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