Ewan Birney


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


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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AUTHOR - Jason Stajich

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 _


 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


 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


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


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


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


 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


 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


 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


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