From 4dc85eb74a70648e2f323109a4fec32b8df69e3f Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 6 Apr 2006 15:36:45 +0000
Subject: [PATCH] added optional argument of a compara dbadaptor to
get_all_compara_DnaAlignFeatures and get_all_compara_Syntenies to make it
easier for users who may not have configured the databases properly
---
modules/Bio/EnsEMBL/Slice.pm | 26 ++++++++++++++++----------
1 file changed, 16 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 69bb712137..19a1dc4aa4 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -2388,6 +2388,7 @@ sub get_all_MarkerFeatures {
The name of the assembly to retrieve similarity features from
Arg [3] : string $type
The type of the alignment to retrieve similarity features from
+ Arg [4] : <optional> compara dbadptor to use.
Example : $fs = $slc->get_all_compara_DnaAlignFeatures('Mus musculus',
'MGSC3',
'WGA');
@@ -2405,7 +2406,7 @@ sub get_all_MarkerFeatures {
=cut
sub get_all_compara_DnaAlignFeatures {
- my ($self, $qy_species, $qy_assembly, $alignment_type) = @_;
+ my ($self, $qy_species, $qy_assembly, $alignment_type, $compara_db) = @_;
if(!$self->adaptor()) {
warning("Cannot retrieve DnaAlignFeatures without attached adaptor");
@@ -2417,11 +2418,13 @@ sub get_all_compara_DnaAlignFeatures {
throw("Query species and assembly and alignmemt type arguments are required");
}
- my $compara_db = $self->adaptor->db->get_db_adaptor('compara');
-
+ if(!defined($compara_db)){
+ $compara_db = $self->adaptor->db->get_db_adaptor('compara');
+ }
unless($compara_db) {
- warning("Compara database must be attached to core database to " .
- "retrieve compara information");
+ warning("Compara database must be attached to core database or passed ".
+ "as an argument to " .
+ "retrieve compara information");
return [];
}
@@ -2433,6 +2436,7 @@ sub get_all_compara_DnaAlignFeatures {
Arg [1] : string $query_species e.g. "Mus_musculus" or "Mus musculus"
Arg [2] : string $method_link_type, default is "SYNTENY"
+ Arg [3] : <optional> compara dbadptor to use.
Description: gets al the conpara syntenys fro a specfic species
Returns : arrayref of Bio::EnsEMBL::Compara::SyntenyRegion
Status : Stable
@@ -2440,7 +2444,7 @@ sub get_all_compara_DnaAlignFeatures {
=cut
sub get_all_compara_Syntenies {
- my ($self, $qy_species, $method_link_type) = @_;
+ my ($self, $qy_species, $method_link_type, $compara_db) = @_;
if(!$self->adaptor()) {
warning("Cannot retrieve features without attached adaptor");
@@ -2455,11 +2459,13 @@ sub get_all_compara_Syntenies {
$method_link_type = "SYNTENY";
}
- my $compara_db = $self->adaptor->db->get_db_adaptor('compara');
-
+ if(!defined($compara_db)){
+ $compara_db = $self->adaptor->db->get_db_adaptor('compara');
+ }
unless($compara_db) {
- warning("Compara database must be attached to core database to " .
- "retrieve compara information");
+ warning("Compara database must be attached to core database or passed ".
+ "as an argument to " .
+ "retrieve compara information");
return [];
}
my $binomial = $self->adaptor->db->get_MetaContainer->get_Species->binomial;
--
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