From d3dabd767ae58b2274136ef4e62a6d9e5239375d Mon Sep 17 00:00:00 2001
From: Alistair Rust <rust@sanger.ac.uk>
Date: Fri, 3 Jan 2003 17:49:26 +0000
Subject: [PATCH] Added a very simple update method that modifies the
display_xref_id field and checks on whether the number of attached exons has
increased.
---
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 54 +++++++++++++++++++
1 file changed, 54 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 5c762fe395..0fa5402bb7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -446,5 +446,59 @@ sub get_display_xref_id {
}
+=head2 update
+
+ Arg [1] : Bio::EnsEMBL::Transcript
+ Example : $transcript_adaptor->update($transcript);
+ Description: Updates a transcript in the database
+ Returntype : None
+ Exceptions : thrown if the $transcript is not a Bio::EnsEMBL::Transcript
+ warn if trying to update the number of attached exons. This
+ is a far more complex process and is not yet implemented.
+ warn if the method is called on a transcript that does not exist
+ in the database.
+ Caller : general
+
+=cut
+
+sub update {
+ my ($self,$transcript) = @_;
+ my $update = 0;
+
+ if( !defined $transcript || !ref $transcript || !$transcript->isa('Bio::EnsEMBL::Transcript') ) {
+ $self->throw("Must update a transcript object, not a $transcript");
+ }
+
+ my $sth = $self->prepare("SELECT exon_count, display_xref_id
+ FROM transcript
+ WHERE transcript_id = ?
+ ");
+
+ $sth->execute($transcript->dbID);
+
+ if ( my ($exons, $dxref_id) = $sth->fetchrow_array() ){
+
+ if ( $exons != scalar(@{$transcript->get_all_Exons})) {
+ $self->warn("Trying to update the number of exons on a stored transcript. Not yet implemented.");
+ }
+
+ if ( $dxref_id != $transcript->display_xref ) {
+
+ $sth = $self->prepare("UPDATE transcript
+ SET display_xref_id = ?
+ WHERE transcript_id = ?
+ ");
+
+ $sth->execute($transcript->display_xref, $transcript->dbID);
+ }
+ }
+ else {
+ $self->warn("Trying to update a transcript that is not in the database. Try store\'ing first.");
+ }
+}
+
+
+
+
1;
--
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