/ 
bioperl-1.0.2
/ Bio::Map::CytoMap

NAME

Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands

SYNOPSIS

    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);
    }

DESCRIPTION

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.

FEEDBACK

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://bioperl.org/bioperl-bugs/

AUTHOR - Heikki Lehvaslaiho

Email heikki@ebi.ac.uk

CONTRIBUTORS

Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org

APPENDIX

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