NAME

Bio::Map::MarkerI - Interface for basic marker functionality

SYNOPSIS

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

DESCRIPTION

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.

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/wiki/Mailing_lists  - 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.open-bio.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Chad Matsalla bioinformatics1@dieselwurks.com Sendu Bala bix@sendu.me.uk

APPENDIX

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

get_position_object

 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
           attributes.

position

 Title   : position
 Usage   : my $position = $mappable->position();
		   $mappable->position($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
            OR
           Bio::Map::MapI AND
           scalar
            OR
           scalar, but only if the marker has a default map

positions

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

default_map

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>

in_map

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