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