Raw content of Bio::Map::LinkageMap
<![CDATA[# BioPerl module for Bio::Map::LinkageMap
#
# 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::LinkageMap - A representation of a genetic linkage map.
=head1 SYNOPSIS
use Bio::Map::LinkageMap;
# create a new map
my $map = new Bio::Map::LinkageMap(-name => 'Chads Superterriffic Map',
-type => 'Linkage',
-units=> 'cM');
# create the location of a marker for that map
my $position = new Bio::Map::LinkagePosition( -positions => 1,
-distance => "22.3");
# create a marker and place it at that position
my $marker = new Bio::Map::Marker::Microsatellite(
-name => 'SuuuperMarker',
-position => $position);
# place that marker on that map
$map->add_element($marker);
# done!
=head1 DESCRIPTION
This object describes the basic functionality of a genetic linkage map in
Bioperl. Each 'position' can have one or more markers that map some number of
units from the markers at the previous 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 - 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::LinkageMap;
use vars qw(@ISA);
use strict;
use Bio::Map::SimpleMap;
@ISA = qw(Bio::Map::SimpleMap);
=head2 new
Title : new
Usage : my $linkage_map = new Bio::Map::LinkageMap();
Function: Builds a new Bio::Map::LinkageMap object
Returns : Bio::Map::LinkageMap
Args : -name => the name of the map (string) [optional]
-type => the type of this map (string, defaults to Linkage) [optional]
-species => species for this map (Bio::Species) [optional]
-units => the map units (string, defaults to cM) [optional]
-elements=> elements to initialize with
(arrayref of Bio::Map::MappableI objects) [optional]
-uid => Unique ID of this map
=cut
# new provided by SimpleMap
=head2 length()
Title : length()
Usage : my $length = $map->length();
Function: Retrieves the length of the map. In the case of a LinkageMap, the
length is the sum of all marker distances.
Returns : An integer representing the length of this LinkageMap. Will return
undef if length is not calculateable
Args : None.
=cut
sub length {
my ($self) = @_;
my $total_distance;
foreach (@{$self->{'_elements'}}) {
if ($_) {
$total_distance += ($_->position()->each_position_value($self))[0];
}
}
return $total_distance;
}
=head2 add_element($marker)
Title : add_element($marker)
Usage : $map->add_element($marker)
Function: Add a Bio::Map::MappableI object to the Map
Returns : none
Args : Bio::Map::MappableI object
Notes : It is strongly recommended that you use a
Bio::Map::LinkagePosition as the position in any
Bio::Map::Mappable that you create to place on this
map. Using some other Bio::Map::Position might work but might
be unpredictable.
N.B. I've added Bio::Map::OrderedPosition which should achieve
similar things from LinkagePosition and will work for
RH markers too.
=cut
#'
sub _add_element {
my ($self,$marker) = @_;
my $o_position = $marker->position();
$self->debug( "marker position is ". $marker->position());
# print("add_element: \$o_position is $o_position\n");
# print("add_element: \$marker is $marker\n");
my $position;
unless ( $o_position->isa('Bio::Map::LinkagePosition') ||
$o_position->isa('Bio::Map::OrderedPosition')
) {
$self->warn("You really should use a Linkage Position for this object. This insures that there is only one position. Trying anyway...");
my @p = ( $o_position->each_position_value($self));
$position = shift @p;
if( ! defined $position ) {
$self->throw("This marker ($marker) does not have a position in this map ($self)");
}
} else {
$position = $o_position->order;
}
if ($self->{'_elements'}[$position]) {
$self->warn("Replacing the marker in position $position because in a linkage map the position is a key.");
}
$self->{'_elements'}[$position] = $marker;
}
=head2 each_element
Title : each_element
Usage : my @elements = $map->each_element;
Function: Retrieves all the elements in a map
_ordered_.
Returns : An array containing MappableI objects.
Args : None.
Notes : This is a useless concept in the context of a linkage map but is
included if you want a list of all of the marker names on the map.
=cut
sub each_element {
my ($self) = @_;
return @{$self->{'_elements'}};
}
=head2 implemented by Bio::Map::SimpleMap
=cut
=head2 name($new_name)
Title : name($new_name)
Usage : my $name = $map->name($new_name) _or_
my $length = $map->name()
Function: Get/set the name of the map.
Returns : The current name of the map.
Args : If provided, the name of the map is set to $new_name.
=head2 species
Title : species
Usage : my $species = $map->species;
Function: Get/Set Species for a map
Returns : Bio::Species object
Args : (optional) Bio::Species
=head2 units
Title : units
Usage : $map->units('cM');
Function: Get/Set units for a map
Returns : units for a map
Args : units for a map (string)
=head2 type
Title : type
Usage : my $type = $map->type
Function: Get/Set Map type
Returns : String coding map type
Args : (optional) string
=head2 unique_id
Title : unique_id
Usage : my $id = $map->unique_id;
Function: Get/Set the unique ID for this map
Returns : a unique identifier
Args : [optional] new identifier to set
=cut
1;
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