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