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In a rarefaction curve, an increasing number of randomly drawn members is
sampled from the given communities and alpha diversity is calculated. In a
collector curve, an increasing number of communities is randomly drawn and
combined and their cumulative alpha diversity is determined. 

The average alpha diversity for the different sampling sizes is reported either
as array references or a tab-delimited string. Note that no plot is actually
drawn.

=head1 AUTHOR

Florent Angly L<florent.angly@gmail.com>

=head1 SUPPORT AND BUGS

User feedback is an integral part of the evolution of this and other Bioperl
modules. Please direct usage questions or support issues to the mailing list, 
L<bioperl-l@bioperl.org>, rather than to the module maintainer directly. Many
experienced and reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem with code and
data examples if at all possible.

If you have found a bug, please report it on the BioPerl bug tracking system
to help us keep track the bugs and their resolution:
L<https://redmine.open-bio.org/projects/bioperl/>

=head1 COPYRIGHT

Copyright 2011-2014 by Florent Angly <florent.angly@gmail.com>

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=head2 new

 Function: Create a new Bio::Community::Tool::Accumulator object
 Usage   : my $accumulator = Bio::Community::Tool::Accumulator->new( );
 Args    : -metacommunity: see metacommunity()
           -type            : 'rarefaction' or 'collector'
           -num_repetitions : see num_repetitions()
           -num_ticks       : see num_ticks()
           -tick_spacing    : see tick_spacing()
           -alpha_types     : see alpha_types()
           -seed            : see set_seed()
 Returns : a new Bio::Community::Tools::Accumulator object

=cut


package Bio::Community::Tools::Accumulator;

use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use namespace::autoclean;
use Bio::Community::Alpha;
use Bio::Community::Meta;
use Bio::Community::Tools::Rarefier;
use List::Util qw( shuffle );
use Method::Signatures;

extends 'Bio::Root::Root';


=head2 metacommunity

 Function: Get or set the metacommunity to normalize.
 Usage   : my $meta = $accumulator->metacommunity;
 Args    : A Bio::Community::Meta object
 Returns : A Bio::Community::Meta object

=cut

has metacommunity => (
   is => 'rw',
   isa => 'Maybe[Bio::Community::Meta]',
   required => 0,
   default => undef,
   lazy => 1,
   init_arg => '-metacommunity',
);


=head2 type

 Function: Get or set the type of accumulation curve to produce.
 Usage   : my $type = $accumulator->type;
 Args    : String of the accumulation type: 'rarefaction' (default) or 'collector'
 Returns : String of the accumulation type

=cut

has type => (
   is => 'rw',
   isa => 'AccumulationType',
   required => 0,
   default => 'rarefaction',
   lazy => 1,
   init_arg => '-type',
);


=head2 num_repetitions

 Function: Get or set the number of num_repetitions to do at each sampling depth.
 Usage   : my $num_repetitions = $accumulator->num_repetitions;
 Args    : positive integer for the number of repetitions
 Returns : positive integer for the number of repetitions

=cut

has num_repetitions => (
   is => 'rw',
   isa => 'Maybe[PositiveInt | Str]',
   required => 0,