/ 
Bio-Phylo-0.03
River stage two • 8 direct dependents • 17 total dependents
/ Bio::Phylo::Matrices::Datum

NAME

Bio::Phylo::Matrices::Datum - An object-oriented module for storing single observations.

SYNOPSIS

use Bio::Phylo::Matrices::Matrix;

#instantiating a datum object...
my $datum = Bio::Phylo::Matrices::Datum->new(
   -name=>'Homo_sapiens,
   -type=>DNA,
   -desc=>'Cytochrome B, mtDNA',
   -pos=>1,
   -weight=>2,
   -char=>'C'
);

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

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.

MUTATORS

set_name()
Type    : Mutator
Title   : set_name
Usage   : $datum->set_name($name);
Function: Assigns a datums's name (i.e. the name of the taxon it refers to).
Returns :
Args    : $name must not contain [;|,|:|(|)]
set_taxon()
Type    : Mutator
Title   : set_taxon
Usage   : $datum->set_taxon($taxon);
Function: Assigns the taxon a datum refers to.
Returns :
Args    : $taxon must be a Bio::Phylo::Taxa::Taxon object.
set_desc()
Type    : Mutator
Title   : set_desc
Usage   : $datum->set_desc($desc);
Function: Assigns a description of the current datum.
Returns :
Args    : The $desc argument is a string of arbitrary length.
set_weight()
Type    : Mutator
Title   : set_weight
Usage   : $datum->set_weight($weight);
Function: Assigns a datums's weight.
Returns :
Args    : The $weight argument may 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 datums's type.
Returns :
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 datums's character value.
Returns :
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 datums's position.
Returns :
Args    : $pos must be an integer.

ACCESSORS

get_name()
Type    : Accessor
Title   : get_name
Usage   : $name = $datum->get_name();
Function: Retrieves a datums's name (i.e. the name of the taxon it refers to).
Returns : SCALAR
Args    :
get_taxon()
Type    : Accessor
Title   : get_taxon
Usage   : $taxon = $datum->get_taxon();
Function: Retrieves the taxon a datum refers to.
Returns : Phylo::Taxa::Taxon object
Args    :
get_desc()
Type    : Accessor
Title   : get_desc
Usage   : $desc = $datum->get_desc();
Function: Retrieves a description of the current datum.
Returns : SCALAR
Args    :
get_weight()
Type    : Accessor
Title   : get_weight
Usage   : $weight = $datum->get_weight();
Function: Retrieves a datums's weight.
Returns : SCALAR
Args    :
get_type()
Type    : Accessor
Title   : get_type
Usage   : $type = $datum->get_type();
Function: Retrieves a datums's type.
Returns : One of [DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS]
Args    :
get_char()
Type    : Accessor
Title   : get_char
Usage   : $char = $datum->get_char();
Function: Retrieves a datums's character value.
Returns : A single character.
Args    :
get_position()
Type    : Accessor
Title   : get_position
Usage   : $pos = $datum->get_position();
Function: Retrieves a datums's position.
Returns : a SCALAR integer.
Args    :

CONTAINER

container()
Type    : Internal method
Title   : container
Usage   : $datum->container;
Function:
Returns : SCALAR
Args    :
container_type()
Type    : Internal method
Title   : container_type
Usage   : $datum->container_type;
Function:
Returns : SCALAR
Args    :

AUTHOR

Rutger Vos, <rvosa@sfu.ca> http://www.sfu.ca/~rvosa/

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.

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