NAME

Bio::Phylo::Matrices::Matrix - The matrix object to aggregate datum objects.

SYNOPSIS

 use Bio::Phylo::Matrices::Matrix;
 use Bio::Phylo::Matrices::Datum;
 
 # instantiate matrix object
 my $matrix = Bio::Phylo::Matrices::Matrix->new;

 # instantiate 1000 datum objects and insert them in the matrix
 for my $i ( 0 .. 1000 ) {
    my $datum = Bio::Phylo::Matrices::Datum->new( -pos => $i );
    $matrix->insert($datum);
 }
 
 # retrieve all datum objects whose position >= 500
 my @second_half_of_matrix = @{ $matrix->get_by_value(
    -value => 'get_position',
    -ge    => 500
 ) };
 

DESCRIPTION

This module defines a container object that holds Bio::Phylo::Matrices::Datum objects. The matrix object inherits from Bio::Phylo::Listable, so the methods defined there apply here.

METHODS

CONSTRUCTOR

new()

 Type    : Constructor
 Title   : new
 Usage   : my $matrix = Bio::Phylo::Matrices::Matrix->new;
 Function: Instantiates a Bio::Phylo::Matrices::Matrix object.
 Returns : A Bio::Phylo::Matrices::Matrix object.
 Args    : NONE required, but look up the inheritance tree to the SUPER class
           Bio::Phylo::Listable, and its parent Bio::Phylo

SEE ALSO

Bio::Phylo::Listable

This object inherits from Bio::Phylo::Listable, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix 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: Matrix.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.