| Bio::Map::MapI(3pm) | User Contributed Perl Documentation | Bio::Map::MapI(3pm) |
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.
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
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.
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
Email jason@bioperl.org
Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
| 2018-10-27 | perl v5.26.2 |