Raw content of Bio::EnsEMBL::Compara::Production::GeneSet
<![CDATA[#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Compara::Production::GeneSet
=cut
=head1 SYNOPSIS
An abstract data class for holding an arbitrary collection of
(ENSEMBLGENE)Member objects and providing set operations and
cross-reference operations to compare to another GeneSet object.
Also used by HomologySet.
=cut
=head1 DESCRIPTION
A 'set' object of Gene objects. Uses Member::stable_id to identify unique genes.
Is used for comparing GeneSet objects with each other and building comparison
matrixes.
Not really a production object, but more an abstract data type for use by
post analysis scripts. Placed in Production since I could not think of a better location.
The design of this object essentially was within the homology_diff.pl script
but has now been formalized into a proper object design.
=cut
=head1 CONTACT
Contact Jessica Severin on module implemetation/design detail: jessica@ebi.ac.uk
Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::Production::GeneSet;
use strict;
use Bio::EnsEMBL::Compara::Member;
use Bio::EnsEMBL::Compara::Graph::CGObject;
our @ISA = qw(Bio::EnsEMBL::Compara::Graph::CGObject);
sub init {
my $self = shift;
$self->SUPER::init;
$self->clear;
return $self;
}
sub dealloc {
my $self = shift;
return $self->SUPER::dealloc;
}
sub clear {
my $self = shift;
$self->{'gene_hash'} = {};
}
sub add {
my $self = shift;
my @gene_list = @_;
foreach my $gene (@gene_list) {
next if(defined($self->{'gene_hash'}->{$gene->stable_id}));
$self->{'gene_hash'}->{$gene->stable_id} = $gene;
}
return $self;
}
sub merge {
my $self = shift;
my $other_set = shift;
$self->add(@{$other_set->list});
return $self;
}
### gene ###
sub size {
my $self = shift;
return scalar(@{$self->list});
}
sub list {
my $self = shift;
my @genes = values(%{$self->{'gene_hash'}});
return \@genes;
}
sub includes {
my $self = shift;
my $gene = shift;
return 1 if(defined($self->{'gene_hash'}->{$gene->stable_id}));
return 0;
}
sub find_gene_like {
my $self = shift;
my $gene = shift;
return $self->{'gene_hash'}->{$gene->stable_id};
}
### debug printing ###
sub print_stats {
my $self = shift;
printf("%d unique genes\n", $self->size);
}
sub hashref_by_genome {
my $self = shift;
my %types;
foreach my $gene (@{$self->list}) {
unless(defined($types{$gene->genome_db_id})) {
$types{$gene->genome_db_id} =
new Bio::EnsEMBL::Compara::Production::GeneSet;
}
$types{$gene->genome_db_id}->add($gene);
}
return \%types;
}
############################################
#
# set theory operations
#
############################################
sub relative_complement {
my $self = shift;
my $other_set = shift;
#genes in other_set that are not in my set
my $new_set = new Bio::EnsEMBL::Compara::Production::GeneSet;
foreach my $gene (@{$other_set->list}) {
unless($self->includes($gene)) {
$new_set->add($gene);
}
}
return $new_set;
}
sub intersection {
my $self = shift;
my $other_set = shift;
my $new_set = new Bio::EnsEMBL::Compara::Production::GeneSet;
foreach my $gene (@{$self->list}) {
if($other_set->includes($gene)) {
$new_set->add($gene);
}
}
return $new_set;
}
1;
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