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  Sequence.6	Sample.2	1

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

Note that member counts (the third column) is optional. Example:

  Sequence.1	Sample.1
  Sequence.1	Sample.2
  Sequence.2	Sample.1
  Sequence.3	Sample.1
  Sequence.4	Sample.2
  Sequence.5	Sample.1
  Sequence.6	Sample.3
  Sequence.6	Sample.2

In this case the data is to be interpreted as presence/absence data. When
reading a Unifrac file without counts, all members are given a count of 1.
Conversely, when writing a Unifrac file, if all members have a count of 1, then
the third column is not written. Also, when writing Unifrac files, any spaces in
community member name or member description is replaced by a dot.

=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::unifrac;

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 => 0,
   lazy => 1,
);


has '_col' => (
   is => 'rw',
   isa => 'PositiveInt',
   required => 0,
   init_arg => undef,
   default => 2,
   lazy => 1,
);


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


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


has '_community_names' => (
   is => 'rw',
   isa => 'ArrayRef', # Arrayref[Str] but keep it lean
   required => 0,