/ 
bioperl-1.2.3
/ Bio::Map::SimpleMap

NAME

Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map

SYNOPSIS

    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);
    }

DESCRIPTION

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().

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://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Heikki Lehvaslaiho heikki@ebi.ac.uk Lincoln Stein lstein@cshl.org

APPENDIX

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