Raw content of Bio::Map::SimpleMap
<![CDATA[# $Id: SimpleMap.pm,v 1.8 2002/10/22 07:45:16 lapp Exp $
#
# BioPerl module for Bio::Map::SimpleMap
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map
=head1 SYNOPSIS
use Bio::Map::SimpleMap;
my $map = new Bio::Map::SimpleMap(-name => 'genethon',
-type => 'Genetic',
-units=> 'cM',
-species => $human);
foreach my $marker ( @markers ) { # get a list of markers somewhere
$map->add_element($marker);
}
=head1 DESCRIPTION
This is the basic implementation of a 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.
Subclasses might need to redefine or hardcode type(), length() and
units().
=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 - Jason Stajich
Email jason@bioperl.org
=head1 CONTRIBUTORS
Heikki Lehvaslaiho heikki@ebi.ac.uk
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::SimpleMap;
use vars qw(@ISA $MAPCOUNT);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Map::MapI;
@ISA = qw(Bio::Root::Root Bio::Map::MapI);
BEGIN { $MAPCOUNT = 1; }
=head2 new
Title : new
Usage : my $obj = new Bio::Map::SimpleMap();
Function: Builds a new Bio::Map::SimpleMap object
Returns : Bio::Map::SimpleMap
Args : -name => name of map (string)
-species => species for this map (Bio::Species) [optional]
-units => map units (string)
-elements=> elements to initialize with
(arrayref of Bio::Map::MappableI objects) [optional]
-uid => Unique Id
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_elements'} = [];
$self->{'_name'} = '';
$self->{'_species'} = '';
$self->{'_units'} = '';
$self->{'_type'} = '';
$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 species
Title : species
Usage : my $species = $map->species;
Function: Get/Set Species for a map
Returns : Bio::Species object or string
Args : (optional) Bio::Species or string
=cut
sub species{
my ($self,$value) = @_;
if( defined $value ) {
$self->{'_species'} = $value;
}
return $self->{'_species'};
}
=head2 units
Title : units
Usage : $map->units('cM');
Function: Get/Set units for a map
Returns : units for a map
Args : units for a map (string)
=cut
sub units{
my ($self,$value) = @_;
if( defined $value ) {
$self->{'_units'} = $value;
}
return $self->{'_units'};
}
=head2 type
Title : type
Usage : my $type = $map->type
Function: Get/Set Map type
Returns : String coding map type
Args : (optional) string
=cut
sub type {
my ($self,$value) = @_;
# this may be hardcoded/overriden by subclasses
if( defined $value ) {
$self->{'_type'} = $value;
}
return $self->{'_type'};
}
=head2 name
Title : name
Usage : my $name = $map->name
Function: Get/Set Map name
Returns : Map name
Args : (optional) string
=cut
sub name {
my ($self,$value) = @_;
if( defined $value ) {
$self->{'_name'} = $value;
}
return $self->{'_name'};
}
=head2 length
Title : length
Usage : my $length = $map->length();
Function: Retrieves the length of the map,
It is possible for the length to be unknown
for maps such as Restriction Enzyme, will return undef
in that case
Returns : integer representing length of map in current units
will return undef if length is not calculateable
Args : none
=cut
sub length {
my ($self) = @_;
my ($len ) = 0;
foreach my $marker ($self->each_element) {
$len = $marker->position->numeric if $marker->position->numeric > $len;
}
return $len;
}
=head2 unique_id
Title : unique_id
Usage : my $id = $map->unique_id;
Function: Get/Set the unique ID for this map
Returns : a unique identifier
Args : [optional] new identifier to set
=cut
sub unique_id {
my ($self,$id) = @_;
if( defined $id ) {
$self->{'_uid'} = $id;
}
return $self->{'_uid'};
}
=head2 add_element
Title : add_element
Usage : $map->add_element($marker)
Function: Add a Bio::Map::MappableI object to the Map
Returns : none
Args : Bio::Map::MappableI object
=cut
sub add_element{
my ($self,$mapelement) = @_;
return unless ( defined $mapelement);
$self->throw("This is not a Bio::Map::MarkerI object but a [$self]")
unless $mapelement->isa('Bio::Map::MarkerI');
$mapelement->map($self); # tell the marker its default map
push @{$self->{'_elements'}}, $mapelement;
}
=head2 each_element
Title : each_element
Usage : my @elements = $map->each_element;
Function: Retrieves all the elements in a map
unordered
Returns : Array of Bio::Map::MappableI objects
Args : none
=cut
sub each_element{
my ($self) = @_;
return @{$self->{'_elements'}};
}
1;
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