Bio-Community

 view release on metacpan or  search on metacpan

lib/Bio/Community/IO.pm  view on Meta::CPAN

           function is implemented by the Bio::Community::IO::Driver used to
           parse the given file format.
 Args    : None
 Returns : An array containing:
             A Bio::Community::Member object (or undef)
             A positive number (or undef)

=cut

method next_member () {
   $self->throw_not_implemented;
}


=head2 next_community

 Usage   : my $community = $in->next_community;
 Function: Get the next community. Note that communities without members are
           skipped.
 Args    : None
 Returns : A Bio::Community object

lib/Bio/Community/IO.pm  view on Meta::CPAN

      }

   }
   # Community is undef if all communities have been seen
   return $community;
}


method _next_community_init () {
   # Driver-side method to initialize new community and return its name
   $self->throw_not_implemented;
}


method _next_community_finish () {
   # Driver-side method to finalize a community
   $self->throw_not_implemented;
}


=head2 next_metacommunity

 Usage   : my $meta = $in->next_metacommunity;
 Function: Get the next metacommunity. It may contain one or several communities
           depending on the format of the file read,
 Args    : None
 Returns : A Bio::Community::Meta object

lib/Bio/Community/IO.pm  view on Meta::CPAN

         $self->_meta->add_communities([$community]);
      }
      # _next_metacommunity_finish will happen before close()
   }
   return $meta;
}


method _next_metacommunity_init () {
   # Driver-side method to initialize new metacommunity and return its name
   $self->throw_not_implemented;
}


method _next_metacommunity_finish () {
   # Driver-side method to finalize reading a metacommunity
   $self->throw_not_implemented;
}


=head2 write_member

 Usage   : $out->write_member($member, $abundance);
 Function: Write the next member from the community and its count or relative
           abundance. This function is implemented by a Bio::Community::IO::Driver
           specific to the given file format.
 Args    : A Bio::Community::Member object
           A positive number
 Returns : 1 for success

=cut

method write_member (Bio::Community::Member $member, Count $count) {
   $self->throw_not_implemented;
}


=head2 write_community

 Usage   : $out->write_community($community);
 Function: Write the next community.
 Args    : A Bio::Community object
 Returns : 1 for success

lib/Bio/Community/IO.pm  view on Meta::CPAN

   if ( ($self->_meta->get_communities_count > 1) && (not $self->multiple_communities) ) {
      $self->throw('Format '.$self->format.' only supports writing one community per file');
   }

   return 1;
}


method _write_community_init (Bio::Community $community) {
   # Driver-side method to initialize writing a community
   $self->throw_not_implemented;
}


method _write_community_finish (Bio::Community $community) {
   # Driver-side method to finalize writing a community
   $self->throw_not_implemented;
}


=head2 write_metacommunity

 Usage   : $out->write_metacommunity($meta);
 Function: Write a metacommunity.
 Args    : A Bio::Community::Meta object
 Returns : 1 for success

lib/Bio/Community/IO.pm  view on Meta::CPAN

      # _write_metacommunity_finish will happen before close()
   } else {
      $self->throw('Can write only one metacommunity');
   }
   return 1;
}


method _write_metacommunity_init (Bio::Community::Meta $meta) {
   # Driver-side method to initialize writing a metacommunity
   $self->throw_not_implemented;
}


method _write_metacommunity_finish (Bio::Community::Meta $meta) {
   # Driver-side method to finalize writing a metacommunity
   $self->throw_not_implemented;
}


before 'close' => sub {
   my $self = shift;
   if ($self->mode eq 'r') {
      $self->_next_metacommunity_finish();
   } else {
      # Finish preparing the metacommunity for writing
      $self->_write_metacommunity_finish($self->_meta);

lib/Bio/Community/Meta/Beta.pm  view on Meta::CPAN

   $p /= 100;

   # Calculate the Maxiphi index
   my $m = 1 - $s * (2-$p) / 2;
   return $m;
}


method _unifrac ($meta, $tree) {
   #### TODO: unifrac
   $self->throw_not_implemented;
}


#######
# TODO:
# Many more beta diversity indices to calculate:
#    Unifrac
#    ...
#######