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Bio::Community::IO::Driver::generic - Driver to read and write files in a generic tab-delimited site-by-species table format

=head1 SYNOPSIS

   my $in = Bio::Community::IO->new( -file => 'gaas_communities.txt', -format => 'generic' );

   # See Bio::Community::IO for more information

=head1 DESCRIPTION

This Bio::Community::IO::Driver::generic driver reads and writes files in a generic
format. Multiple communities can be written in a file to generate a site-by-
species table (OTU table), in which the entries are tab-delimited. Example:

  Species	site A	site B
  species 1	321	94
  species 2	0	58
  species 3	47	26

For each Bio::Community::Member $member generated from a generic site-by-species
file, $member->desc() contains the content of the species field. Since the
generic format does not specify a member ID, one is automatically generated
and can be retrieved using $member->id().

=head1 CONSTRUCTOR

See L<Bio::Community::IO>.

=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.

=cut


package Bio::Community::IO::Driver::generic;

use Moose;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::Member;

extends 'Bio::Community::IO';
with 'Bio::Community::Role::IO',
     'Bio::Community::Role::Table';


our $multiple_communities   =  1;      # format supports several communities per file
our $explicit_ids           =  0;      # IDs are not explicitly recorded
#### sorting only effective for first community???
our $default_sort_members   =  0;      # unsorted
our $default_abundance_type = 'count'; # absolute count (positive integer)
our $default_missing_string =  0;      # empty members get a '0'


has '_line' => (
   is => 'rw',
   isa => 'PositiveInt',
   required => 0,
   init_arg => undef,
   default => 1,
   lazy => 1,
);


has '_col' => (
   is => 'rw',
   isa => 'PositiveInt',
   required => 0,
   init_arg => undef,
   default => 1,
   lazy => 1,
);


has '_members' => (
   is => 'rw',
   isa => 'ArrayRef', # ArrayRef[Bio::Community::Member] but keep it lean
   required => 0,
   init_arg => undef,
   default => sub { [] },
   lazy => 1,
   predicate => '_has_members',
);


has '_id2line' => (
   is => 'rw',
   isa => 'HashRef', # HashRef[String] but keep it lean
   required => 0,
   init_arg => undef,
   default => sub { {} },
   lazy => 1,
);


has '_write_desc' => (
   is => 'rw',
   isa => 'Bool',
   required => 0,