comparison variant_effect_predictor/Bio/EnsEMBL/SplicingEventFeature.pm @ 0:1f6dce3d34e0

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author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
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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::SplicingEventFeature - Object representing an alternative splicing event
24
25 =head1 SYNOPSIS
26
27 my $ase = Bio::EnsEMBL::SplicingEventFeature->new(
28 -START => 123,
29 -END => 1045,
30 -EXON_ID => $exon->dbID
31 );
32
33 # set some additional attributes
34 $ase->type('flanking_exon');
35
36 =head1 DESCRIPTION
37
38 A representation of an Alternative Splicing Event Feature within the Ensembl system.
39
40 =head1 METHODS
41
42 =cut
43
44 package Bio::EnsEMBL::SplicingEventFeature;
45
46 use strict;
47
48 use POSIX;
49 use Bio::EnsEMBL::Feature;
50 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
51 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
52
53 use vars qw(@ISA);
54 @ISA = qw(Bio::EnsEMBL::Feature);
55
56
57
58 ## Add to gene get_all_splicing_events
59
60
61
62 sub exon_id{
63 my $self = shift;
64 $self->{'exon_id'} = shift if (@_);
65
66 if (defined $self->{'exon_id'}) {
67 return $self->{'exon_id'};
68 }
69
70 return undef;
71 }
72
73 sub transcript_id{
74 my $self = shift;
75 $self->{'transcript_id'} = shift if (@_);
76
77 if (defined $self->{'transcript_id'}) {
78 return $self->{'transcript_id'};
79 }
80
81 return undef;
82 }
83
84 sub feature_order{
85 my $self = shift;
86 $self->{'feature_order'} = shift if (@_);
87
88 if (defined $self->{'feature_order'}) {
89 return $self->{'feature_order'};
90 }
91
92 return undef;
93 }
94
95 sub type{
96 my $self = shift;
97 $self->{'type'} = shift if (@_);
98
99 if (defined $self->{'type'}) {
100 return $self->{'type'};
101 }
102
103 return undef;
104 }
105
106 sub start{
107 my $self = shift;
108 $self->{'start'} = shift if (@_);
109
110 if (defined $self->{'start'}) {
111 return $self->{'start'};
112 }
113
114 return undef;
115 }
116
117 sub end{
118 my $self = shift;
119 $self->{'end'} = shift if (@_);
120
121 if (defined $self->{'end'}) {
122 return $self->{'end'};
123 }
124
125 return undef;
126 }
127
128
129 sub transcript_association{
130 my $self = shift;
131 $self->{'transcript_association'} = shift if (@_);
132
133 if (defined $self->{'transcript_association'}) {
134 return $self->{'transcript_association'};
135 }
136
137 return undef;
138 }
139
140
141
142
143 1;