Bio::Map::SimpleMap(3pm)				User Contributed Perl Documentation				  Bio::Map::SimpleMap(3pm)

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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02						  Bio::Map::SimpleMap(3pm)