Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps. # get map objects somehow # a marker with complex localisation $o_usat = new Bio::Map::Marker (-name=>'Chad Super Marker 2', -positions => [ [$map1, $position1], [$map1, $position2] ] ); # The markers deal with Bio::Map::Position objects which can also # be explicitely created and passed on to markers as an array ref: $o_usat2 = new Bio::Map::Marker (-name=>'Chad Super Marker 3', -positions => [ $pos1, $pos2 ] ); # a marker with unique position in a map $marker1 = new Bio::Map::Marker (-name=>'hypervariable1', -map => $map1, -position => 100 ); # an other way of creating a marker with unique position in a map: $marker2 = new Bio::Map::Marker (-name=>'hypervariable2'); $map1->add_marker($marker2); $marker2->position(100); # position method is a short cut for get/set'ing unigue positions # which overwrites previous values # to place a marker to other maps or to have multiple positions # for a map within the same map use add_position() $marker2->add_position(200); # new position in the same map $marker2->add_position($map2,200); # new map # setting a map() in a marker or adding a marker into a map are # identical mathods. Both set the bidirectional connection which is # used by the marker to remember its latest, default map. # Regardes of how marker positions are created, they are stored and # returned as Bio::Map::PositionI objects: # unique position print $marker1->position->value, "\n"; # several positions foreach $pos ($marker2->each_position($map1)) { print $pos->value, "\n"; } See Bio::Map::Position and Bio::Map::PositionI for more information. This object handles the notion of a generic marker. This marker will have a name and a position in a map. This object is intended to be used by a marker parser like Mapmaker.pm and then blessed into the proper type of marker (ie Microsatellite) by the calling script.

Design principles
A Marker is a central object in Bio::Map name space. A Map is a holder class for objects. A Marker has a Position in a Map. A Marker can be compared to an other Markers using boolean methods. Positions can have non-numeric values or other methods to store the locations, so they have a method numeric() which does the conversion. A Marker has a convinience method position() which is able to create Positions of required class from scalars by calling method get_position_object(). For more complex situations, a Marker can have multiple positions in multiple Maps. It is therefore possible to extract Positions (all or belonging to certain Map) and compare Markers to them. It is up to the programmer to make sure position values and Maps they belong to can be sensibly compared.

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email bioinformatics1@dieselwurks.com Heikki Lehvaslaiho heikki@ebi.ac.uk Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $o_marker = new Bio::Map::Marker( -name => 'Whizzy marker', -position => $position); Function: Builds a new Bio::Map::Marker object Returns : Bio::Map::Marker Args : -name => name of this microsatellite [optional], string,default 'Unknown' -positions => map position for this marker, [optional] Bio::Map::PositionI-inherited obj, no default)

name
Title : name Usage : $o_usat->name($new_name) _or_ my $name = $o_usat->name() Function: Get/Set the name for this Microsatellite Returns : A scalar representing the current name of this marker Args : If provided, the current name of this marker will be set to $new_name.

map
Title : map Usage : my $mymap = $marker->map(); Function: Get/Set the default map for the marker. This is set by L<Bio::Map::CytoMap::add_element> method Returns : L<Bio::Map::MapI> Args : [optional] new L<Bio::Map::MapI>

get_position_object
Title : get_position_class Usage : my $pos = $marker->get_position_object(); Function: To get an object of the default Position class for this Marker. Subclasses should redefine this method. The Position needs to be Bio::Map::PositionI. Returns : Bio::Map::Position Args : none See Bio::Map::Position and Bio::Map::PositionI for more information.

position
Title : position Usage : $position = $mappable->position($map); OR $mappable->position($position); # $position can be Bio::Map::PositionI $mappable->position(100); # or scalar if the marker has a default map $mappable->position($map, 100); # if not give explicit $map Function: Get/Set the Bio::Map::PositionI for a mappable element in a specific Map Adds the marker to a map automatically if Map is given. Altenaitvely, you can add the merker to the map first (L<Bio::Map::Map::add_element>) to set the default map Returns : Bio::Map::PositionI Args : $position - Bio::Map::PositionI # Position we want to set OR $map - Bio::Map::MapI AND scalar OR scalar, but only if the marker has been added to a map

add_position
Title : add_position Usage : $position->add_position($position) Function: Add the Position to the Marker container. If you are using this method, you need to add the Marker to the Map yourself Returns : none Args : Position - Reference to Bio::Map::PositionI

positions
Title : positions Usage : $mappable->positions([$pos1, $pos2, $pos3]); Function: Add multiple Bio::Map::PositionI for a mappable element in a Map. Returns : boolean Args : array ref of $map/value tuples or array ref of Positions

each_position
Title : each_position Usage : my @positions = $position->each_position('mapname'); Function: Retrieve a list of Positions Returns : Array of L<Bio::Map::PositionI> Args : none

purge_positions
Title : purge_positions Usage : $marker->purge_positions Function: Remove all the position values stored for a Marker Returns : none Args : [optional] only purge values for a given map

known_maps
Title : known_maps Usage : my @maps = $marker->known_maps Function: Returns the list of maps that this position has values for Returns : list of Bio::Map::MapI unique ids Args : none

in_map
Title : in_map Usage : if ( $position->in_map($map) ) {} Function: Tests if a position has values in a specific map Returns : boolean Args : a map unique id OR Bio::Map::MapI

Comparison methods

tuple
Title : tuple Usage : ($me, $you) = $self->_tuple($compare) Function: Utility ethod to extract numbers and test for missing values. Returns : tuple values Args : Bio::Map::MappableI or Bio::Map::PositionI

equals
Title : equals Usage : if( $mappable->equals($mapable2)) ... Function: Test if a position is equal to another position Returns : boolean Args : Bio::Map::MappableI or Bio::Map::PositionI

less_than
Title : less_than Usage : if( $mappable->less_than($m2) ) ... Function: Tests if a position is less than another position Returns : boolean Args : Bio::Map::MappableI or Bio::Map::PositionI

greater_than
Title : greater_than Usage : if( $mappable->greater_than($m2) ) ... Function: Tests if position is greater than another position Returns : boolean Args : Bio::Map::MappableI or Bio::Map::PositionI