Raw content of Bio::Map::OrderedPosition
<![CDATA[# BioPerl module for Bio::Map::OrderedPosition
#
# Cared for by Chad Matsalla <bioinformatics1@dieselwurks.com>
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::OrderedPosition - Abstracts the notion of a member
of an ordered list of markers. Each marker is a certain distance
from the one in the ordered list before it.
=head1 SYNOPSIS
use Bio::Map::OrderedPosition;
# the first marker in the sequence
my $position = new Bio::Map::OrderedPosition(-order => 1,
-positions => [ [ $map, 22.3] ] );
# the second marker in the sequence, 15.6 units from the fist one
my $position2 = new Bio::Map::OrderedPosition(-order => 2,
-positions => [ [ $map, 37.9] ] );
# the third marker in the sequence, coincidental with the second
# marker
my $position3 = new Bio::Map::OrderedPosition(-order => 3,
-posititions => [ [ $map, 37.9]] );
=head1 DESCRIPTION
This object is an implementation of the PositionI interface and the
Position object handles the specific values of a position.
OrderedPosition is intended to be slightly more specific then Position
but only specific enough for a parser from the MarkerIO subsystem to
create and then pass to a client application to bless into the proper
type. For an example of how this is intended to work, see the
Mapmaker.pm.
No units are assumed here - units are handled by context of which Map
a position is placed in.
Se Bio::Map::Position for additional information.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Chad Matsalla
Email bioinformatics1@dieselwurks.com
=head1 CONTRIBUTORS
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki@ebi.ac.uk
Jason Stajich, jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::OrderedPosition;
use vars qw(@ISA);
use strict;
use Bio::Map::Position;
@ISA = qw(Bio::Map::Position);
=head2 new
Title : new
Usage : my $obj = new Bio::Map::OrderedPosition();
Function: Builds a new Bio::Map::OrderedPosition object
Returns : Bio::Map::OrderedPosition
Args : -order - The order of this position
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
# $self->{'_order'} = [];
my ($map, $marker, $value, $order) =
$self->_rearrange([qw( MAP
MARKER
VALUE
ORDER
)], @args);
# print join ("|-|", ($map, $marker, $value, $order)), "\n";
$map && $self->map($map);
$marker && $self->marker($marker);
$value && $self->value($value);
$order && $self->order($order);
return $self;
}
=head2 order
Title : order
Usage : $o_position->order($new_position) _or_
$o_position->order()
Function: get/set the order position of this position in a map
Returns :
Args : If $new_position is provided, the current position of this Position
will be set to $new_position.
=cut
sub order {
my ($self,$order) = @_;
if ($order) {
# no point in keeping the old ones
$self->{'_order'} = $order;
}
return $self->{'_order'};
}
=head2 Bio::Map::Position functions
=cut
=head2 known_maps
Title : known_maps
Usage : my @maps = $position->known_maps
Function: Returns the list of maps that this position has values for
Returns : list of Bio::Map::MapI unique ids
Args : none
=head2 in_map
Title : in_map
Usage : if ( $position->in_map($map) ) {}
Function: Tests if a position has values in a specific map
Returns : boolean
Args : a map unique id OR Bio::Map::MapI
=head2 each_position_value
Title : positions
Usage : my @positions = $position->each_position_value($map);
Function: Retrieve a list of positions coded as strings or ints
Returns : Array of position values for a Map
Args : Bio::Map::MapI object to get positions for
=head2 add_position_value
Title : add_position_value
Usage : $position->add_position_value($map,'100');
Function: Add a numeric or string position to the PositionI container
and assoiciate it with a Bio::Map::MapI
Returns : none
Args : $map - Bio::Map::MapI
String or Numeric coding for a position on a map
=head2 purge_position_values
Title : purge_position_values
Usage : $position->purge_position_values
Function: Remove all the position values stored for a position
Returns : none
Args : [optional] only purge values for a given map
=head2 equals
Title : equals
Usage : if( $mappable->equals($mapable2)) ...
Function: Test if a position is equal to another position.
Returns : boolean
Args : Bio::Map::PositionI
=cut
sub equals{
my ($self,$compare) = @_;
return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
return ( $compare->order == $self->order);
}
# admittedly these are really the best comparisons in the world
# but it is a first pass we'll need to refine the algorithm or not
# provide general comparisions and require these to be implemented
# by objects closer to the specific type of data
=head2 less_than
Title : less_than
Usage : if( $mappable->less_than($m2) ) ...
Function: Tests if a position is less than another position
It is assumed that 2 positions are in the same map.
Returns : boolean
Args : Bio::Map::PositionI
=cut
sub less_than{
my ($self,$compare) = @_;
return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
return ( $compare->order < $self->order);
}
=head2 greater_than
Title : greater_than
Usage : if( $mappable->greater_than($m2) ) ...
Function: Tests if position is greater than another position.
It is assumed that 2 positions are in the same map.
Returns : boolean
Args : Bio::Map::PositionI
=cut
sub greater_than{
my ($self,$compare) = @_;
return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
return ( $compare->order > $self->order);
}
1;
]]>