Bio::Map LinkageMap
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Summary
Bio::Map::LinkageMap - A representation of a genetic linkage map.
Package variables
No package variables defined.
Inherit
Bio::Map::SimpleMap
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!
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.
Methods
lengthDescriptionCode
_add_element_will_be_deleted
No description
Code
Methods description
lengthcode    nextTop
 Title   : length
Usage : my $length = $map->length();
Function: Retrieves the length of the map. In the case of a LinkageMap, the
length is the sum of all marker distances.
Returns : An integer representing the length of this LinkageMap. Will return
0 if length is not calculateable
Args : None.
Methods code
lengthdescriptionprevnextTop
sub length {
    my ($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 $total_distance;
}
_add_element_will_be_deleteddescriptionprevnextTop
sub _add_element_will_be_deleted {
    my ($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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chad MatsallaTop
Email bioinformatics1@dieselwurks.com
CONTRIBUTORSTop
Lincoln Stein lstein@cshl.org
Heikki Lehvaslaiho heikki-at-bioperl-dot-org
Jason Stajich jason@bioperl.org
Sendu Bala bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $linkage_map = Bio::Map::LinkageMap->new();
Function: Builds a new Bio::Map::LinkageMap object
Returns : Bio::Map::LinkageMap
Args : -name => the name of the map (string) [optional]
-type => the type of this map (string, defaults to Linkage) [optional]
-species => species for this map (Bio::Species) [optional]
-units => the map units (string, defaults to cM) [optional]
-elements=> elements to initialize with
(arrayref of Bio::Map::MappableI objects) [optional]
-uid => Unique ID of this map
add_element($marker)Top
 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.