Mercurial > repos > mahtabm > ensembl
comparison variant_effect_predictor/Bio/EnsEMBL/SeqRegionSynonym.pm @ 0:1f6dce3d34e0
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author | mahtabm |
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date | Thu, 11 Apr 2013 02:01:53 -0400 |
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-1:000000000000 | 0:1f6dce3d34e0 |
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1 =head1 LICENSE | |
2 | |
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and | |
4 Genome Research Limited. All rights reserved. | |
5 | |
6 This software is distributed under a modified Apache license. | |
7 For license details, please see | |
8 | |
9 http://www.ensembl.org/info/about/code_licence.html | |
10 | |
11 =head1 CONTACT | |
12 | |
13 Please email comments or questions to the public Ensembl | |
14 developers list at <dev@ensembl.org>. | |
15 | |
16 Questions may also be sent to the Ensembl help desk at | |
17 <helpdesk@ensembl.org>. | |
18 | |
19 =cut | |
20 | |
21 =head1 NAME | |
22 | |
23 Bio::EnsEMBL::SeqRegionSynonym - | |
24 Object representing an alternatice name. | |
25 | |
26 =head1 SYNOPSIS | |
27 | |
28 =head1 DESCRIPTION | |
29 | |
30 This object holds information about alternative name to | |
31 Ensembl seq regions. | |
32 | |
33 =head1 METHODS | |
34 | |
35 =cut | |
36 | |
37 package Bio::EnsEMBL::SeqRegionSynonym; | |
38 | |
39 use strict; | |
40 use warnings; | |
41 no warnings qw(uninitialized); | |
42 | |
43 use Bio::EnsEMBL::Storable; | |
44 use Bio::Annotation::DBLink; | |
45 | |
46 use Bio::EnsEMBL::Utils::Argument qw(rearrange); | |
47 use Bio::EnsEMBL::Utils::Exception qw(deprecate); | |
48 | |
49 our @ISA = qw(Bio::EnsEMBL::Storable); | |
50 | |
51 =head2 new | |
52 | |
53 Args [...] : list of named parameters | |
54 Example : my $srs = new Bio::EnsEMBL::SeqRegionSynonym( | |
55 -adaptor => $adaptor, | |
56 -synonym => $alt_name, | |
57 -external_db_id => 1234 | |
58 -seq_region_id => 12); | |
59 Description: Creates a new SeqRegionSynonym object | |
60 Returntype : Bio::EnsEMBL::SeqRegionSynonym | |
61 Exceptions : none | |
62 Caller : Bio::EnsEMBL::SeqRegionSynonymAdaptor | |
63 Status : At Risk | |
64 =cut | |
65 | |
66 sub new { | |
67 my ($class, @args) = @_; | |
68 | |
69 my $self = bless {},$class; | |
70 | |
71 my ( $adaptor, $synonym, $ex_db, $seq_region_id, $dbid) = | |
72 rearrange ( ['ADAPTOR','SYNONYM','EXTERNAL_DB_ID','SEQ_REGION_ID','DBID'], @args ); | |
73 | |
74 $self->adaptor($adaptor); | |
75 | |
76 if( defined $ex_db ) { $self->external_db_id( $ex_db ) } | |
77 if( defined $seq_region_id ) { $self->seq_region_id( $seq_region_id ) } | |
78 if (defined $dbid) { $self->{'dbID'} = $dbid} | |
79 | |
80 if( defined $synonym ) { | |
81 $self->name( $synonym ) ; | |
82 } else { | |
83 warn "No alternative name given\n"; | |
84 return undef; | |
85 } | |
86 | |
87 return $self; | |
88 } | |
89 | |
90 sub name{ | |
91 my $self = shift; | |
92 $self->{'name'} = shift if(@_); | |
93 return $self->{'name'}; | |
94 } | |
95 | |
96 sub external_db_id{ | |
97 my $self = shift; | |
98 $self->{'ex_db'} = shift if(@_); | |
99 return $self->{'ex_db'}; | |
100 } | |
101 | |
102 sub seq_region_id{ | |
103 my $self = shift; | |
104 $self->{'seq_region_id'} = shift if(@_); | |
105 return $self->{'seq_region_id'}; | |
106 } | |
107 | |
108 1; |