/ 
Bio-Phylo-0.05
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Matrices::Datum

NAME

Bio::Phylo::Matrices::Datum - The single observations object.

SYNOPSIS

use Bio::Phylo::Matrices::Matrix;
use Bio::Phylo::Matrices::Datum;
use Bio::Phylo::Taxa::Taxon;

# instantiating a datum object...
my $datum = Bio::Phylo::Matrices::Datum->new(
   -name   => 'Tooth comb size,
   -type   => 'STANDARD',
   -desc   => 'Records the number of teeth in lower jaw tooth comb',
   -pos    => 1,
   -weight => 2,
   -char   => 6
);

# ...and linking it to a taxon object
$datum->set_taxon( Bio::Phylo::Taxa::Taxon->new( -name => 'Lemur_catta' ) );

# instantiating a matrix...
my $matrix = Bio::Phylo::Matrices::Matrix->new;

# ...and insert datum in matrix
$matrix->insert($datum);

DESCRIPTION

The datum object models a single observation, which can be crossreferenced with a taxon object.

METHODS

CONSTRUCTOR

new()
Type    : Constructor
Title   : new
Usage   : my $datum = new Bio::Phylo::Matrices::Datum;
Function: Instantiates a Bio::Phylo::Matrices::Datum object.
Returns : A Bio::Phylo::Matrices::Datum object.
Args    : None required. Optional:
          -taxon  => $taxon (A Bio::Phylo::Taxa::Taxon object)
          -weight => 0.234 (a perl number)
          -type   => (one of DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS)
          -char   => 3 (a single character state)
          -pos    => 2 (position in the matrix object)

MUTATORS

set_taxon()
Type    : Mutator
Title   : set_taxon
Usage   : $datum->set_taxon($taxon);
Function: Assigns the taxon a datum refers to.
Returns : Modified object.
Args    : $taxon must be a Bio::Phylo::Taxa::Taxon object.
set_weight()
Type    : Mutator
Title   : set_weight
Usage   : $datum->set_weight($weight);
Function: Assigns a datum's weight.
Returns : Modified object.
Args    : The $weight argument must be a number in any of Perl's number
          formats.
set_type()
Type    : Mutator
Title   : set_type
Usage   : $datum->set_type($type);
Function: Assigns a datum's type.
Returns : Modified object.
Args    : $type must be one of [DNA|RNA|STANDARD|PROTEIN|
          NUCLEOTIDE|CONTINUOUS]. If DNA, RNA or NUCLEOTIDE is defined, the
          subsequently set char is validated against the IUPAC nucleotide one
          letter codes. If PROTEIN is defined, the char is validated against
          IUPAC one letter amino acid codes. Likewise, a STANDARD char has to
          be a single integer [0-9], while for CONTINUOUS all of Perl's number
          formats are allowed.
set_char()
Type    : Mutator
Title   : set_char
Usage   : $datum->set_char($char);
Function: Assigns a datum's character value.
Returns : Modified object.
Args    : The $char argument is checked against the allowed ranges for the
          various character types: IUPAC nucleotide (for types of
          DNA|RNA|NUCLEOTIDE), IUPAC single letter amino acid codes
          (for type PROTEIN), integers (STANDARD) or any of perl's
          decimal formats (CONTINUOUS).
set_position()
Type    : Mutator
Title   : set_position
Usage   : $datum->set_position($pos);
Function: Assigns a datum's position.
Returns : Modified object.
Args    : $pos must be an integer.

ACCESSORS

get_taxon()
Type    : Accessor
Title   : get_taxon
Usage   : my $taxon = $datum->get_taxon;
Function: Retrieves the taxon a datum refers to.
Returns : Bio::Phylo::Taxa::Taxon
Args    : NONE
get_weight()
Type    : Accessor
Title   : get_weight
Usage   : my $weight = $datum->get_weight;
Function: Retrieves a datum's weight.
Returns : FLOAT
Args    : NONE
get_type()
Type    : Accessor
Title   : get_type
Usage   : my $type = $datum->get_type;
Function: Retrieves a datum's type.
Returns : One of [DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS]
Args    : NONE
get_char()
Type    : Accessor
Title   : get_char
Usage   : my $char = $datum->get_char;
Function: Retrieves a datum's character value.
Returns : A single character.
Args    : NONE
get_position()
Type    : Accessor
Title   : get_position
Usage   : my $pos = $datum->get_position;
Function: Retrieves a datum's position.
Returns : a SCALAR integer.
Args    : NONE

SEE ALSO

Bio::Phylo

This object inherits from Bio::Phylo, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Datum objects.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Datum.pm,v 1.20 2005/09/29 20:31:18 rvosa Exp $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca
web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.