Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::Map::MapI - Interface for describing Map objects in bioperl


           # get a MapI somehow
           my $name   = $map->name();     # string
           my $length = $map->length();   # integer
           my $species= $map->species;    # Bio::Species
           my $type   = $map->type();     # genetic/sts/rh/


       This object describes the basic functionality of a Map in bioperl.  Maps are anything from
       Genetic Map to Sequence Map to Assembly Map to Restriction Enzyme to FPC.


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AUTHOR - Jason Stajich



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


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

   EntityI methods
        These are fundamental to coordination of Maps and other entities, so are
        implemented at the interface level

        Title   : get_position_handler
        Usage   : my $position_handler = $entity->get_position_handler();
        Function: Gets a PositionHandlerI that $entity is registered with.
        Returns : Bio::Map::PositionHandlerI object
        Args    : none

   PositionHandlerI-related methods
        These are fundamental to coordination of Maps and other entities, so are
        implemented at the interface level

        Title   : get_positions
        Usage   : my @positions = $mappable->get_positions();
        Function: Get all the Positions on this Map (sorted).
        Returns : Array of L<Bio::Map::PositionI> objects
        Args    : none for all, OR
                  L<Bio::Map::MappableI> object for positions of the given Mappable

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

        Title   : purge_positions
        Usage   : $map->purge_position();
        Function: Remove all positions from this map. Notifies the positions they are
                  no longer on this map.
        Returns : n/a
        Args    : none to remove all positions, OR
                  L<Bio::Map::PositionI> object to remove just that Position, OR
                          L<Bio::Map::MappableI> object to remove only those positions of the
                  given mappable

        Title   : get_elements
        Usage   : my @elements = $map->get_elements;
        Function: Retrieves all the elements on a map (unordered)
        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   : common_elements
        Usage   : my @common_elements = $map->common_elements(\@other_maps);
                  my @common_elements = Bio::Map::SimpleMap->common_elements(\@maps);
        Function: Find the elements that are common to multiple maps.
        Returns : array of Bio::Map::MappableI
        Args    : arg #1 = L<Bio::Map::MapI> to compare this one to, or an array ref
                           of such objects (mandatory)
                  arg #2 = optionally, one or more of the key => value pairs below
                  -min_num => int        : the minimum number of input maps an element
                                           must be found on before before returned
                                           [default is 1]
                  -min_percent => number : as above, but the minimum percentage of
                                           input maps [default is 100 - note that this
                                           will effectively override all other options]
                  -require_self => 1|0   : require that all output elements at least
                                           be on the calling map [default is 1, has no
                                           effect when the second usage form is used]
                  -required => \@maps    : require that all output elements be on at
                                           least all the maps supplied here

   MapI-specific methods
        Title   : species
        Usage   : my $species = $map->species;
        Function: Get/Set Species for a map
        Returns : L<Bio::Species> object
        Args    : (optional) Bio::Species

        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 undef if length is not calculateable
        Args    : none