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SENDU / bioperl-1.5.2_004-RCb / Bio / Map / CytoMap.pm 

            

              
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# $Id: CytoMap.pm,v 1.10.4.1 2006/10/02 23:10:21 sendu Exp $
#
# BioPerl module for Bio::Map::CytoMap
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands 
=head1 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);
    }
=head1 DESCRIPTION
This is the simple implementation of cytogenetic maps based on
L<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.
=head1 FEEDBACK
=head2 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
=head2 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:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email heikki-at-bioperl-dot-org
=head1 CONTRIBUTORS
Jason Stajich      jason@bioperl.org
Lincoln Stein      lstein@cshl.org
Sendu Bala         bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Map::CytoMap;
use vars qw($MAPCOUNT);
use strict;
use base qw(Bio::Map::SimpleMap);
BEGIN { $MAPCOUNT = 1; }
=head2 new
 Title   : new
 Usage   : my $obj = new Bio::Map::CytoMap();
 Function: Builds a new Bio::Map::CytoMap object
 Returns : Bio::Map::CytoMap
 Args    : -name    => name of map (string)
           -species => species for this map (Bio::Species) [optional]
           -elements=> elements to initialize with
                       (arrayref of Bio::Map::MappableI objects) [optional]
           -uid     => Unique Id
=cut
sub new {
    my ($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;
}
=head2 type
 Title   : type
 Usage   : my $type = $map->type
 Function: Get hard-coded Map type
 Returns : String coding Map type (always 'cyto')
 Args    : none
=cut
sub type {
   return 'cyto';
}
=head2 length
 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
=cut
sub length {
   return 0;
}
1;