———# BioPerl module for Bio::Map::LinkageMap
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# 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 = Bio::Map::LinkageMap->new(-name => 'Chads Superterriffic Map',
-type => 'Linkage',
-units=> 'cM');
# create the location of a marker for that map
my $position = Bio::Map::LinkagePosition->new( -positions => 1,
-distance => "22.3");
# create a marker and place it at that position
my $marker = Bio::Map::Marker::Microsatellite->new(
-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/wiki/Mailing_lists - 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 the
web:
=head1 AUTHOR - Chad Matsalla
Email bioinformatics1@dieselwurks.com
=head1 CONTRIBUTORS
Lincoln Stein lstein@cshl.org
Heikki Lehvaslaiho heikki-at-bioperl-dot-org
Jason Stajich jason@bioperl.org
Sendu Bala bix@sendu.me.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::LinkageMap;
use
strict;
=head2 new
Title : new
Usage : my $linkage_map = Bio::Map::LinkageMap->new();
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
=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
0 if length is not calculateable
Args : None.
=cut
sub
length
{
my
(
$self
) =
@_
;
$self
->throw(
"Not yet implemented correctly"
);
my
$total_distance
;
foreach
my
$element
(@{
$self
->get_elements}) {
#*** there is no such method ->each_position_value!
$total_distance
+= (
$element
->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
#*** what is this? what calls it? note that it seems to be private
sub
_add_element_will_be_deleted {
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
;
}
1;