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

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0:1f6dce3d34e0

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::SplicingEventFeature - Object representing an alternative splicing event

=head1 SYNOPSIS

  my $ase = Bio::EnsEMBL::SplicingEventFeature->new(
    -START  => 123,
    -END    => 1045,
    -EXON_ID => $exon->dbID
  );

  # set some additional attributes
  $ase->type('flanking_exon');

=head1 DESCRIPTION

A representation of an Alternative Splicing Event Feature within the Ensembl system.

=head1 METHODS

=cut

package Bio::EnsEMBL::SplicingEventFeature;

use strict;

use POSIX;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);

use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature);



## Add to gene get_all_splicing_events



sub exon_id{
  my $self = shift;
  $self->{'exon_id'} = shift if (@_);

  if (defined $self->{'exon_id'}) {
    return $self->{'exon_id'};
  }

  return undef;
}

sub transcript_id{
  my $self = shift;
  $self->{'transcript_id'} = shift if (@_);

  if (defined $self->{'transcript_id'}) {
    return $self->{'transcript_id'};
  }

  return undef;
}

sub feature_order{
  my $self = shift;
  $self->{'feature_order'} = shift if (@_);

  if (defined $self->{'feature_order'}) {
    return $self->{'feature_order'};
  }

  return undef;
}

sub type{
  my $self = shift;
  $self->{'type'} = shift if (@_);

  if (defined $self->{'type'}) {
    return $self->{'type'};
  }

  return undef;
}

sub start{
  my $self = shift;
  $self->{'start'} = shift if (@_);

  if (defined $self->{'start'}) {
    return $self->{'start'};
  }

  return undef;
}

sub end{
  my $self = shift;
  $self->{'end'} = shift if (@_);

  if (defined $self->{'end'}) {
    return $self->{'end'};
  }

  return undef;
}


sub transcript_association{
  my $self = shift;
  $self->{'transcript_association'} = shift if (@_);

  if (defined $self->{'transcript_association'}) {
    return $self->{'transcript_association'};
  }

  return undef;
}




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