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Bio::Map::MarkerI.3pm

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
 
 

Support

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

bioperl-l@bioperl.org

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:

   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