IndelCoordinate.pm

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=head1 LICENSE
 
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Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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     http://www.apache.org/licenses/LICENSE-2.0
 
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
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  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::Mapper::IndelCoordinate
 
=head1 SYNOPSIS
 
=head1 DESCRIPTION
 
Representation of a indel in a sequence; returned from Mapper.pm when
the target region is in a deletion.
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::Mapper::IndelCoordinate;
 
use Bio::EnsEMBL::Mapper::Gap;
use Bio::EnsEMBL::Mapper::Coordinate;
 
use vars qw(@ISA);
use strict;
 
@ISA = qw(Bio::EnsEMBL::Mapper::Coordinate Bio::EnsEMBL::Mapper::Gap);
 
 
=head2 new
 
  Arg [1]    : Bio::EnsEMBL::Mapper::Gap $gap
  Arg [2]    : Bio::EnsEMBL::Mapper::Coordinate $coordinate
  Example    : $indelCoord = Bio::EnsEMBL::Mapper::IndelCoordinate($gap, $coordinate);
  Description: Creates a new IndelCoordinate object.
  Returntype : Bio::EnsEMBL::Mapper::IndelCoordinate
  Exceptions : none
  Caller     : Bio::EnsEMBL::Mapper
 
=cut
 
sub new {
  my ( $proto, $gap, $coordinate ) = @_;
 
  my $class = ref($proto) || $proto;
 
  return
    bless( { 'start'        => $coordinate->start(),
             'end'          => $coordinate->end(),
             'strand'       => $coordinate->strand(),
             'id'           => $coordinate->id(),
             'coord_system' => $coordinate->coord_system(),
             'gap_start'    => $gap->start(),
             'gap_end'      => $gap->end()
           },
           $class );
}
 
=head2 gap_start
 
  Arg[1]      : (optional) int $gap_start
  Example     : $gap_start = $ic->gap_start()
  Description : Getter/Setter for the start of the Gap region
  ReturnType  : int
  Exceptions  : none
  Caller      : general
 
=cut
 
sub gap_start {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'gap_start'} = $value;
  }
 
  return $self->{'gap_start'};
}
 
=head2 gap_end
 
  Arg[1]      : (optional) int $gap_end
  Example     : $gap_end = $ic->gap_end()
  Description : Getter/Setter for the end of the Gap region
  ReturnType  : int
  Exceptions  : none
  Caller      : general
 
=cut
 
sub gap_end {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'gap_end'} = $value;
  }
 
  return $self->{'gap_end'};
}
 
=head2 gap_length
 
  Args        : None
  Example     : $gap_length = $ic->gap_length()
  Description : Getter for the length of the Gap region
  ReturnType  : int
  Exceptions  : none
  Caller      : general
 
=cut
 
sub gap_length {
  my ($self) = @_;
 
  return $self->{'gap_end'} - $self->{'gap_start'} + 1;
}
 
1;