Raw content of Bio::Map::Position
<![CDATA[# $Id: Position.pm,v 1.9 2002/10/22 07:45:16 lapp Exp $
#
# BioPerl module for Bio::Map::Position
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::Position - A single position of a Marker in a Map
=head1 SYNOPSIS
use Bio::Map::Position;
my $position = new Bio::Map::Position(-map => $map,
-marker => $marker
-value => 100
);
=head1 DESCRIPTION
This object is an implementation of the PositionI interface that
handles the specific values of a position. This allows an element
(e.g. Marker) to have multiple positions within a map and still be
treated as a single entity.
This does not directly handle the concept of a relative map in which
no known exact positions exist but markers are just ordered relative
to one another - in that case arbitrary values must be assigned for
position values.
No units are assumed here - units are handled by context of which Map
a position is placed in or the subclass of this Position.
=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 - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki@ebi.ac.uk
Chad Matsalla, bioinformatics1@dieselwurks.com
=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::Position;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Map::PositionI;
@ISA = qw(Bio::Root::Root Bio::Map::PositionI );
=head2 new
Title : new
Usage : my $obj = new Bio::Map::Position();
Function: Builds a new Bio::Map::Position object
Returns : Bio::Map::Position
Args : -map a <Bio::Map::MapI> object
-marker a <Bio::Map::MarkerI> object
-value string or number
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($map, $marker, $value) =
$self->_rearrange([qw( MAP
MARKER
VALUE
)], @args);
$map && $self->map($map);
$marker && $self->marker($marker);
$value && $self->value($value);
return $self;
}
=head2 map
Title : map
Usage : my $id = map->$map;
Function: Get/Set the map the position is in.
Returns : L<Bio::Map::MapI>
Args : [optional] new L<Bio::Map::MapI>
=cut
sub map {
my ($self,$map) = @_;
if( defined $map ) {
$self->throw("This is [$map], not a Bio::Map::MapI object")
unless $map->isa('Bio::Map::MapI');
$self->{'_map'} = $map;
}
return $self->{'_map'};
}
=head2 marker
Title : marker
Usage : my $id = marker->$marker;
Function: Get/Set the marker the position is in.
Returns : L<Bio::Map::MarkerI>
Args : [optional] new L<Bio::Map::MarkerI>
=cut
sub marker {
my ($self,$marker) = @_;
if( defined $marker ) {
$self->thow("This is [$marker], not a Bio::Map::MarkerI object")
unless $marker->isa('Bio::Map::MarkerI');
$self->{'_marker'} = $marker;
}
return $self->{'_marker'};
}
=head2 value
Title : value
Usage : my $pos = $position->value;
Function: Get/Set the value for this postion
Returns : scalar, value
Args : [optional] new value to set
=cut
sub value {
my ($self,$value) = @_;
if( defined $value ) {
$self->{'_value'} = $value;
}
return $self->{'_value'};
}
=head2 numeric
Title : numeric
Usage : my $num = $position->numeric;
Function: Read-only method that is guarantied to return a numeric
representation for this position.
Returns : numeric (int or real)
Args : none
=cut
sub numeric {
my ($self) = @_;
my $num = $self->{'_value'} || 0;
# expand this to cover scientific notation, too!
$self->throw("This value [$num] is not numeric!")
unless $num && $num =~ /^[+-]?[\d.]+$/;
return $num;
}
1;
]]>