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 => '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_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). 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_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 : 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
METHODS
- copy_atts()
-
Type : Method Title : copy_atts Usage : my $copy = $datum->copy_atts; Function: Creates an empty copy of invocant (i.e. no data, but all the attributes). Returns : Bio::Phylo::Matrices::Datum (shallow copy) Args : None - reverse()
-
Type : Method Title : reverse Usage : my $reversed = $datum->reverse; Function: Reverse a datum's character string. Returns : Reversed datum. Args : NONE - to_xml()
-
Type : Format converter Title : to_xml Usage : my $xml = $datum->to_xml; Function: Reverse a datum's XML representation. Returns : Valid XML string. Args : NONE
DESTRUCTOR
- DESTROY()
-
Type : Destructor Title : DESTROY Usage : $phylo->DESTROY Function: Destroys Phylo object Alias : Returns : TRUE Args : none Comments: You don't really need this, it is called automatically when the object goes out of scope.
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 1.28 2006/04/12 22:38:22 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.