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NCTreeAdaptor.pm
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00001 =head1 LICENSE
00002 
00003   Copyright (c) 1999-2012 The European Bioinformatics Institute and
00004   Genome Research Limited.  All rights reserved.
00005 
00006   This software is distributed under a modified Apache license.
00007   For license details, please see
00008 
00009    http://www.ensembl.org/info/about/code_licence.html
00010 
00011 =head1 CONTACT
00012 
00013   Please email comments or questions to the public Ensembl
00014   developers list at <dev@ensembl.org>.
00015 
00016   Questions may also be sent to the Ensembl help desk at
00017   <helpdesk@ensembl.org>.
00018 
00019 =head1 NAME
00020 
00021 Bio::EnsEMBL::Compara::DBSQL::NCTreeAdaptor
00022 
00023 =head1 DESCRIPTION
00024 
00025 Specialization of Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor for non-coding genes
00026 
00027 =head1 INHERITANCE TREE
00028 
00029   Bio::EnsEMBL::Compara::DBSQL::NCTreeAdaptor
00030   `- Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor
00031      `- Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor
00032 
00033 =head1 AUTHORSHIP
00034 
00035 Ensembl Team. Individual contributions can be found in the CVS log.
00036 
00037 =head1 MAINTAINER
00038 
00039 $Author: mm14 $
00040 
00041 =head VERSION
00042 
00043 $Revision: 1.7 $
00044 
00045 =head1 APPENDIX
00046 
00047 The rest of the documentation details each of the object methods.
00048 Internal methods are usually preceded with an underscore (_)
00049 
00050 =cut
00051 
00052 package Bio::EnsEMBL::Compara::DBSQL::NCTreeAdaptor;
00053 
00054 use strict;
00055 
00056 use base ('Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor');
00057 
00058 sub default_where_clause {
00059     return "tr.tree_type IN ('ncrnaclusterset', 'ncrnatree')";
00060 }
00061 
00062 
00063 sub _get_canonical_Member {
00064   my $self = shift;
00065   my $member = shift;
00066 
00067   return $member->get_canonical_transcript_Member;
00068 }
00069 
00070 1;