Bio::Map::MarkerI(3) Interface for basic marker functionality


# do not use this module directly
# See Bio::Map::Marker for an example of
# implementation.


A Marker is a Bio::Map::Mappable with some properties particular to markers. It also offers a number of convienience methods to make dealing with map elements easier.


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AUTHOR - Jason Stajich

Email [email protected]


Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein [email protected] Jason Stajich [email protected] Chad Matsalla [email protected] Sendu Bala [email protected]


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


 Title   : get_position_class
 Usage   : my $position = $marker->get_position_object();
 Function: To get an object of the default Position class
           for this Marker. Subclasses should redefine this method.
           The Position returned needs to be a L<Bio::Map::PositionI> with
                   -element set to self.
 Returns : L<Bio::Map::PositionI>
 Args    : none for an 'empty' PositionI object, optionally
           Bio::Map::MapI and value string to set the Position's -map and -value


 Title   : position
 Usage   : my $position = $mappable->position();
 Function: Get/Set the Position of this Marker (where it is on which map),
           purging all other positions before setting.
 Returns : L<Bio::Map::PositionI>
 Args    : Bio::Map::PositionI
           Bio::Map::MapI AND
           scalar, but only if the marker has a default map


 Title   : positions
 Usage   : $marker->positions([$pos1, $pos2, $pos3]);
 Function: Add multiple Bio::Map::PositionI to this marker
 Returns : n/a
 Args    : array ref of $map/value tuples or array ref of Bio::Map::PositionI


 Title   : default_map
 Usage   : my $map = $marker->default_map();
 Function: Get/Set the default map for the marker.
 Returns : L<Bio::Map::MapI>
 Args    : [optional] new L<Bio::Map::MapI>


 Title   : in_map
 Usage   : if ( $marker->in_map($map) ) {}
 Function: Tests if this marker is found on a specific map
 Returns : boolean
 Args    : a map unique id OR Bio::Map::MapI