Raw content of Bio::Map::OrderedPositionWithDistance
<![CDATA[# BioPerl module for Bio::Map::OrderedPositionWithDistance
#
# 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::OrderedPositionWithDistance - 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::OrderedPositionWithDistance;
# the first marker in the sequence
my $position = new Bio::Map::OrderedPositionWithDistance(-positions => 1,
-distance => 22.3 );
# the second marker in the sequence, 15.6 units from the fist one
my $position2 = new Bio::Map::OrderedPositionWithDistance(-positions => 2,
-distance => 15.6 );
# the third marker in the sequence, coincidental with the second
# marker
my $position3 = new Bio::Map::OrderedPositionWithDistance(-positions => 3,
-distance => 0 );
=head1 DESCRIPTION
This object is an implementation of the PositionI interface and the
Position object handles the specific values of a position.
OrderedPositionWithDistance 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
=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::OrderedPositionWithDistance;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Map::Position;
@ISA = qw(Bio::Map::Position);
=head2 new
Title : new
Usage : my $obj = new Bio::Map::OrderedPositionWithDistance();
Function: Builds a new Bio::Map::OrderedPositionWithDistance object
Returns : Bio::Map::OrderedPositionWithDistance
Args : -positions - Should be a single value representing the order
of this marker within the list of markers
-distance - The distance this marker is from the marker before it.
0 reflects coincidentality.
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_positions'} = [];
my ($positions,$distance) = $self->_rearrange([qw(POSITIONS DISTANCE)], @args);
if( ref($positions) =~ /array/i ) {
foreach my $p ( @$positions ) {
$self->add_position($p);
}
} else {
$self->add_position($positions);
}
$distance && $self->distance($distance);
return $self;
}
=head2 distance($new_distance)
Title : distance($new_distance)
Usage : $position->distance(new_distance) _or_
$position->distance()
Function: get/set the distance of this position from the previous marker
Returns : A scalar representing the current distance for this position.
Args : If $new_distance is provided the distance of this Position will
be set to $new_distance
=cut
sub distance {
my ($self,$distance) = @_;
if ($distance) {
$self->{'_distance'} = $distance;
}
return $self->{'_distance'};
}
1;
]]>