Bio::Map::MarkerI(3) 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. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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: 

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email [email protected]

CONTRIBUTORS

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

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

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