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1
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2 =head1 LICENSE
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3
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4 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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5 Genome Research Limited. All rights reserved.
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6
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7 This software is distributed under a modified Apache license.
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8 For license details, please see
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9
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10 http://www.ensembl.org/info/about/code_licence.html
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11
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12 =head1 CONTACT
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13
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14 Please email comments or questions to the public Ensembl
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15 developers list at <dev@ensembl.org>.
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16
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17 Questions may also be sent to the Ensembl help desk at
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18 <helpdesk@ensembl.org>.
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19
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20 =cut
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21
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22 =head1 NAME
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23
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24 Bio::EnsEMBL::SlicingEvent - Object representing an alternative splicing event
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25
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26 =head1 SYNOPSIS
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27
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28 my $ase =
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29 Bio::EnsEMBL::SplicingEvent->new( -START => 123,
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30 -END => 1045,
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31 -STRAND => 1,
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32 -GENE_ID => $gene->dbID,
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33 -SLICE => $slice );
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34
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35 # set some additional attributes
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36 $ase->name('ENSG00000000003-CNE-3');
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37 $ase->type('CNE');
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38
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39 =head1 DESCRIPTION
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40
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41 A representation of an Alternative Splicing Event within the Ensembl system.
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42
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43 =head1 METHODS
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44
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45 =cut
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46
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47 package Bio::EnsEMBL::SplicingEvent;
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48
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49 use strict;
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50
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51 use POSIX;
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52 use Bio::EnsEMBL::Feature;
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53 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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54 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
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55
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56 use vars qw(@ISA);
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57 @ISA = qw(Bio::EnsEMBL::Feature);
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58
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59 ## Add to gene get_all_splicing_events
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60
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61 sub gene_id {
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62 my ( $self, $value ) = @_;
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63
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64 if ( defined($value) ) {
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65 $self->{'gene_id'} = $value;
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66 }
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67
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68 return $self->{'gene_id'};
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69 }
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70
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71 sub name {
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72 my ( $self, $value ) = @_;
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73
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74 if ( defined($value) ) {
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75 $self->{'name'} = $value;
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76 }
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77
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78 return $self->{'name'};
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79 }
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80
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81 sub type {
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82 my ( $self, $value ) = @_;
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83
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84 if ( defined($value) ) {
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85 $self->{'type'} = $value;
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86 }
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87
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88 return $self->{'type'};
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89 }
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90
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91 sub add_Feature {
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92 my ( $self, $feature ) = @_;
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93
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94 if ( !ref($feature)
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95 || !$feature->isa("Bio::EnsEMBL::SplicingEventFeature") )
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96 {
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97 throw("$feature is not a Bio::EnsEMBL::SplicingEventFeature!");
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98 }
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99
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100 $self->{'_feature_array'} ||= [];
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101
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102 push( @{ $self->{'_feature_array'} }, $feature );
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103 }
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104
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105 sub get_all_Features {
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106 my ($self) = @_;
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107
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108 if ( !exists( $self->{'_feature_array'} ) ) {
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109 if ( defined( $self->adaptor() ) ) {
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110 my $fta =
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111 $self->adaptor()->db()->get_SplicingEventFeatureAdaptor();
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112 my $features = $fta->fetch_all_by_SplicingEvent($self);
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113 $self->{'_feature_array'} = $features;
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114 }
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115 }
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116
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117 return $self->{'_feature_array'};
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118 }
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119
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120 sub add_Pair {
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121 my ( $self, $feature ) = @_;
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122
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123 if ( !ref($feature)
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124 || !$feature->isa("Bio::EnsEMBL::SplicingEventPair") )
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125 {
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126 throw("$feature is not a Bio::EnsEMBL::SplicingEventPair!");
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127 }
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128
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129 $self->{'_pair_array'} ||= [];
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130
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131 push( @{ $self->{'_pair_array'} }, $feature );
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132 }
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133
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134 sub get_all_Pairs {
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135 my ($self) = @_;
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136
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137 if ( !exists( $self->{'_pair_array'} ) ) {
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138 if ( defined( $self->adaptor() ) ) {
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139 my $pa =
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140 $self->adaptor()->db()->get_SplicingTranscriptPairAdaptor();
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141 my $pairs = $pa->fetch_all_by_SplicingEvent($self);
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142 $self->{'_pair_array'} = $pairs;
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143 }
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144 }
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145
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146 return $self->{'_pair_array'};
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147 }
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148
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149 1;
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