Raw content of Bio::EnsEMBL::UnconventionalTranscriptAssociation
<![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::UnconventionalTranscriptAssociation - A class representing
an some sort of unconventional association between a gene and a
transcript.
=head1 SYNOPSIS
$ex = new Bio::EnsEMBL::UnconventionalTranscriptAssociation( $gene,
$transcript, $type );
=head1 METHODS
=cut
package Bio::EnsEMBL::UnconventionalTranscriptAssociation;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
=head2 new
Args [1] : Bio::EnsEMBL::Gene - the gene which is associated.
Args [2] : Bio::EnsEMBL::Transcript - the transcript which is associated.
Args [3] : String type - the type of assocation, e.g. "antisense",
"sense_intronic","sense_overlaping_exonic","chimeric_sense_exonic".
Example : $uta = new Bio::EnsEMBL::UnconventionalTranscriptAssociation($gene, $transcript, "antisense")
Description: create an UnconventionalTranscriptAssociation object.
Returntype : Bio::EnsEMBL::UnconventionalTranscriptAssociation.
Exceptions : Wrong argument types
Caller : general
Status : At risk
=cut
sub new {
my ($class, $transcript, $gene, $type) = @_;
$class = ref $class || $class;
my $self = {};
if( !ref $gene || ! $gene->isa("Bio::EnsEMBL::Gene") ) {
throw("$gene is not a Bio::EnsEMBL::Gene!");
}
if( !ref $transcript || ! $transcript->isa("Bio::EnsEMBL::Transcript") ) {
throw("$transcript is not a Bio::EnsEMBL::Transcript!");
}
$self->{'gene'} = $gene;
$self->{'transcript'} = $transcript;
$self->{'type'} = $type;
return bless $self, $class;
}
=head2 gene
Args : none
Example : $gene = $uta->gene()
Description: Getter/setter for the gene part of this association.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : At risk
=cut
sub gene {
my ($self) = shift;
$self->{'gene'} = shift if (@_);
return $self->{'gene'};
}
=head2 transcript
Args : none
Example : $transcript = $uta->transcript()
Description: Getter/setter for the transcript part of this association.
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : General
Status : At risk
=cut
sub transcript {
my ($self) = shift;
$self->{'transcript'} = shift if (@_);
return $self->{'transcript'};
}
=head2 interaction_type
Args : none
Example : $type = $uta->interaction_type()
Description: Getter/setter for the interaction_type of this association.
Returntype : String
Exceptions : none
Caller : General
Status : At risk
=cut
sub interaction_type {
my ($self) = shift;
$self->{'interaction_type'} = shift if (@_);
return $self->{'interaction_type'};
}
1;
]]>