File Coverage

blib/lib/Bio/Polloc/GroupCriteria/operator/num.pm

Criterion	Covered	Total	%
statement	7	42	16.6
branch	0	36	0.0
condition	0	3	0.0
subroutine	3	5	60.0
pod	2	2	100.0
total	12	88	13.6

=head1 NAME

Bio::Polloc::GroupCriteria::operator::num - A numeric operator

=head1 AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

=cut

package Bio::Polloc::GroupCriteria::operator::num;
use base qw(Bio::Polloc::GroupCriteria::operator);
use strict;
our $VERSION = 1.0503; # [a-version] from Bio::Polloc::Polloc::Version


=head1 APPENDIX

Methods provided by the package

=head2 new

Generic initialization method.

=head3 Arguments

See L<Bio::Polloc::GroupCriteria::operator->new()>

=head3 Returns

A L<Bio::Polloc::GroupCriteria::operator::bool> object.

=cut

sub new {
   my($caller,@args) = @_;
   my $self = $caller->SUPER::new(@args);
   $self->_initialize(@args);
   return $self;
}

=head2 operate

=head3 Returns

A numeric value.

=cut

sub operate {
   my $self = shift;
   return $self->val if defined $self->val;
   $self->throw('Bad operators', $self->operators)
   	unless ref($self->operators)
	and ref($self->operators)=~/ARRAY/;
   my $o1 = $self->operators->[0]->operate;
   $self->throw("Undefined first operator") unless defined $o1;
   my $o2 = $self->operators->[1]->operate;
   $self->throw("Undefined second operator") unless defined $o2;
   return ($o1 + $o2)	if $self->operation =~ /^\s*(?:\+)\s*$/i;
   return ($o1 - $o2)	if $self->operation =~ /^\s*(?:\-)\s*$/i;
   return ($o1 * $o2)	if $self->operation =~ /^\s*(?:\*)\s*$/i;
   return ($o1 / $o2)	if $self->operation =~ /^\s*(?:\/)\s*$/i;
   return ($o1 % $o2)	if $self->operation =~ /^\s*(?:%)\s*$/i;
   return ($o1 ** $o2)	if $self->operation =~ /^\s*(?:\*\*|\^)\s*$/i;
   if($self->operation =~ /^\s*aln-(sim|score)(?: with)?\s*$/i){
      my $ret = lc $1;
      return unless $self->_load_module('Bio::Tools::Run::Alignment::Muscle');
      my $factory = Bio::Tools::Run::Alignment::Muscle->new();
      $factory->quiet(1);
      UNIVERSAL::can($o1, 'isa') or $self->throw('First operator must be an object', $o1);
      UNIVERSAL::can($o2, 'isa') or $self->throw('First operator must be an object', $o2);
      $o1->isa('Bio::Seq') or $self->throw('First operator must be a Bio::Seq object', $o1);
      $o2->isa('Bio::Seq') or $self->throw('Second operator must be a Bio::Seq object', $o2);
      $o1->id('op1');
      $o2->id('op2');
      my $aln = $factory->align([$o1, $o2]);
      my $out = 0;
      $out = ($ret eq 'sim') ? $aln->overall_percentage_identity('long')/100 : $aln->score;
      $factory->cleanup(); # This is to solve the issue #1
      defined $out or $self->throw('Empty value for '.$ret, $self, 'Bio::Polloc::Polloc::UnexpectedException');
      return $out;
   }
   $self->throw("Unknown numeric operation", $self->operation);
}

=head1 INTERNAL METHODS

Methods intended to be used only within the scope of Bio::Polloc::*

=head2 _initialize

=cut

sub _initialize { }

1;