From eb65588c27c18da95c6dc41a5a2c7a65c6b56e42 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 22 Apr 2008 08:52:48 +0000
Subject: [PATCH] attach lazy loading chado feature to GFFStreamFeature
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@7275 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/GFFDocumentEntry.java | 27 ++++++++++++++++---
1 file changed, 23 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
index d933bcaa0..e89732f47 100644
--- a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.52 2007-10-15 08:39:29 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.53 2008-04-22 08:52:48 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -43,7 +43,7 @@ import java.sql.Timestamp;
* A DocumentEntry that can read an GFF entry from a Document.
*
* @author Kim Rutherford
- * @version $Id: GFFDocumentEntry.java,v 1.52 2007-10-15 08:39:29 tjc Exp $
+ * @version $Id: GFFDocumentEntry.java,v 1.53 2008-04-22 08:52:48 tjc Exp $
**/
public class GFFDocumentEntry extends SimpleDocumentEntry
@@ -266,9 +266,28 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
}
//
- // load /similarity - lazily
+ //
if(getDocument() instanceof DatabaseDocument)
- loadSimilarityLazyData(original_features);
+ {
+ DatabaseDocument doc = (DatabaseDocument)getDocument();
+
+ if(!doc.isLazyFeatureLoad())
+ loadSimilarityLazyData(original_features); // load /similarity - lazily
+ else
+ {
+ // using lazy loading - add the lazy chado feature to GFFStreamFeature
+ final Hashtable idFeatureStore = doc.getIdFeatureStore();
+ for(int i = 0 ; i < original_features.size() ; ++i)
+ {
+ this_feature = original_features.featureAt(i);
+ String featureId = (String) this_feature.getQualifierByName("feature_id").getValues().get(0);
+ org.gmod.schema.sequence.Feature chadoLazyFeature =
+ (org.gmod.schema.sequence.Feature)idFeatureStore.get(featureId);
+ ((GFFStreamFeature)this_feature).setChadoLazyFeature(chadoLazyFeature);
+ }
+ idFeatureStore.clear();
+ }
+ }
// now join exons
//combineFeatures();
--
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