Mercurial > repos > mahtabm > ensembl
comparison variant_effect_predictor/Bio/EnsEMBL/SplicingEventFeature.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::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; |