Raw content of Bio::Map::CytoMap
<![CDATA[# $Id: CytoMap.pm,v 1.2 2002/10/22 07:45:15 lapp Exp $
#
# BioPerl module for Bio::Map::CytoMap
#
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.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/MailList.shtml - 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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email heikki@ebi.ac.uk
=head1 CONTRIBUTORS
Jason Stajich jason@bioperl.org
Lincoln Stein lstein@cshl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::CytoMap;
use vars qw(@ISA $MAPCOUNT);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Map::SimpleMap;
@ISA = qw(Bio::Root::Root Bio::Map::SimpleMap);
BEGIN { $MAPCOUNT = 1; }
=head2 Modified methods
All methods present in L<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.
=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->{'_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;
}
=head2 type
Title : type
Usage : my $type = $map->type
Function: Get hard-coded Map type
Returns : String coding map type
Args :
=cut
sub type {
my ($self) = @_;
return $self->{'_type'};
}
=head2 length
Title : length
Usage : my $length = $map->length();
Function: Retrieves the length of the map,
Returns : undef since length is not calculatable for
cytogenetic maps
Args : none
=cut
sub length{
my ($self,@args) = @_;
return undef;
}
=head2 Methods inherited from L<Bio::Map::SimpleMap>
=cut
=head2 species
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
=cut
=head2 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)
=cut
=head2 name
Title : name
Usage : my $name = $map->name
Function: Get/Set Map name
Returns : Map name
Args : (optional) string
=cut
=head2 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
=cut
=head2 each_element
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
=cut
=head2 New methods
=cut
1;
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