From c395eb23e28b3c8e0e058995c937d3a85d2f070f Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 9 Jan 2013 17:28:13 +0000
Subject: [PATCH] added method fetch_all allows to fetch all density features
without for all slices also takes an optional logic_name argument
---
.../EnsEMBL/DBSQL/DensityFeatureAdaptor.pm | 44 +++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
index 31c5f8a0f2..9ac705b1c8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
@@ -60,6 +60,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
our $DENSITY_FEATURE_CACHE_SIZE = 20;
+
=head2 new
Arg [1] : list of args @args
@@ -305,6 +306,49 @@ sub fetch_all_by_Slice {
}
+sub fetch_all {
+ my $self = shift;
+ my $logic_name = shift;
+
+ my ($sth, $seq_region_id, $start, $end, $density_value, $density_type_id);
+ my ($slice, $density_type, @out);
+ my $sa = $self->db()->get_SliceAdaptor();
+ my $dta = $self->db()->get_DensityTypeAdaptor();
+
+ if ($logic_name) {
+ $sth = $self->prepare("SELECT df.seq_region_id, df.seq_region_start, df.seq_region_end, df.density_value, df.density_type_id "
+ . "FROM density_feature df, density_type dt, analysis a "
+ . "WHERE df.density_type_id = dt.density_type_id "
+ . "AND dt.analysis_id = a.analysis_id "
+ . "AND logic_name = ?" );
+ $sth->bind_param(1, $logic_name, SQL_VARCHAR);
+ $sth->execute();
+ } else {
+ $sth = $self->prepare("SELECT df.seq_region_id, df.seq_region_start, df.seq_region_end, df.density_value, df.density_type_id "
+ . "FROM density_feature df, density_type dt "
+ . "WHERE df.density_type_id = dt.density_type_id" );
+ $sth->execute();
+ }
+
+
+ $sth->bind_columns(\($seq_region_id, $start, $end, $density_value, $density_type_id));
+
+
+ while ($sth->fetch()) {
+ $slice = $sa->fetch_by_seq_region_id($seq_region_id);
+ $density_type = $dta->fetch_by_dbID($density_type_id);
+ push (@out, Bio::EnsEMBL::DensityFeature->new
+ (-seq_region => $slice,
+ -start => $start,
+ -end => $end,
+ -density_type => $density_type,
+ -density_value => $density_value));
+ }
+ return \@out;
+}
+
+
+
sub _tables {
my $self = shift;
--
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