From dd3856c8ead2fad5ae94840dbb60fb3298233e06 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 29 Oct 2007 15:55:42 +0000
Subject: [PATCH] added 2 optional parameters to fetch_all_by_Slice these bieng
biotype and source
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 7925ae40bf..03df844d36 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -439,6 +439,10 @@ sub fetch_all_by_Slice_and_external_dbname_link {
Arg [3] : (optional) boolean $load_transcripts
if true, transcripts will be loaded immediately rather than
lazy loaded later.
+ Arg [4] : (optional) string $source
+ the source name of the features to obtain.
+ Arg [5] : (optional) string biotype
+ the biotype of the features to obtain.
Example : @genes = @{$gene_adaptor->fetch_all_by_Slice()};
Description: Overrides superclass method to optionally load transcripts
immediately rather than lazy-loading them later. This
@@ -456,9 +460,20 @@ sub fetch_all_by_Slice {
my $slice = shift;
my $logic_name = shift;
my $load_transcripts = shift;
+ my $source = shift;
+ my $biotype = shift;
+
+ my $constraint = 'g.is_current = 1';
+
+ if(defined($source)){
+ $constraint .= " and g.source = '$source'";
+ }
+ if(defined($biotype)){
+ $constraint .= " and g.biotype = '$biotype'" ;
+ }
my $genes = $self->SUPER::fetch_all_by_Slice_constraint($slice,
- 'g.is_current = 1', $logic_name);
+ $constraint , $logic_name);
# if there are 0 or 1 genes still do lazy-loading
if(!$load_transcripts || @$genes < 2) {
--
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