Gap.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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distributed under the License is distributed on an "AS IS" BASIS,
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
  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::Mapper::Gap
 
=head1 SYNOPSIS
 
=head1 DESCRIPTION
 
Representation of a gap in a sequence; returned from Mapper.pm when the
target region is in a gap.
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::Mapper::Gap;
 
use strict;
 
=head2 new
 
  Arg [1]    : int $start
  Arg [2]    : int $end
  Example    : $gap = Bio::EnsEMBL::Mapper::Gap($start, $end);
  Description: Creates a new Gap object.
  Returntype : Bio::EnsEMBL::Mapper::Gap
  Exceptions : none
  Caller     : Bio::EnsEMBL::Mapper
  Status     : Stable
 
=cut
 
sub new {
  my ( $proto, $start, $end, $rank ) = @_;
 
  my $class = ref($proto) || $proto;
 
  return bless( { 'start' => $start, 'end' => $end, 'rank' => $rank  || 0 }, $class );
}
 
=head2 start
 
  Arg [1]    : (optional) int $start
               start coordinate of gap region
  Example    : $start = $gap->start();
  Description: Getter/Setter for the start attribute
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub start {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'start'} = $value;
  }
 
  return $self->{'start'};
}
 
=head2 end
 
  Arg [1]    : (optional) int $newval
               The new value to set the end coordinate to
  Example    : $end = $gap->end()
  Description: Getter/Setter for the end coordinate of the gap region
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub end {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'end'} = $value;
  }
 
  return $self->{'end'};
}
 
=head2 length
 
  Arg [1]    : none
  Example    : $len = $gap->length();
  Description: Getter for the length of this gap region
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub length {
  my ($self) = @_;
 
  return $self->{'end'} - $self->{'start'} + 1;
}
 
sub rank {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'rank'} = $value;
  }
 
  return $self->{'rank'};
}
 
1;