From 1c5fe21cd5e61e84d9d54d9dc416385dcecfc0b0 Mon Sep 17 00:00:00 2001
From: Will Spooner <whs@sanger.ac.uk>
Date: Mon, 16 Feb 2004 12:23:33 +0000
Subject: [PATCH] Ported changes from branch-ensembl-19
---
modules/Bio/EnsEMBL/External/BlastAdaptor.pm | 35 ++++++++++++++++----
1 file changed, 29 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/External/BlastAdaptor.pm b/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
index 4e40198bbc..71e7a94f33 100644
--- a/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
+++ b/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
@@ -197,6 +197,26 @@ sub new {
#----------------------------------------------------------------------
+=head2 ticket
+
+ Arg [1] : string ticket (optional)
+ Function : Get/get the blast ticket attribute
+ Returntype: string ticket
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub ticket{
+ my $key = "_ticket";
+ my $self = shift;
+ if( @_ ){ $self->{$key} = shift }
+ return $self->{$key};
+}
+
+#----------------------------------------------------------------------
+
=head2 store
Arg [1] :
@@ -384,9 +404,10 @@ sub store_result{
my $dbh = $self->db->db_handle;
- my $ticket = $res->group_ticket;
my ( $id, $use_date ) = split( '!!', $res->token || '' );
$use_date ||= $self->use_date('RESULT');
+ #my $ticket = $res->group_ticket || warn( "Result $id has no ticket" );
+ my $ticket = $self->ticket || warn("Result $id BlastAdaptor has no ticket");
my $rv = 0;
if( $id ){
@@ -460,9 +481,10 @@ sub store_hit{
my $dbh = $self->db->db_handle;
- my $ticket = $hit->group_ticket;
my ( $id, $use_date ) = split( '!!', $hit->token || '' );
$use_date ||= '';
+ #my $ticket = $hit->group_ticket || warn( "Hit $id has no ticket" );
+ my $ticket = $self->ticket || warn("Hit $id BlastAdaptor has no ticket");
my $rv = 0;
if( $id ){
@@ -535,9 +557,10 @@ sub store_hsp{
my $dbh = $self->db->db_handle;
- my $ticket = $hsp->group_ticket;
my ( $id, $use_date ) = split( '!!', $hsp->token || '');
$use_date ||= $self->use_date('HSP');
+ #my $ticket = $hsp->group_ticket || warn( "HSP $id has no ticket" );
+ my $ticket = $self->ticket || warn( "HSP $id BlastAdaptor has no ticket" );
my $chr_name = 'NULL';
my $chr_start = 'NULL';
@@ -627,7 +650,7 @@ sub get_all_HSPs {
my $SQL = qq(
SELECT object
FROM blast_hsp%s
-WHERE \(ticket = ? OR ticket = ?\) );
+WHERE ticket = ? );
my $CHR_SQL = qq(
AND chr_name = ? );
@@ -637,7 +660,7 @@ AND chr_start <= ?
AND chr_end >= ? );
my $q = sprintf( $SQL, $use_date );
- my @binded = ( $id, substr($id,6) );
+ my @binded = ( $id );
if( $chr_name ){
$q .= $CHR_SQL;
@@ -648,7 +671,7 @@ AND chr_end >= ? );
push @binded, $chr_end, $chr_start;
}
}
-# warn( "$q: ", join( ', ',@binded ) );
+ #warn( "$q: ", join( ', ',@binded ) );
my $sth = $self->db->db_handle->prepare($q);
my $rv = $sth->execute( @binded ) || $self->throw( $sth->errstr );
--
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