Provided by: libbio-perl-perl_1.7.2-3_all bug


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


           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

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


       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().


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AUTHOR - Jason Stajich



       Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein Sendu Bala


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        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]

        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

        Title   : units
        Usage   : $map->units('cM');
        Function: Get/Set units for a map
        Returns : units for a map
        Args    : units for a map (string)

        Title   : type
        Usage   : my $type = $map->type
        Function: Get/Set Map type
        Returns : String coding map type
        Args    : (optional) string

        Title   : name
        Usage   : my $name = $map->name
        Function: Get/Set Map name
        Returns : Map name
        Args    : (optional) string

        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

        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

        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

        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

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

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

        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