Raw content of Bio::EnsEMBL::Collection::Exon =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 package Bio::EnsEMBL::Collection::Exon; =head1 NAME Bio::EnsEMBL::Collection::Exon - Feature collection implementation for exon features. =head1 DESCRIPTION =head2 Extended feature representation An exon is represented by the basic feature representation (see documentation of Bio::EnsEMBL::Collection) and by the following extended feature representation: =over 4 =item 1. Phase =item 2. End phase =item 3. Is-current =item 4. Stable ID =item 5. Version =item 6. Created date =item 7. Modified date =back =cut use strict; use warnings; use Bio::EnsEMBL::Utils::Argument ('rearrange'); use Bio::EnsEMBL::Utils::Exception ('throw'); use base( 'Bio::EnsEMBL::Collection', 'Bio::EnsEMBL::DBSQL::ExonAdaptor' ); sub _create_feature { my ( $this, $feature_type, $args ) = @_; my $feature = $this->SUPER::_create_feature( $feature_type, $args ); if ( !$this->lightweight() ) { my ( $phase, $end_phase, $is_current, $stable_id, $version, $created_date, $modified_date ) = rearrange( [ 'PHASE', 'END_PHASE', 'IS_CURRENT', 'STABLE_ID', 'VERSION', 'CREATED_DATE', 'MODIFIED_DATE' ], %{$args} ); push( @{$feature}, $phase, $end_phase, $is_current, $stable_id, $version, $created_date, $modified_date ); } return $feature; } sub _create_feature_fast { my ( $this, $feature_type, $args ) = @_; throw( '_create_feature_fast() ' . 'is not implemented for ' . 'exon collections' ); } sub _tables { my ($this) = @_; my @tables = $this->SUPER::_tables(); if ( $this->lightweight() ) { return ( $tables[0] ) } return @tables; } sub _columns { my ($this) = @_; my @columns = $this->SUPER::_columns(); if ( $this->lightweight() ) { @columns[ Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ] = map( 1, Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ); } return @columns; } sub _default_where_clause { my ($this) = @_; if ( $this->lightweight() ) { return '' } return $this->SUPER::_default_where_clause(); } 1; # $Id: Exon.pm,v 1.11 2009/03/04 10:58:13 ak4 Exp $