Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands use Bio::Map::CytoMap; my $map = new Bio::Map::CytoMap(-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.

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email heikki@ebi.ac.uk Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Modified methods
All methods present in Bio::Map::SimpleMap are implemted by this class. Most of the methods are inherited from SimpleMap. The following methods have been modified to refelect the needs of cytogenetic maps.

new
Title : new Usage : my $obj = new Bio::Map::CytoMap(); 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 Args :

length
Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map, Returns : undef since length is not calculatable for cytogenetic maps Args : none

Methods inherited from Bio::Map::SimpleMap

species
Title : species Usage : my $species = $map->species; Function: Get/Set Species for a map Returns : Bio::Species object or string Args : (optional) Bio::Species or string

units
Title : units Usage : $map->units('cM'); Function: Get/Set units for a map Returns : units for a map Args : units for a map (string)

name
Title : name Usage : my $name = $map->name Function: Get/Set Map name Returns : Map name Args : (optional) string

unique_id
Title : unique_id Usage : my $id = $map->unique_id; Function: Get/Set the unique ID for this map Returns : a unique identifier Args : [optional] new identifier to set

each_element
Title : each_element Usage : my @elements = $map->each_element; Function: Retrieves all the elements in a map unordered Returns : Array of Bio::Map::MappableI objects Args : none

New methods