Raw content of Bio::EnsEMBL::GoXref
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::GoXref
=head1 DESCRIPTION
This class extends the DBEntry in order to associate Evidence Tags
to the relationship between EnsEMBL objects and GO identifiers. The
relationship to GO that is stored in the database is actually derived
through the relationship of EnsEMBL peptides to SwissProt peptides, i.e.
the relationship is derived like this:
ENSP -> SWISSPROT -> GO
And the evidence tag describes the relationship between the SwissProt
Peptide and the GO entry.
In reality, however, we store this in the database like this:
ENSP -> SWISSPROT
ENSP -> GO
and the evidence tag hangs off of the relationship between the ENSP and
the GO identifier. Some ENSPs are associated with multiple closely
related Swissprot entries which may both be associated with the same GO
identifier but with different evidence tags. For this reason a single
'GoXref' can have multiple evidence tags.
=head1 SYNOPSIS
my $goxref = Bio::EnsEMBL::GoXref->new();
$goxref->add_linkage_type('IEA');
foreach my $evtag ( @{ $goxref->get_all_linkage_types() } ) {
print "$evtag\n";
}
=head1 METHODS
=cut
package Bio::EnsEMBL::GoXref;
use vars qw(@ISA);
use strict;
@ISA = qw( Bio::EnsEMBL::DBEntry );
=head2 add_linkage_type
Arg [1] : string $value
allowed values:
'IC', 'IDA', 'IEA', 'IEP', 'IGI', 'IMP', 'IPI',
'ISS', NAS', 'ND', 'TAS', 'NR', 'RCA'
Arg [2] : (optional) Bio::EnsEMBL::DBEntry $source
Example : $go_xref->add_linkage_type('IGI');
Description: Associates a linkage type and source DBEntry with this go_xref
Returntype : integer; number of linkages
Exceptions : thrown if $linkage_type argument not supplied or
the optional DBEntry is not a DBEntry object.
Caller : DBEntryAdaptor
Status : Experimantal
=cut
sub add_linkage_type {
my ( $self, $lt, $source_dbentry ) = @_;
if ( !defined($lt) ) {
$self->throw("linkage type argument required");
}
if ( defined($source_dbentry)
&& !$source_dbentry->isa('Bio::EnsEMBL::DBEntry') )
{
$self->throw("source_dbentry must be a Bio::EnsEMBL::DBEntry");
}
$self->{'linkage_types'} ||= [];
push @{ $self->{'linkage_types'} },
[ $lt, ( $source_dbentry || () ) ];
}
=head2 get_all_linkage_info
Arg [1] : none
Example : foreach (@{$gox->get_all_linkage_info})
{ print "evidence: $_->[0] via $_->[1]->display_id" }
Description: Retrieves a list of evidence-tag/source-DBEntry pairs
associated with this go_xref
Returntype : listref of listrefs
Exceptions : none
Caller : geneview? general.
Status : Experimental
=cut
sub get_all_linkage_info {
my ($self) = @_;
return $self->{'linkage_types'} || [];
}
=head2 get_all_linkage_types
Arg [1] : none
Example : print( join( ' ',
@{ $goxr->get_all_linkage_types() } ),
"\n" );
Description: Retrieves a unique list of evidence tags associated with
this go_xref
Returntype : none
Exceptions : none
Caller : geneview? general
Status : Stable
=cut
sub get_all_linkage_types {
my ($self) = @_;
my %seen;
return [ grep { !$seen{$_}++ }
map { $_->[0] } @{ $self->{'linkage_types'} } ];
#return [ map{ $_->[0]} @{ $self->{'linkage_types'} || [] } ];
}
=head2 flush_linkage_types
Arg [1] : none
Example : $goxr->flush_linkage_types
Description: Removes any associated evidence tags
Returntype : none
Exceptions : none
Caller : general
Status : Stable
=cut
sub flush_linkage_types {
my ($self) = @_;
$self->{'linkage_types'} = [];
}
1;
]]>