Bio::Map::CytoMap(3pm) User Contributed Perl Documentation Bio::Map::CytoMap(3pm)
NAME
Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
SYNOPSIS
use Bio::Map::CytoMap;
my $map = Bio::Map::CytoMap->new(-name => 'human1',
-species => $human);
foreach my $marker ( @markers ) { # get a list of markers somewhere
$map->add_element($marker);
}
DESCRIPTION
This is the simple implementation of cytogenetic maps based on Bio::Map::MapI. It handles the essential storage of name, species, type,
and units as well as in memory representation of the elements of a map.
For CytoMaps type is hard coded to be 'cytogeneticmap' and units are set to '' but can be set to something else.
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki Lehvaslaiho
Email heikki-at-bioperl-dot-org
CONTRIBUTORS
Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org 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 _
new
Title : new
Usage : my $obj = Bio::Map::CytoMap->new();
Function: Builds a new Bio::Map::CytoMap object
Returns : Bio::Map::CytoMap
Args : -name => name of map (string)
-species => species for this map (Bio::Species) [optional]
-elements=> elements to initialize with
(arrayref of Bio::Map::MappableI objects) [optional]
-uid => Unique Id
type
Title : type
Usage : my $type = $map->type
Function: Get hard-coded Map type
Returns : String coding Map type (always 'cyto')
Args : none
length
Title : length
Usage : my $length = $map->length();
Function: Retrieves the length of the map,
Returns : 0 since length is not calculatable for cytogenetic maps
Args : none
perl v5.14.2 2012-03-02 Bio::Map::CytoMap(3pm)