/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Map::SimpleMap

NAME

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

SYNOPSIS

    use Bio::Map::SimpleMap;

    my $map = Bio::Map::SimpleMap->new(-name => 'genethon',
				      -type => 'Genetic',
				      -units=> 'cM',
				      -species => $human);

    foreach my $marker ( @markers ) { # get a list of markers somewhere
		$map->add_element($marker);
    }

    foreach my $marker ($map->get_elements) {
        # do something with this Bio::Map::MappableI
    }

DESCRIPTION

This is the basic implementation of a Bio::Map::MapI. It handles the essential storage of name, species, type, and units.

It knows which map elements (mappables) belong to it, and their position.

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/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk

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 = Bio::Map::SimpleMap->new();
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)
          -uid     => Unique Id [defaults to a unique integer]

species

Title   : species
Usage   : my $species = $map->species;
Function: Get/Set Species for a map
Returns : Bio::Taxon object or string
Args    : (optional) Bio::Taxon 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 0 in that case.
Returns : integer representing length of map in current units
          will return 0 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   : $map->add_element($element)
 Function: Tell a Bio::Map::MappableI object its default Map is this one; same
           as calling $element->default_map($map).

		   *** does not actually add the element to this map! ***

 Returns : none
 Args    : Bio::Map::MappableI object
 Status  : Deprecated, will be removed in next version

get_elements

Title   : get_elements
Usage   : my @elements = $map->get_elements;
Function: Retrieves all the elements on a map (unordered unless all elements
          have just 1 position on the map, in which case sorted)
Returns : Array of Map elements (L<Bio::Map::MappableI>)
Args    : none

each_element

Title   : each_element
Function: Synonym of the get_elements() method.
Status  : deprecated, will be removed in the next version

purge_element

Title   : purge_element
Usage   : $map->purge_element($element)
Function: Purge an element from the map.
Returns : none
Args    : Bio::Map::MappableI object

annotation

Title   : annotation
Usage   : $map->annotation($an_col);
          my $an_col = $map->annotation();
Function: Get the annotation collection (see Bio::AnnotationCollectionI)
          for this annotatable object.
Returns : a Bio::AnnotationCollectionI implementing object, or undef
Args    : none to get, OR
          a Bio::AnnotationCollectionI implementing object to set