SYNOPSIS
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
}
DESCRIPTION
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().
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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
AUTHOR - Jason Stajich
Email [email protected]CONTRIBUTORS
Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein [email protected] Sendu Bala [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
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]
species
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
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 0 if length is not calculateable Args : none
unique_id
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
add_element
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
get_elements
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
each_element
Title : each_element Function: Synonym of the get_elements() method. Status : deprecated, will be removed in the next version
purge_element
Title : purge_element Usage : $map->purge_element($element) Function: Purge an element from the map. Returns : none Args : Bio::Map::MappableI object
annotation
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