Bio::Map::MarkerI - Interface for basic marker functionality Give standard usage here Describe the interface here

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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 jason@bioperl.org Describe contact details here Heikki Lehvaslaiho heikki@ebi.ac.uk Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Chad Matsalla bioinformatics1@dieselwurks.com The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

name($new_name)
Title : name($new_name) Usage : my $name = $o_usat->name($new_name) _or_ my $name = $o_usat->name() Function: Get/Set the name for this Marker 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.

add_position
Title : add_position Usage : $position->add_position($map,'100') Function: Add a numeric or string position to the PositionI container Returns : none Args : Map - Reference to Bio::Map::MapI String or Numeric coding for a position on a map

each_position
Title : positions Usage : my @positions = $position->each_position_value('mapname'); Function: Retrieve a list of positions coded as strings or ints Returns : Array of position values Args : none

purge_positions
Title : purge_positions Usage : $position->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

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 L<Bio::Map::PositionI>. Returns : L<Bio::Map::PositionI> Args : none

tuple
Title : tuple Usage : ($me, $you) = $self->_tuple($compare) Function: Utility method to extract numbers and test for missing values. Makes writing subsequent tests easier. Returns : a tuple of values or ranges Args : Bio::Map::MappableI or Bio::Map::PositionI

Bio::Map::MappableI methods

position
Title : position Usage : my position_string = $position->position('mapname'); Function: Get/Set method for single value positions. Gives a simplified interface when only one map and one position per marker is used. Returns : a position value Args : optional: Map - Reference to Bio::Map::MapI String or Numeric coding for a position on a map

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

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

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