Bio::Map
CytoMap
Summary
Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Map::CytoMap;
my $map = new Bio::Map::CytoMap(-name => 'human1',
-species => $human);
foreach my $marker ( @markers ) { # get a list of markers somewhere
$map->add_element($marker);
}
Description
This is the simple implementation of cytogenetic maps based on
Bio::Map::MapI. It handles the essential storage of name, species,
type, and units as well as in memory representation of the elements of
a map.
For CytoMaps type is hard coded to be 'cytogeneticmap' and
units are set to '' but can be set to something else.
Methods
Methods description
Title : new
Usage : my $obj = new Bio::Map::CytoMap();
Function: Builds a new Bio::Map::CytoMap object
Returns : Bio::Map::CytoMap
Args : -name => name of map (string)
-species => species for this map (Bio::Species) [optional]
-elements=> elements to initialize with
(arrayref of Bio::Map::MappableI objects) [optional]
-uid => Unique Id |
Title : type
Usage : my $type = $map->type
Function: Get hard-coded Map type
Returns : String coding map type
Args : |
Title : length
Usage : my $length = $map->length();
Function: Retrieves the length of the map,
Returns : undef since length is not calculatable for
cytogenetic maps
Args : none |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_elements'} = [];
$self->{'_name'} = '';
$self->{'_species'} = '';
$self->{'_units'} = '';
$self->{'_type'} = 'cyto';
$self->{'_uid'} = $MAPCOUNT++;
my ($name, $type,$species, $units,
$elements,$uid) = $self->_rearrange([qw(NAME TYPE
SPECIES UNITS
ELEMENTS UID)], @args);
defined $name && $self->name($name);
defined $species && $self->species($species);
defined $units && $self->units($units);
defined $type && $self->type($type);
defined $uid && $self->unique_id($uid);
if( $elements && ref($elements) =~ /array/ ) {
foreach my $item ( @$elements ) {
$self->add_element($item);
}
}
return $self;} | sub type
{ my ($self) = @_;
return $self->{'_type'};} | sub length
{ my ($self,@args) = @_;
return undef; } | General documentation
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/MailList.shtml - About the mailing lists
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
email or the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/
| AUTHOR - Heikki Lehvaslaiho | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
All methods present in
Bio::Map::SimpleMap are implemted by this
class. Most of the methods are inherited from SimpleMap. The following
methods have been modified to refelect the needs of cytogenetic maps.
Title : species
Usage : my $species = $map->species;
Function: Get/Set Species for a map
Returns : Bio::Species object or string
Args : (optional) Bio::Species 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 : name
Usage : my $name = $map->name
Function: Get/Set Map name
Returns : Map name
Args : (optional) string
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 : each_element
Usage : my @elements = $map->each_element;
Function: Retrieves all the elements in a map
unordered
Returns : Array of Bio::Map::MappableI objects
Args : none