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