Coordinate.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.
You may obtain a copy of the License at
 
     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.
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::Mapper::Coordinate
 
=head1 SYNOPSIS
 
=head1 DESCRIPTION
 
Representation of a mapped region in a sequence; returned from Mapper.pm
when the target region maps on to valid sequence.
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::Mapper::Coordinate;
 
use strict;
 
=head2 new
 
  Arg [1]     char|int id of object in mapped region
  Arg [2]     int start of region   
  Arg [3]     int end of region
  Arg [4]     int strand if region
  Arg [5]     Bio::EnsEMBL::CoordSystem  coordsytem of the region
  Function    creates a new Coordinate object
  Returntype  Bio::EnsEMBL::Mapper::Coordinate
  Exceptions  none
  Status      Stable
 
=cut
 
sub new {
  my ( $proto, $id, $start, $end, $strand, $coord_system, $rank ) = @_;
 
  my $class = ref($proto) || $proto;
 
  return
    bless( { 'id'           => $id,
             'start'        => $start,
             'end'          => $end,
             'strand'       => $strand,
             'coord_system' => $coord_system,
             'rank'         => $rank || 0
           },
           $class );
}
 
 
=head2 start
 
  Arg  1      int $start
              start coordinate of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
 
=cut
 
sub start {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'start'} = $value;
  }
 
  return $self->{'start'};
}
 
 
=head2 end
 
  Arg  1      int $end
              end coordinate of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
 
=cut
 
sub end {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'end'} = $value;
  }
 
  return $self->{'end'};
}
 
=head2 strand
 
  Arg  1      int $strand
              strand of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
 
=cut
 
sub strand {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'strand'} = $value;
  }
 
  return $self->{'strand'};
}
 
=head2 id
 
  Arg  1      char|int $id
              id of object in mapped region
          e.g. seq_region_id
  Function    getter/setter method
  Returntype  char|int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
 
=cut
 
sub id {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'id'} = $value;
  }
 
  return $self->{'id'};
}
 
=head2 name
 
  Arg  1      char name
              name of object in mapped region
          e.g. seq_region_name
  Function    getter/setter method
  Returntype  char
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
 
=cut
 
sub name {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'name'} = $value;
  }
 
  return $self->{'name'};
}
 
=head2 coord_system
 
  Arg  1      Bio::EnsEMBL::CoordSystem
  Function    getter/setter method
  Returntype  Bio::EnsEMBL::CoordSystem
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
 
=cut
 
sub coord_system {
  my ( $self, $value ) = @_;
 
  if ( defined($value) ) {
    $self->{'coord_system'} = $value;
  }
 
  return $self->{'coord_system'};
}
 
=head2 length
 
  Function    getter method
  Returntype  int
  Exceptions  none
  Caller      ?
  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;