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SplicingEventFeature.pm
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00001 =head1 LICENSE
00002 
00003   Copyright (c) 1999-2012 The European Bioinformatics Institute and
00004   Genome Research Limited.  All rights reserved.
00005 
00006   This software is distributed under a modified Apache license.
00007   For license details, please see
00008 
00009     http://www.ensembl.org/info/about/code_licence.html
00010 
00011 =head1 CONTACT
00012 
00013   Please email comments or questions to the public Ensembl
00014   developers list at <dev@ensembl.org>.
00015 
00016   Questions may also be sent to the Ensembl help desk at
00017   <helpdesk@ensembl.org>.
00018 
00019 =cut
00020 
00021 =head1 NAME
00022 
00023 Bio::EnsEMBL::SplicingEventFeature - Object representing an alternative splicing event
00024 
00025 =head1 SYNOPSIS
00026 
00027   my $ase = Bio::EnsEMBL::SplicingEventFeature->new(
00028     -START  => 123,
00029     -END    => 1045,
00030     -EXON_ID => $exon->dbID
00031   );
00032 
00033   # set some additional attributes
00034   $ase->type('flanking_exon');
00035 
00036 =head1 DESCRIPTION
00037 
00038 A representation of an Alternative Splicing Event Feature within the Ensembl system.
00039 
00040 =head1 METHODS
00041 
00042 =cut
00043 
00044 package Bio::EnsEMBL::SplicingEventFeature;
00045 
00046 use strict;
00047 
00048 use POSIX;
00049 use Bio::EnsEMBL::Feature;
00050 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
00051 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
00052 
00053 use vars qw(@ISA);
00054 @ISA = qw(Bio::EnsEMBL::Feature);
00055 
00056 
00057 
00058 ## Add to gene get_all_splicing_events
00059 
00060 
00061 
00062 sub exon_id{
00063   my $self = shift;
00064   $self->{'exon_id'} = shift if (@_);
00065 
00066   if (defined $self->{'exon_id'}) {
00067     return $self->{'exon_id'};
00068   }
00069 
00070   return undef;
00071 }
00072 
00073 sub transcript_id{
00074   my $self = shift;
00075   $self->{'transcript_id'} = shift if (@_);
00076 
00077   if (defined $self->{'transcript_id'}) {
00078     return $self->{'transcript_id'};
00079   }
00080 
00081   return undef;
00082 }
00083 
00084 sub feature_order{
00085   my $self = shift;
00086   $self->{'feature_order'} = shift if (@_);
00087 
00088   if (defined $self->{'feature_order'}) {
00089     return $self->{'feature_order'};
00090   }
00091 
00092   return undef;
00093 }
00094 
00095 sub type{
00096   my $self = shift;
00097   $self->{'type'} = shift if (@_);
00098 
00099   if (defined $self->{'type'}) {
00100     return $self->{'type'};
00101   }
00102 
00103   return undef;
00104 }
00105 
00106 sub start{
00107   my $self = shift;
00108   $self->{'start'} = shift if (@_);
00109 
00110   if (defined $self->{'start'}) {
00111     return $self->{'start'};
00112   }
00113 
00114   return undef;
00115 }
00116 
00117 sub end{
00118   my $self = shift;
00119   $self->{'end'} = shift if (@_);
00120 
00121   if (defined $self->{'end'}) {
00122     return $self->{'end'};
00123   }
00124 
00125   return undef;
00126 }
00127 
00128 
00129 sub transcript_association{
00130   my $self = shift;
00131   $self->{'transcript_association'} = shift if (@_);
00132 
00133   if (defined $self->{'transcript_association'}) {
00134     return $self->{'transcript_association'};
00135   }
00136 
00137   return undef;
00138 }
00139 
00140 
00141 
00142 
00143 1;