Bio::Map::LinkageMap(3)

NAME
Bio::Map::LinkageMap - A representation of a genetic linkage map.

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!

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.

FEEDBACK

  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

  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:

  http://bugzilla.bioperl.org/

AUTHOR - Chad Matsalla
Email bioinformatics1@dieselwurks.com

CONTRIBUTORS
Lincoln Stein lstein@cshl.org Heikki Lehvaslaiho heikki@ebi.ac.uk Jason Stajich jason@bioperl.org

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  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

  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.

  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;
}

  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.

  implemented by Bio::Map::SimpleMap

  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.

  species
 Title   : species
 Usage   : my $species = $map->species;
 Function: Get/Set Species for a map
 Returns : Bio::Species object
 Args    : (optional) Bio::Species

  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)

  type
 Title   : type
 Usage   : my $type = $map->type
 Function: Get/Set Map type
 Returns : String coding map type
 Args    : (optional) string

  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