Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map use Bio::Map::SimpleMap; my $map = new Bio::Map::SimpleMap(-name => 'genethon', -type => 'Genetic', -units=> 'cM', -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); } This is the basic implementation of a 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. Subclasses might need to redefine or hardcode type(), length() and units().

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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 jason@bioperl.org Heikki Lehvaslaiho heikki@ebi.ac.uk Lincoln Stein lstein@cshl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Map::SimpleMap(); Function: Builds a new Bio::Map::SimpleMap object Returns : Bio::Map::SimpleMap Args : -name => name of map (string) -species => species for this map (Bio::Species) [optional] -units => map units (string) -elements=> elements to initialize with (arrayref of Bio::Map::MappableI objects) [optional] -uid => Unique Id

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)

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

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

length
Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map, It is possible for the length to be unknown for maps such as Restriction Enzyme, will return undef in that case Returns : integer representing length of map in current units will return undef if length is not calculateable Args : none

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

add_element
Title : add_element Usage : $map->add_element($marker) Function: Add a Bio::Map::MappableI object to the Map Returns : none Args : Bio::Map::MappableI object

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