TinyExon.pm

Go to the documentation of this file.

=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::TinyExon - lightweight exon object
 
=head1 SYNOPSIS
 
  # fetch an exon from the db and create a lightweight exon object
  # from it
  my $exon = $exon_adaptor->fetch_by_stable_id('ENSE000345437');
  my $lightweight_exon = Bio::EnsEMBL::IdMapping::TinyExon->new_fast( [
      $exon->dbID,
      $exon->stable_id,
      $exon->version,
      $exon->created_date,
      $exon->modified_date,
      $exon->start,
      $exon->end,
      $exon->strand,
      $exon->slice->seq_region_name,
      $exon->slice->coord_system_name,
      $exon->slice->coord_system->version,
      $exon->slice->subseq( $exon->start, $exon->end, $exon->strand ),
      $exon->phase,
      $need_project,
  ] );
 
=head1 DESCRIPTION
 
This is a lightweight exon object for the stable Id mapping. See the
documentation in TinyFeature for general considerations about its
design.
 
=head1 METHODS
 
  start
  end
  strand
  seq_region_name
  coord_system_name
  coord_system_version
  seq
  phase
  need_project
  common_start
  common_end
  common_strand
  common_sr_name
  length
 
=cut
 
 
package Bio::EnsEMBL::IdMapping::TinyExon;
 
# internal data structure (array indices):
#
#  0-4 see TinyFeature
#  5  start
#  6  end
#  7  strand
#  8  seq_region_name
#  9  coord_system_name
# 10  coord_system_version
# 11  seq
# 12  phase
# 13  need_project
# 14  common_start
# 15  common_end
# 16  common_strand
# 17  common_sr_name
 
 
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 exon's start coordinate
  Description : Getter/setter for the exon'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 exon's end coordinate
  Description : Getter/setter for the exon'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 exon's strand
  Description : Getter/setter for the exon'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 seq_region_name
 
  Arg[1]      : (optional) String - seq_region name
  Description : Getter/setter for the seq_region name of the slice the exon is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub seq_region_name {
  my $self = shift;
  $self->[8] = shift if (@_);
  return $self->[8];
}
 
 
=head2 coord_system_name
 
  Arg[1]      : (optional) String - coord_system name
  Description : Getter/setter for the coord_system name of the slice the exon is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub coord_system_name {
  my $self = shift;
  $self->[9] = shift if (@_);
  return $self->[9];
}
 
 
=head2 coord_system_version
 
  Arg[1]      : (optional) String - coord_system version
  Description : Getter/setter for the coord_system version of the slice the
                exon is on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub coord_system_version {
  my $self = shift;
  $self->[10] = shift if (@_);
  return $self->[10];
}
 
 
=head2 seq
 
  Arg[1]      : (optional) String - the exon's sequence
  Description : Getter/setter for the exon's sequence.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub seq {
  my $self = shift;
  $self->[11] = shift if (@_);
  return $self->[11];
}
 
 
=head2 phase
 
  Arg[1]      : (optional) Int - the exon's phase
  Description : Getter/setter for the exon's phase.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub phase {
  my $self = shift;
  $self->[12] = shift if (@_);
  return $self->[12];
}
 
 
=head2 need_project
 
  Arg[1]      : (optional) Boolean - attribute to set
  Description : Getter/setter for the attribute determining whether an exon
                needs to be projected onto a common coord_system. You don't need
                to do so if the native coord_system is common to the source and
                target assemblies, or if no common coord_system is found (the
                Cache object has methods to determine this).
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub need_project {
  my $self = shift;
  $self->[13] = shift if (@_);
  return $self->[13];
}
 
 
=head2 common_start
 
  Arg[1]      : (optional) Int - the exon's start in common coord_system
                coordinates
  Description : Getter/setter for the exon's start in common coord_system
                coordinates. Will return $self->start if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub common_start {
  my $self = shift;
 
  # when used as a setter, always set a value
  $self->[14] = shift if (@_);
 
  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[14];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->start;
  }
}
 
 
=head2 common_end
 
  Arg[1]      : (optional) Int - the exon's end in common coord_system
                coordinates
  Description : Getter/setter for the exon's end in common coord_system
                coordinates. Will return $self->end if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub common_end {
  my $self = shift;
 
  # when used as a setter, always set a value
  $self->[15] = shift if (@_);
 
  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[15];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->end;
  }
}
 
 
=head2 common_strand
 
  Arg[1]      : (optional) Int - the exon's strand in common coord_system
                coordinates
  Description : Getter/setter for the exon's strand in common coord_system
                coordinates. Will return $self->strand if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub common_strand {
  my $self = shift;
 
  # when used as a setter, always set a value
  $self->[16] = shift if (@_);
 
  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[16];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->strand;
  }
}
 
 
=head2 common_sr_name
 
  Arg[1]      : (optional) String - seq_region name of the exon's slice on the
                common coord_system
  Description : Getter/setter for the seq_region name of the exon's slice on the
                common coord_system coordinates. Will return
                $self->seq_region_name if no projection to a common coord_system
                is required.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub common_sr_name {
  my $self = shift;
 
  # when used as a setter, always set a value
  $self->[17] = shift if (@_);
 
  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[17];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->seq_region_name;
  }
}
 
 
=head2 length
 
  Description : Returns the exon length (distance between start and end).
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub length {
  my $self = shift;
  return ($self->end - $self->start + 1);
}
 
 
 
1;