Bio::Map::CytoMap(3) 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


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.


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AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org


Jason Stajich [email protected] Lincoln Stein [email protected] Sendu Bala [email protected]


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