| Bio::Map::SimpleMap(3pm) | User Contributed Perl Documentation | Bio::Map::SimpleMap(3pm) |
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
$map->add_element($marker);
}
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().
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
Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.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 _
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
| 2018-10-27 | perl v5.26.2 |