/ 
Bio-Phylo-0.10
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Matrices::Sequence

NAME

Bio::Phylo::Matrices::Sequence - The molecular sequence object.

SYNOPSIS

use Bio::Phylo::Matrices::Sequence;
use Bio::Phylo::Matrices::Alignment;
use Bio::Phylo::Taxa::Taxon;

#instantiating a sequence object...
my $sequence = Bio::Phylo::Matrices::Sequence->new;
$sequence->set_type('DNA');
$sequence->set_seq('ACGCATCGACTCAGAC');

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

#instantiate an alignment object...
my $alignment = Bio::Phylo::Matrices::Alignment->new;

#...and insert the sequence into the alignment
$alignment->insert($sequence);

DESCRIPTION

The sequence object models a character sequence, which can be crossreferenced with a taxon object, and inserted in an alignment object.

METHODS

CONSTRUCTOR

new()
Type    : Constructor
Title   : new
Usage   : my $sequence = 
          Bio::Phylo::Matrices::Sequence->new;
Function: Instantiates a 
          Bio::Phylo::Matrices::Sequence object.
Returns : A Bio::Phylo::Matrices::Sequence object.
Args    : Optional arguments:
          -type  => 'DNA', (a string)
          -seq   => 'ACGCATCGACTACGCAG', (a string)
          -taxon => $taxon (a Bio::Phylo::Taxa::Taxon 
                    object)

MUTATORS

set_taxon()
Type    : Mutator
Title   : set_taxon
Usage   : $sequence->set_taxon($taxon);
Function: Assigns the taxon a sequence refers to.
Returns : Modified Bio::Phylo::Matrices::Sequence object.
Args    : $taxon must be a Bio::Phylo::Taxa::Taxon object.
set_type()
Type    : Mutator
Title   : set_type
Usage   : $sequence->set_type($type);
Function: Assigns a sequence'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 seq is validated against 
          the IUPAC nucleotide one letter codes. If 
          PROTEIN is defined, the seq is validated 
          against IUPAC one letter amino acid codes. 
          Likewise, a STANDARD seq has to be a single 
          integer [0-9], while for CONTINUOUS all of 
          Perl's number formats are allowed.
set_seq()
Type    : Mutator
Title   : set_seq
Usage   : $sequence->set_seq('GATTACA');
Function: Assigns a character string 
          to the sequence object.
Returns : The modified invocant.
Args    : A character string.
Comments: The string 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 
          character type must be specified first 
          using the $sequence->set_type method.

ACCESSORS

get_taxon()
Type    : Accessor
Title   : get_taxon
Usage   : my $taxon = $sequence->get_taxon;
Function: Retrieves the taxon a sequence refers to.
Returns : Bio::Phylo::Taxa::Taxon
Args    : NONE
get_type()
Type    : Accessor
Title   : get_type
Usage   : my $type = $sequence->get_type;
Function: Retrieves a sequence's type.
Returns : One of [DNA|RNA|STANDARD|PROTEIN|
          NUCLEOTIDE|CONTINUOUS]
Args    : NONE
get_seq()
Type    : Accessor
Title   : get_seq
Usage   : my $string = $sequence->get_char;
Function: Retrieves a sequence object's raw 
          character string;
Returns : A character 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::Sequence 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: Sequence.pm,v 1.14 2006/03/14 12:01:57 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.