Raw content of Bio::EnsEMBL::Pipeline::Alignment
<![CDATA[# Cared for by Dan Andrews <dta@sanger.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Pipeline::Alignment.pm
=head1 SYNOPSIS
=head1 DESCRIPTION
A very basic object that contains sequences of an alignment
(as AlignmentSeq objects). Stores (or at least will store)
information about the alignment too.
=head1 CONTACT
Post general queries to B<ensembl-dev@ebi.ac.uk>
=cut
package Bio::EnsEMBL::Pipeline::Alignment;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
@ISA = qw();
sub new {
my ($class, @args) = @_;
my $self = bless {},$class;
my ($name,
$align_seqs) = rearrange([qw(NAME
SEQS)],@args);
if ($align_seqs) {
foreach my $align_seq (@$align_seqs){
$self->add_sequence($align_seq);
}
}
$self->alignment_name($name) if $name;
return $self;
}
sub alignment_name {
my $self = shift;
if (@_) {
$self->{'_name'} = shift;
}
return $self->{'_name'};
}
sub add_sequence {
my ($self, $align_seq) = @_;
$self->throw("Must attach AlignmentSeq objects to Alignment, not [$align_seq]")
unless $align_seq->isa("Bio::EnsEMBL::Pipeline::Alignment::AlignmentSeq");
push (@{$self->{'_alignment_seqs'}}, $align_seq);
return 1;
}
sub fetch_AlignmentSeqs {
my $self = shift;
return $self->{'_alignment_seqs'};
}
return 1;
]]>