Bio::Map CytoMap
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
Package variables
No package variables defined.
Inherit
Bio::Map::SimpleMap
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
BEGIN Code
newDescriptionCode
typeDescriptionCode
lengthDescriptionCode
Methods description
newcode    nextTop
 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
typecodeprevnextTop
 Title   : type
 Usage   : my $type = $map->type
 Function: Get hard-coded Map type
 Returns : String coding Map type (always 'cyto')
 Args    : none
lengthcodeprevnextTop
 Title   : length
 Usage   : my $length = $map->length();
 Function: Retrieves the length of the map,
 Returns : 0 since length is not calculatable for cytogenetic maps
 Args    : none
Methods code
BEGINTop
BEGIN {
 $MAPCOUNT = 1;
}
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
	
    my $self = $class->SUPER::new(@args);
	
    $self->{'_uid'} = $MAPCOUNT++;
    my ($uid) = $self->_rearrange([qw(UID)], @args);
    defined $uid && $self->unique_id($uid);
	
    return $self;
}
typedescriptionprevnextTop
sub type {
   return 'cyto';
}
lengthdescriptionprevnextTop
sub length {
   return 0;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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:
  http://bugzilla.open-bio.org/
AUTHOR - Heikki LehvaslaihoTop
Email heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Jason Stajich jason@bioperl.org
Lincoln Stein lstein@cshl.org
Sendu Bala bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _