
+
+ fr.setFeatureByObjectId(objectFeature);
+ fr.setFeatureBySubjectId(subjectFeature);
+ fr.setCvTerm(cvterm);
+
+ ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ fr,
+ null, (GFFStreamFeature)null, feature.getKey().getKeyString(),
+ qualifierName.toUpperCase()+ ": ID="+uniquename+" "+qualifierString);
+ sql.add(tsn);
+
+
+ fr.setFeatureByObjectId(subjectFeature);
+ fr.setFeatureBySubjectId(objectFeature);
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ fr,
+ null, (GFFStreamFeature)null, feature.getKey().getKeyString(),
+ qualifierName.toUpperCase()+ ": ID="+uniquename+" "+qualifierString);
+ sql.add(tsn);
+ }
+
public static CvTerm getCvTerm(final String cvTermName, final String cvName,
final String definition,
final String dbName)
diff --git a/uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java b/uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java
index 2dd48b219..5053caaae 100644
--- a/uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java
+++ b/uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java
@@ -204,7 +204,9 @@ public class ClusterLazyQualifierValue implements LazyQualifierValue
String product = getProduct(matchFeature);
if(product != null)
- value = value.concat("; product="+product);
+ value = value.concat(";product="+product);
+
+ value = value.concat(";match_name="+matchFeature.getUniqueName());
}
continue;
--
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