NAME

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

SYNOPSIS

           # 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/

DESCRIPTION

       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.

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

       Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-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 _

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

   get_position_handler
        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

   get_positions
        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

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

   purge_positions
        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

   get_elements
        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

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

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

   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 undef if length is not calculateable
        Args    : none