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

NAME

Bio::Phylo::Matrices::Alignment - The alignment object to aggregate sequences.

SYNOPSIS

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

my $alignment = Bio::Phylo::Matrices::Alignment->new;
my $sequence  = Bio::Phylo::Matrices::Sequence->new;

$alignment->insert($sequence);

DESCRIPTION

This module aggregates sequence objects in a larger container object. The alignment object inherits from the Bio::Phylo::Listable object, so look there for more methods applicable to alignment objects.

METHODS

CONSTRUCTOR

new()
Type    : Constructor
Title   : new
Usage   : my $alignment = 
          Bio::Phylo::Matrices::Alignment->new;
Function: Instantiates a 
          Bio::Phylo::Matrices::Alignment object.
Returns : A Bio::Phylo::Matrices::Alignment object.
Args    : NONE required.

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::Listable

This object inherits from Bio::Phylo::Listable, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Alignment 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: Alignment.pm,v 1.11 2006/03/14 12:01:56 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.