TinyTranscript.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::IdMapping::TinyTranscript - lightweight transcript object
 
=head1 SYNOPSIS
 
  # fetch a transcript from the db and create a lightweight
  # transcript object from it
  my $tr = $transcript_adaptor->fetch_by_stable_id('ENST000345437');
  my $lightweight_tr =
    Bio::EnsEMBL::IdMapping::TinyTranscript->new_fast( [
      $tr->dbID,          $tr->stable_id,
      $tr->version,       $tr->created_date,
      $tr->modified_date, $tr->start,
      $tr->end,           $tr->strand,
      $tr->length,        md5_hex( $tr->spliced_seq ),
    ] );
 
=head1 DESCRIPTION
 
This is a lightweight transcript object for the stable Id mapping. See
the documentation in TinyFeature for general considerations about its
design.
 
=head1 METHODS
 
  start
  end
  strand
  length
  seq_md5_sum
  add_Translation
  translation
  add_Exon
  get_all_Exons
 
=cut
 
package Bio::EnsEMBL::IdMapping::TinyTranscript;
 
# internal data structure (array indices):
#
#  0-4 see TinyFeature
#  5  start
#  6  end
#  7  strand
#  8  length
#  9  seq_md5_sum
# 10  translation
# 11  [exons]
# 12  biotype
# 13  slice
 
 
use strict;
use warnings;
no warnings 'uninitialized';
 
use Bio::EnsEMBL::IdMapping::TinyFeature;
our @ISA = qw(Bio::EnsEMBL::IdMapping::TinyFeature);
 
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 
 
=head2 start
 
  Arg[1]      : (optional) Int - the transcript's start coordinate
  Description : Getter/setter for the transcript's start coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub start {
  my $self = shift;
  $self->[5] = shift if (@_);
  return $self->[5];
}
 
 
=head2 end
 
  Arg[1]      : (optional) Int - the transcript's end coordinate
  Description : Getter/setter for the transcript's end coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub end {
  my $self = shift;
  $self->[6] = shift if (@_);
  return $self->[6];
}
 
 
=head2 strand
 
  Arg[1]      : (optional) Int - the transcript's strand
  Description : Getter/setter for the transcript's strand.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub strand {
  my $self = shift;
  $self->[7] = shift if (@_);
  return $self->[7];
}
 
 
=head2 length
 
  Arg[1]      : (optional) Int - the transcript's length
  Description : Getter/setter for the transcript's length. Note that this is
                *not* the distance between start and end, but rather the sum of
                the lengths of all exons.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub length {
  my $self = shift;
  $self->[8] = shift if (@_);
  return $self->[8];
}
 
 
=head2 seq_md5_sum
 
  Arg[1]      : (optional) String - the md5 digest of the transcript's sequence
  Description : Getter/setter for the md5 digest of the transcript's sequence.
                Note that when used as a setter, you are expected to pass a
                digest, not the raw sequence (i.e. the digest is not created for
                you).
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub seq_md5_sum {
  my $self = shift;
  $self->[9] = shift if (@_);
  return $self->[9];
}
 
 
 
=head2 add_Translation
 
  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyTranslation $tl - the translation
                to add
  Example     : $tiny_transcript->add_Translation($tiny_translation);
  Description : Adds a translation to this transcript.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub add_Translation {
  my $self = shift;
  my $tl = shift;
 
  unless ($tl && $tl->isa('Bio::EnsEMBL::IdMapping::TinyTranslation')) {
    throw('Need a Bio::EnsEMBL::IdMapping::TinyTranslation.');
  }
 
  $self->[10] = $tl;
}
 
 
=head2  translation
 
  Description : Getter for the transcript's translation.
  Return type : Bio::EnsEMBL::IdMapping::TinyTranslation
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub translation {
  return $_[0]->[10];
}
 
 
=head2 add_Exon
 
  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyExon $exon - the exon to add
  Example     : $tiny_transcript->add_Exon($tiny_exon);
  Description : Adds an exon to this transcript.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub add_Exon {
  my $self = shift;
  my $exon = shift;
 
  unless ($exon && $exon->isa('Bio::EnsEMBL::IdMapping::TinyExon')) {
    throw('Need a Bio::EnsEMBL::IdMapping::TinyExon.');
  }
 
  push @{ $self->[11] }, $exon;
}
 
 
=head2 get_all_Exons
 
  Example     : foreach my $exon (@{ $tiny_transcript->get_all_Exons }) {
                  # do something with exon
                }
  Description : Returns all exons attached to that transcript.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyExon objects
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub get_all_Exons {
  return $_[0]->[11] || [];
}
 
=head2 biotype
 
  Arg[1]      : (optional) String - the gene's biotype
  Description : Getter/setter for the gene's biotype.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub biotype {
  my $self = shift;
  $self->[12] = shift if (@_);
  return $self->[12];
}
 
=head2 seq_region_name
 
  Arg[1]      : (optional) String - seq_region name
  Description : Getter/setter for the seq_region name of the slice the gene is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub seq_region_name {
  my $self = shift;
  $self->[13] = shift if (@_);
  return $self->[13];
}
 
 
1;