|
0
|
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::UnconventionalTranscriptAssociation - A class representing
|
|
|
24 an some sort of unconventional association between a gene and a
|
|
|
25 transcript.
|
|
|
26
|
|
|
27 =head1 SYNOPSIS
|
|
|
28
|
|
|
29 $ex = new Bio::EnsEMBL::UnconventionalTranscriptAssociation( $gene,
|
|
|
30 $transcript, $type );
|
|
|
31
|
|
|
32 =head1 METHODS
|
|
|
33
|
|
|
34 =cut
|
|
|
35
|
|
|
36 package Bio::EnsEMBL::UnconventionalTranscriptAssociation;
|
|
|
37 use vars qw(@ISA);
|
|
|
38 use strict;
|
|
|
39
|
|
|
40 use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
|
|
|
41 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
|
|
|
42
|
|
|
43 =head2 new
|
|
|
44
|
|
|
45 Args [1] : Bio::EnsEMBL::Gene - the gene which is associated.
|
|
|
46 Args [2] : Bio::EnsEMBL::Transcript - the transcript which is associated.
|
|
|
47 Args [3] : String type - the type of assocation, e.g. "antisense",
|
|
|
48 "sense_intronic","sense_overlaping_exonic","chimeric_sense_exonic".
|
|
|
49 Example : $uta = new Bio::EnsEMBL::UnconventionalTranscriptAssociation($gene, $transcript, "antisense")
|
|
|
50 Description: create an UnconventionalTranscriptAssociation object.
|
|
|
51 Returntype : Bio::EnsEMBL::UnconventionalTranscriptAssociation.
|
|
|
52 Exceptions : Wrong argument types
|
|
|
53 Caller : general
|
|
|
54 Status : At risk
|
|
|
55
|
|
|
56 =cut
|
|
|
57
|
|
|
58 sub new {
|
|
|
59
|
|
|
60 my ($class, $transcript, $gene, $type) = @_;
|
|
|
61
|
|
|
62 $class = ref $class || $class;
|
|
|
63
|
|
|
64 my $self = {};
|
|
|
65
|
|
|
66 if( !ref $gene || ! $gene->isa("Bio::EnsEMBL::Gene") ) {
|
|
|
67 throw("$gene is not a Bio::EnsEMBL::Gene!");
|
|
|
68 }
|
|
|
69
|
|
|
70 if( !ref $transcript || ! $transcript->isa("Bio::EnsEMBL::Transcript") ) {
|
|
|
71 throw("$transcript is not a Bio::EnsEMBL::Transcript!");
|
|
|
72 }
|
|
|
73
|
|
|
74 $self->{'gene'} = $gene;
|
|
|
75 $self->{'transcript'} = $transcript;
|
|
|
76 $self->{'type'} = $type;
|
|
|
77
|
|
|
78 return bless $self, $class;
|
|
|
79 }
|
|
|
80
|
|
|
81
|
|
|
82 =head2 gene
|
|
|
83
|
|
|
84 Args : none
|
|
|
85 Example : $gene = $uta->gene()
|
|
|
86 Description: Getter/setter for the gene part of this association.
|
|
|
87 Returntype : Bio::EnsEMBL::Gene
|
|
|
88 Exceptions : none
|
|
|
89 Caller : general
|
|
|
90 Status : At risk
|
|
|
91
|
|
|
92 =cut
|
|
|
93
|
|
|
94 sub gene {
|
|
|
95 my ($self) = shift;
|
|
|
96
|
|
|
97 $self->{'gene'} = shift if (@_);
|
|
|
98 return $self->{'gene'};
|
|
|
99
|
|
|
100 }
|
|
|
101
|
|
|
102 =head2 transcript
|
|
|
103
|
|
|
104 Args : none
|
|
|
105 Example : $transcript = $uta->transcript()
|
|
|
106 Description: Getter/setter for the transcript part of this association.
|
|
|
107 Returntype : Bio::EnsEMBL::Transcript
|
|
|
108 Exceptions : none
|
|
|
109 Caller : General
|
|
|
110 Status : At risk
|
|
|
111
|
|
|
112 =cut
|
|
|
113
|
|
|
114 sub transcript {
|
|
|
115 my ($self) = shift;
|
|
|
116
|
|
|
117 $self->{'transcript'} = shift if (@_);
|
|
|
118 return $self->{'transcript'};
|
|
|
119
|
|
|
120 }
|
|
|
121
|
|
|
122 =head2 interaction_type
|
|
|
123
|
|
|
124 Args : none
|
|
|
125 Example : $type = $uta->interaction_type()
|
|
|
126 Description: Getter/setter for the interaction_type of this association.
|
|
|
127 Returntype : String
|
|
|
128 Exceptions : none
|
|
|
129 Caller : General
|
|
|
130 Status : At risk
|
|
|
131
|
|
|
132 =cut
|
|
|
133
|
|
|
134 sub interaction_type {
|
|
|
135 my ($self) = shift;
|
|
|
136
|
|
|
137 $self->{'interaction_type'} = shift if (@_);
|
|
|
138 return $self->{'interaction_type'};
|
|
|
139
|
|
|
140 }
|
|
|
141
|
|
|
142 1;
|
|
|
143
|
|
|
144
|
