From bd38fb530b9c31f578a21171fdbdfd1b4286c056 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 14 Nov 2007 12:42:32 +0000
Subject: [PATCH] pass argument to ignore release when storing DBEntry
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 2 +-
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 3 ++-
modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm | 2 +-
3 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 03df844d36..7586e46108 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -999,7 +999,7 @@ sub store {
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$gene->get_all_DBEntries} ) {
- $dbEntryAdaptor->store($dbe, $gene_dbID, "Gene");
+ $dbEntryAdaptor->store($dbe, $gene_dbID, "Gene", 1);
}
# we allow transcripts not to share equal exons and instead have copies
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 7ff944995e..2e6b7fca90 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -690,7 +690,7 @@ sub store {
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$transcript->get_all_DBEntries} ) {
- $dbEntryAdaptor->store($dbe, $transc_dbID, "Transcript");
+ $dbEntryAdaptor->store($dbe, $transc_dbID, "Transcript", 1);
}
#
@@ -775,6 +775,7 @@ sub store {
# store transcript attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
+
$attr_adaptor->store_on_Transcript($transc_dbID,
$transcript->get_all_Attributes);
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index 8d05dc7ce1..6e1a1413d3 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -252,7 +252,7 @@ sub store {
my $dbEntryAdaptor = $self->db()->get_DBEntryAdaptor();
# store each of the xrefs for this translation
foreach my $dbl ( @{$translation->get_all_DBEntries} ) {
- $dbEntryAdaptor->store( $dbl, $transl_dbID, "Translation" );
+ $dbEntryAdaptor->store( $dbl, $transl_dbID, "Translation", 1 );
}
#storing the protein features associated with the translation
--
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