| Bio::Map::CytoMap(3pm) | User Contributed Perl Documentation | Bio::Map::CytoMap(3pm) |
Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
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);
}
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.
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.
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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.
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:
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Email heikki-at-bioperl-dot-org
Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : type Usage : my $type = $map->type Function: Get hard-coded Map type Returns : String coding Map type (always 'cyto') Args : none
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
| 2018-10-27 | perl v5.26.2 |