From d431fb5ea35e3c49dff193764916a21fa6496bdf Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 3 Sep 2009 10:44:13 +0000
Subject: [PATCH] add getChadoGeneByAnyCurrentName()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11694 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 34 +++++++++++++++++--
1 file changed, 31 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 32aa38328..7751d4a73 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -999,7 +999,7 @@ public class DatabaseDocument extends Document
final List schema_search,
GmodDAO dao,
final boolean readChildren)
- throws SQLException, ReadFormatException, ConnectException
+ throws SQLException, ReadFormatException, ConnectException, IOException
{
CvTermThread cvThread = null;
if(DatabaseDocument.cvterms == null)
@@ -1028,8 +1028,11 @@ public class DatabaseDocument extends Document
else
reset((String)getLocation(), (String)schema_search.get(0));
dao = getDAO();
- Feature chadoFeature =
- (Feature)(dao.getFeaturesByUniqueName(search_gene).get(0));
+
+ List features = dao.getFeaturesByUniqueName(search_gene);
+ if(features == null || features.size() == 0)
+ throw new IOException();
+ Feature chadoFeature = (Feature)(features.get(0));
ChadoCanonicalGene chado_gene = new ChadoCanonicalGene();
id_store.put(Integer.toString(chadoFeature.getFeatureId()),
@@ -2099,6 +2102,31 @@ public class DatabaseDocument extends Document
return feature;
}
+ /**
+ * Find the gene by the ID or synonym on the gene or transcript.
+ * @param id
+ * @return
+ */
+ public Feature getChadoGeneByAnyCurrentName(String id)
+ {
+ Feature chadoFeature =
+ (Feature)(getDAOOnly().getFeaturesByAnyCurrentName(id).get(0));
+
+ if(!chadoFeature.getCvTerm().equals("gene"))
+ {
+ Iterator<FeatureRelationship> parents =
+ chadoFeature.getFeatureRelationshipsForSubjectId().iterator();
+ while(parents.hasNext())
+ {
+ FeatureRelationship fr = parents.next();
+ Feature parent = fr.getFeatureByObjectId();
+ if(parent.getCvTerm().getName().equals("gene"))
+ chadoFeature = parent;
+ }
+ }
+ return chadoFeature;
+ }
+
/**
* Get the sequence for a feature.
--
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