Raw content of Bio::EnsEMBL::UnconventionalTranscriptAssociation =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;