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