Bio::Map::MarkerI(3) User Contributed Perl Documentation Bio::Map::MarkerI(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Map::MarkerI(3)