Raw content of Bio::EnsEMBL::Compara::Production::EPOanchors::AnchorAlign
<![CDATA[=head1 NAME - Bio::EnsEMBL::Compara::Production::EPOanchors::AnchorAlign
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONTACT
Ensembl-dev mailing list <ensembl-dev@ebi.ac.uk>
=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::EPOanchors::AnchorAlign;
use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Compara::DnaFrag;
use Bio::EnsEMBL::Utils::Exception;
sub new {
my($class, @args) = @_;
my $self = {};
bless $self,$class;
## First lines are for backward compatibility, middle one is for both versions and
## last ones are for the new schema
my ($adaptor, $dbID, $method_link_species_set, $method_link_species_set_id, $anchor_id,
$dnafrag, $dnafrag_id, $dnafrag_start, $dnafrag_end, $dnafrag_strand,
$score, $num_of_organisms, $num_of_sequences, $anchor_status) =
rearrange([qw(
ADAPTOR DBID METHOD_LINK_SPECIES_SET METHOD_LINK_SPECIES_SET_ID ANCHOR_ID
DNAFRAG DNAFRAG_ID DNAFRAG_START DNAFRAG_END DNAFRAG_STRAND
SCORE NUM_OF_ORGANISMS NUM_OF_SEQUENCES ANCHOR_STATUS)], @args);
$self->adaptor($adaptor) if (defined($adaptor));
$self->dbID($dbID) if (defined($dbID));
$self->method_link_species_set($method_link_species_set) if (defined($method_link_species_set));
$self->method_link_species_set_id($method_link_species_set_id) if (defined($method_link_species_set_id));
$self->anchor_id($anchor_id) if (defined($anchor_id));
$self->dnafrag($dnafrag) if (defined($dnafrag));
$self->dnafrag_id($dnafrag_id) if (defined($dnafrag_id));
$self->dnafrag_start($dnafrag_start) if (defined($dnafrag_start));
$self->dnafrag_end($dnafrag_end) if (defined($dnafrag_end));
$self->dnafrag_strand($dnafrag_strand) if (defined($dnafrag_strand));
$self->score($score) if (defined($score));
$self->num_of_organisms($num_of_organisms) if (defined($num_of_organisms));
$self->num_of_sequences($num_of_sequences) if (defined($num_of_sequences));
$self->anchor_status($anchor_status) if (defined($anchor_status));
return $self;
}
sub adaptor {
my $self = shift;
if (@_) {
$self->{_adaptor} = shift;
}
return $self->{_adaptor};
}
sub dbID {
my $self = shift;
if (@_) {
$self->{_dbID} = shift;
}
return $self->{_dbID};
}
sub method_link_species_set {
my $self = shift;
if (@_) {
$self->{_method_link_species_set} = shift;
}
return $self->{_method_link_species_set};
}
sub method_link_species_set_id {
my $self = shift;
if (@_) {
$self->{_method_link_species_set_id} = shift;
}
if (!defined($self->{_method_link_species_set_id}) and defined($self->{_method_link_species_set})) {
$self->{_method_link_species_set_id} = $self->{_method_link_species_set}->dbID;
}
return $self->{_method_link_species_set_id};
}
sub anchor_id {
my $self = shift;
if (@_) {
$self->{_anchor_id} = shift;
}
return $self->{_anchor_id};
}
sub dnafrag {
my $self = shift;
if (@_) {
$self->{_dnafrag} = shift;
} elsif (!$self->{_dnafrag} and $self->{_dnafrag_id} and $self->{_adaptor}) {
$self->{_dnafrag} = $self->{_adaptor}->db->get_DnaFragAdaptor->fetch_by_dbID($self->{_dnafrag_id});
}
return $self->{_dnafrag};
}
sub dnafrag_id {
my $self = shift;
if (@_) {
$self->{_dnafrag_id} = shift;
}
if (!defined($self->{_dnafrag_id}) and defined($self->{_dnafrag})) {
$self->{_dnafrag_id} = $self->{_dnafrag}->dbID;
}
return $self->{_dnafrag_id};
}
sub dnafrag_start {
my $self = shift;
if (@_) {
$self->{_dnafrag_start} = shift;
}
return $self->{_dnafrag_start};
}
sub dnafrag_end {
my $self = shift;
if (@_) {
$self->{_dnafrag_end} = shift;
}
return $self->{_dnafrag_end};
}
sub dnafrag_strand {
my $self = shift;
if (@_) {
$self->{_dnafrag_strand} = shift;
}
return $self->{_dnafrag_strand};
}
sub score {
my $self = shift;
if (@_) {
$self->{_score} = shift;
}
return $self->{_score};
}
sub num_of_organisms {
my $self = shift;
if (@_) {
$self->{_num_of_organisms} = shift;
}
return $self->{_num_of_organisms};
}
sub num_of_sequences {
my $self = shift;
if (@_) {
$self->{_num_of_sequences} = shift;
}
return $self->{_num_of_sequences};
}
sub anchor_status {
my $self = shift;
if (@_) {
$self->{_anchor_status} = shift;
}
return $self->{_anchor_status};
}
sub seq {
my $self = shift;
return $self->{'_seq'} if ($self->{'_seq'});
my $seq = $self->dnafrag->slice()->subseq($self->{'_dnafrag_start'},
$self->{'_dnafrag_end'}, $self->{'_dnafrag_strand'});
$self->{'_seq'} = $seq;
return $self->{'_seq'};
}
1;
]]>