Raw content of Bio::EnsEMBL::Intron
<![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::Intron - A class representing an Intron
=head1 SYNOPSIS
$ex = new Bio::EnsEMBL::Intron( exon1, exon2 );
=cut
package Bio::EnsEMBL::Intron;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Feature;
use Bio::Seq; # introns have to have sequences...
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Args : exon1, exon2. The two exons to build the Intron from.
Example : $intron = new Bio::EnsEMBL::Intron($exon1, $exon2)
Description: create an Intron object from two exons.
Returntype : Bio::EnsEMBL::Intron
Exceptions : exons not on the same strand or slice.
Caller : general
Status : Stable
=cut
sub new {
my ($class,$e1,$e2) = @_;
$class = ref $class || $class;
my $self = $class->SUPER::new();
if($e1->strand == -1){
$self->{'end'} = ($e1->start)-1;
$self->{'start'} = ($e2->end)+1;
}
else{
$self->{'start'}= ($e1->end)+1;
$self->{'end'} = ($e2->start)-1;
}
if($e1->strand != $e2->strand){
# throw("Exons on different strand. Not allowed");
}
else{
$self->{'strand'} = $e1->strand;
}
if($e1->slice ne $e2->slice){
if($e1->slice->seq_region_name ne $e2->slice->seq_region_name){
throw("Exons on different slices. Not allowed");
}
else{
warn("Exons have different slice references to the same seq_region\n");
}
}
else{
$self->{'slice'} = $e1->slice;
}
$self->{'prev'} = $e1;
$self->{'next'} = $e2;
return $self;
}
=head2 prev_Exon
Args : none
Example : $exon = $intron->prev_Exon
Description: Returns the exon before this Intron
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : general
Status : Stable
=cut
sub prev_Exon {
my ($self) = shift;
return $self->{'prev'};
}
=head2 next_Exon
Args : none
Example : $exon = $intron->next_Exon
Description: Returns the exon after this Intron
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : general
Status : Stable
=cut
sub next_Exon {
my ($self) = shift;
return $self->{'next'};
}
1;
]]>