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.