Raw content of Bio::EnsEMBL::ExternalData::DAS::XrefPeptideMapper
<![CDATA[# Proxy object to make IdentityXref mappers play nice with the core Mapper
# interface. Differences:
# does not use real identifiers for the sequences it is mapping between,
# it uses 'external_id' and 'ensembl_id' strings
# names the from/to coordinate systems as 'external' and 'ensembl'.
package Bio::EnsEMBL::ExternalData::DAS::XrefPeptideMapper;
use strict;
use warnings;
use base qw(Bio::EnsEMBL::Mapper);
sub new {
my ( $proto, $from, $to, $from_cs, $to_cs, $identity_xref, $translation ) = @_;
my $is_forward = 1;
if ($identity_xref->isa('Bio::EnsEMBL::Translation')) {
$is_forward = 0;
($identity_xref, $translation) = ($translation, $identity_xref);
}
$identity_xref->can('get_mapper') || throw('Xref does not support mapping');
my $class = ref $proto || $proto;
my $mapper = $identity_xref->get_mapper;
my $self = {
%{ $mapper }
};
bless $self, $class;
$self->{'from'} = $from;
$self->{'to'} = $to;
$self->{'from_cs'} = $from_cs;
$self->{'to_cs'} = $to_cs;
$self->{'external'} = $is_forward ? $from : $to;
$self->{'ensembl'} = $is_forward ? $to : $from;
$self->{'external_cs'} = $is_forward ? $from_cs : $to_cs;
$self->{'ensembl_cs'} = $is_forward ? $to_cs : $from_cs;
return $self;
}
sub external_id {
my ($self, $tmp) = @_;
if ($tmp) {
$self->{'external_id'} = $tmp;
}
return $self->{'external_id'};
}
sub ensembl_id {
my ($self, $tmp) = @_;
if ($tmp) {
$self->{'ensembl_id'} = $tmp;
}
return $self->{'ensembl_id'};
}
sub map_coordinates {
my $self = shift;
my ($in_id, $out_id, $in_name, $out_cs);
if ( $_[4] eq $self->{'external'} ) {
$in_id = 'external_id';
$in_name = 'external';
$out_id = $self->{'ensembl_id'};
$out_cs = $self->{'ensembl_cs'};
} elsif ( $_[4] eq $self->{'ensembl'} ) {
$in_id = 'ensembl_id';
$in_name = 'ensembl';
$out_id = $self->{'external_id'};
$out_cs = $self->{'external_cs'};
} else {
throw($_[4].' is neither the xref or peptide coordinate system');
}
my @coords = $self->SUPER::map_coordinates( $in_id, @_[1..3], $in_name );
for my $c ( @coords ) {
if ($c->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
$c->id( $out_id );
$c->coord_system( $out_cs ); # IdentityXref mapper doesn't set this
}
}
return @coords;
}
1;]]>