From 639ed3af20b1160949c3237276165193afdb1691 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 5 Aug 2005 09:26:33 +0000
Subject: [PATCH] new merged adaptor needs species and type
---
modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm | 45 +++++++++++++++++-----
1 file changed, 36 insertions(+), 9 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
index ab12b27f79..fcfbccc7ec 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
@@ -13,7 +13,7 @@ Bio::EnsEMBL::DBSQL::MergedAdaptor
=head1 SYNOPSIS
-$merged_adaptor = new Bio::EnsEMBL::DBSQL::MergedAdaptor();
+$merged_adaptor = new Bio::EnsEMBL::DBSQL::MergedAdaptor(-species => "human", -type => "Population");
=head1 DESCRIPTION
@@ -37,23 +37,49 @@ package Bio::EnsEMBL::DBSQL::MergedAdaptor;
use vars qw(@ISA);
use strict;
+use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Registry;
+my $reg = "Bio::EnsEMBL::Registry";
+
=head2 new
- Example : $MergedAdaptor = new Bio::EnsEMBL::DBSQL::MergedAdaptor();
+ Example : $MergedAdaptor = new
+ : Bio::EnsEMBL::DBSQL::MergedAdaptor(-species=> 'human', -type =>'Population');
+ Arg [SPECIES]: (optional) string
+ species name to get adaptors for
+ Arg [TYPE] : (optional) string
+ type to get adaptors for
+
Description: Creates a new MergedAdaptor
Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
- Exceptions : none
- Caller : Bio::EnsEMBL::Registry
+ Exceptions : throws if species or type not specified
+ Caller : general
+ Status : At Risk
+ : Under development
=cut
sub new {
- my ($class) = @_;
+ my ($class,@args) = @_;
my $self ={};
bless $self,$class;
+ my ($species, $type) =
+ rearrange([qw(SPECIES TYPE)], @args);
+
+ if(!defined($species)|| !defined($type)){
+ die "Species and Type must be specified\n";
+ }
+
+ my @adaps = @{$reg->get_all_adaptors(-species => $species, -type => $type)};
+
+ my @list =();
+ push(@list,@adaps);
+ $self->{'list'}= \@list;
+
return $self;
}
@@ -63,6 +89,8 @@ sub new {
Description: adds a list of adaptors to the Merged adaptor list.
Returntype : none
Exceptions : none
+ Status : At Risk
+ : Under development
=cut
@@ -80,6 +108,8 @@ sub add_list{
Description: adds an adaptor to the Merged adaptor list.
Returntype : none
Exceptions : none
+ Status : At Risk
+ : Under development
=cut
@@ -122,10 +152,7 @@ sub AUTOLOAD {
foreach my $adaptor (@{$self->{'list'}}) {
my $ref;
- if($adaptor->can($sub)
-# and !($adaptor->isa("Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor") ||
-# $adaptor->isa("Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor"))
- ){
+ if($adaptor->can($sub)){
$ref = $adaptor->$sub(@args);
my $type= ref($ref);
if($type =~/HASH/){
--
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