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://github.com/bioperl/bioperl-live/issues

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