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Bio-Phylo-0.16_RC4
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Matrices::Datum

NAME

Bio::Phylo::Matrices::Datum - The character state sequence 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   => 'number of teeth in lower jaw comb',
   -pos    => 1,
   -weight => 2,
   -char   => [ 6 ],
);

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

# 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 or a sequence of observations, which can be linked to a taxon object.

METHODS

CONSTRUCTOR

new()
Type    : Constructor
Title   : new
Usage   : my $datum = Bio::Phylo::Matrices::Datum->new;
Function: Instantiates a Bio::Phylo::Matrices::Datum
          object.
Returns : A Bio::Phylo::Matrices::Datum object.
Args    : None required. Optional:
          -taxon  => $taxon,
          -weight => 0.234,
          -type   => DNA,
          -char   => [ 'G','A','T','T','A','C','A' ],
          -pos    => 2,

MUTATORS

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_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). The $char can be:
              * a single character;
              * a string of characters;
              * an array reference of characters;
Comments: Note that on assigning characters to a datum,
          previously set annotations are removed.
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.
set_annotation()
Type    : Mutator
Title   : set_annotation
Usage   : $datum->set_annotation(
              -char       => 1,
              -annotation => { -codonpos => 1 }
          );
Function: Assigns an annotation to a
          character in the datum.
Returns : Modified object.
Args    : Required: -char       => $int
          Optional: -annotation => $hashref
Comments: Use this method to annotate
          a single character. To annotate
          multiple characters, use
          'set_annotations' (see below).
set_annotations()
Type    : Mutator
Title   : set_annotations
Usage   : $datum->set_annotations(
              { '-codonpos' => 1 },
              { '-codonpos' => 2 },
              { '-codonpos' => 3 },
          );
Function: Assign annotations to
          characters in the datum.
Returns : Modified object.
Args    : Hash references, where
          position in the argument
          list matches that of the
          specified characters in
          the character list.
Comments: Use this method to annotate
          multiple characters. To
          annotate a single character,
          use 'set_annotation' (see
          above).

ACCESSORS

get_weight()
Type    : Accessor
Title   : get_weight
Usage   : my $weight = $datum->get_weight;
Function: Retrieves a datum's weight.
Returns : FLOAT
Args    : NONE
get_char()
Type    : Accessor
Title   : get_char
Usage   : my $char = $datum->get_char;
Function: Retrieves a datum's character value.
Returns : In scalar context, returns a single
          character, or a string of characters
          (e.g. a DNA sequence, or a space
          delimited series of continuous characters).
          In list context, returns a list of characters
          (of zero or more characters).
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
get_annotation()
Type    : Accessor
Title   : get_annotation
Usage   : $datum->get_annotation(
              '-char' => 1,
              '-key'  => '-codonpos',
          );
Function: Retrieves an annotation to
          a character in the datum.
Returns : SCALAR or HASH
Args    : Optional: -char => $int
          Optional: -key => $key
get_length()
Type    : Accessor
Title   : get_length
Usage   : my $length = $datum->get_length;
Function: Retrieves a datum's length.
Returns : a SCALAR integer.
Args    : NONE

METHODS

reverse()
Type    : Method
Title   : reverse
Usage   : $datum->reverse;
Function: Reverses a datum's contained characters
Returns : Returns modified $datum
Args    : NONE
concat()
Type    : Method
Title   : reverse
Usage   : $datum->concat($datum1);
Function: Appends $datum1 to $datum
Returns : Returns modified $datum
Args    : NONE
validate()
Type    : Method
Title   : validate
Usage   : $datum->validate;
Function: Validates character data contained by $datum
Returns : True or throws Bio::Phylo::Util::Exceptions::InvalidData
Args    : NONE
copy_atts()
Not implemented!
complement()
Not implemented!
slice()
Not implemented!

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::Taxa::TaxonLinker

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

Bio::Phylo::Util::XMLWritable

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

Bio::Phylo::Matrices::TypeSafeData

This object inherits from Bio::Phylo::Matrices::TypeSafeData, 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 3396 2007-03-26 18:08:40Z rvosa $

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.