From 485046e65736b6b4b00f5107cc880a2ad2921aec Mon Sep 17 00:00:00 2001
From: Felix Kokocinski <fsk@sanger.ac.uk>
Date: Thu, 6 Jul 2006 14:00:09 +0000
Subject: [PATCH] added method to fetch total extend of mapped ditag
---
.../EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm | 33 ++++++++++++-------
1 file changed, 21 insertions(+), 12 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
index 7a4124aeec..2cf4381983 100644
--- a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
@@ -92,10 +92,12 @@ sub fetch_by_dbID {
}
+
=head2 fetch_all_by_ditagID
Arg [1] : ditag dbID
- Example : @my_tags = @{$ditagfeature_adaptor->fetch_by_ditag_id($my_id)};
+ Arg [2] : (optional) ditag-pair dbID
+ 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
Caller : general
@@ -103,17 +105,24 @@ sub fetch_by_dbID {
=cut
sub fetch_all_by_ditagID {
- my ($self, $ditag_id) = @_;
-
-print "\nID=$ditag_id\n";
-
- my $sth = $self->prepare("SELECT ditag_feature_id, ditag_id, seq_region_id, seq_region_start,
- seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
- hit_strand, cigar_line, ditag_side, ditag_pair_id
- FROM ditag_feature
- WHERE ditag_id = ?
- ORDER BY ditag_pair_id" );
- $sth->execute($ditag_id);
+ my ($self, $ditag_id, $ditag_pair_id) = @_;
+
+ my $sql = "SELECT ditag_feature_id, ditag_id, seq_region_id, seq_region_start,
+ seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
+ hit_strand, cigar_line, ditag_side, ditag_pair_id
+ FROM ditag_feature
+ WHERE ditag_id = ? ";
+ if($ditag_pair_id){
+ $sql .= "AND ditag_pair_id = ? ";
+ }
+ $sql .= "ORDER BY ditag_pair_id";
+ my $sth = $self->prepare($sql);
+ if($ditag_pair_id){
+ $sth->execute($ditag_id, $ditag_pair_id);
+ }
+ else{
+ $sth->execute($ditag_id);
+ }
my $result = $self->_fetch($sth);
--
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