Bio::Map::SimpleMap(3pm) User Contributed Perl Documentation Bio::Map::SimpleMap(3pm)
NAME
Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map
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.
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
Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.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 _
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
perl v5.14.2 2012-03-02 Bio::Map::SimpleMap(3pm)