From 217a209eb846dc10719a83b670684319fe3032a7 Mon Sep 17 00:00:00 2001
From: Felix Kokocinski <fsk@sanger.ac.uk>
Date: Thu, 28 Sep 2006 08:21:26 +0000
Subject: [PATCH] use analysis-id when fetching pairs
---
modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm | 6 +++++-
modules/Bio/EnsEMBL/Map/DitagFeature.pm | 10 +++++++---
2 files changed, 12 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
index b39a5edbce..7ae925244d 100644
--- a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
@@ -98,6 +98,7 @@ sub fetch_by_dbID {
Arg [1] : ditag dbID
Arg [2] : (optional) ditag-pair dbID
+ Arg [3] : (optional) analysis ID
Example : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_ditag_id($my_id)};
Description: Retrieves all ditagFeatures from the database linking to a specific ditag-id
Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
@@ -106,7 +107,7 @@ sub fetch_by_dbID {
=cut
sub fetch_all_by_ditagID {
- my ($self, $ditag_id, $ditag_pair_id) = @_;
+ my ($self, $ditag_id, $ditag_pair_id, $analysis_id) = @_;
my $sql = "SELECT ditag_feature_id, ditag_id, seq_region_id, seq_region_start,
seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
@@ -116,6 +117,9 @@ sub fetch_all_by_ditagID {
if($ditag_pair_id){
$sql .= "AND ditag_pair_id = ? ";
}
+ if($analysis_id){
+ $sql .= "AND analysis_id = ? ";
+ }
$sql .= "ORDER BY ditag_pair_id";
my $sth = $self->prepare($sql);
if($ditag_pair_id){
diff --git a/modules/Bio/EnsEMBL/Map/DitagFeature.pm b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
index 6f3bb5dce7..8f0e7c0233 100644
--- a/modules/Bio/EnsEMBL/Map/DitagFeature.pm
+++ b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
@@ -183,14 +183,18 @@ sub get_ditag_location {
else{
my ($ditag_a, $ditag_b, $more);
eval{
- ($ditag_a, $ditag_b, $more) = @{$self->adaptor->fetch_all_by_ditagID($self->ditag_id, $self->ditag_pair_id)};
+ ($ditag_a, $ditag_b, $more) = @{$self->adaptor->fetch_all_by_ditagID($self->ditag_id,
+ $self->ditag_pair_id,
+ $self->analysis->analysis_id)};
};
if($@ or !defined($ditag_a) or !defined($ditag_b)){
- throw("Cannot find 2nd tag of pair (".$self->dbID.", ".$self->ditag_id.", ".$self->ditag_pair_id.")");
+ throw("Cannot find 2nd tag of pair (".$self->dbID.", ".$self->ditag_id.", ".
+ $self->ditag_pair_id.", ".$self->analysis->analysis_id.")");
}
else{
if(defined $more){
- throw("More than two DitagFeatures were returned for ".$self->dbID.", ".$self->ditag_id.", ".$self->ditag_pair_id);
+ throw("More than two DitagFeatures were returned for ".$self->dbID.", ".$self->ditag_id
+ .", ".$self->ditag_pair_id);
}
($ditag_a->start < $ditag_b->start) ? ($start = $ditag_a->start) : ($start = $ditag_b->start);
--
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