--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_psm_comparison_table/lib/CPT/Bio/RBS/Algo/Naive.pm	Tue Jul 05 05:42:59 2022 +0000
@@ -0,0 +1,103 @@
+package CPT::Bio::RBS::Algo::Naive;
+use Moose;
+with 'CPT::Bio::RBS::Algo';
+use CPT::Bio::RBS_Object;
+
+my @SDs = (
+	'aggaggt',
+	'ggaggt',
+	'aggagg',
+	'aggag',
+	'gaggt',
+	'ggagg',
+	'aggt',
+	'gggt',
+	'gagg',
+	'gggg',
+	'agga',
+	'ggag',
+	'gga',
+	'gag',
+	'agg',
+	'ggt',
+);
+
+sub predict {
+	my ( $self, %params ) = @_;
+	my $upstream = $params{sequence};
+	my $only_best = $params{return_best};
+
+	my $length = length($upstream);
+
+	my @results = ();
+	foreach my $rbs ( @SDs ){
+		while ($upstream =~ /$rbs/g) {
+			# Position of regex match
+			my $loc = $-[0];
+			# Seq before RBS
+			my $before = substr($upstream,0, $loc);
+			# Seq after RBS
+			my $after = substr($upstream, $loc + length($rbs));
+			my $rbs_o = CPT::Bio::RBS_Object->new(
+				upstream => sprintf('%s %s %s', $before , uc($rbs) , $after),
+				score => $self->score_match($rbs, length($after)),
+				rbs_seq => uc($rbs),
+				separation => length($after),
+			);
+			push( @results, $rbs_o );
+		}
+	}
+	@results = sort { $b->score() <=> $a->score() } @results;
+	if (@results) {
+		if($only_best){
+			return ($results[0]);
+		}else{
+			return @results;
+		}
+	}
+	else {
+		return (
+			CPT::Bio::RBS_Object->new(
+				upstream =>$upstream,
+				score => '-1',
+				rbs_seq => 'None',
+				separation => -1,
+			)
+		);
+	}
+}
+
+sub score_match {
+	my ($self, $match, $dist) = @_;
+	return length($match);
+}
+
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Bio::RBS::Algo::Naive
+
+=head1 VERSION
+
+version 1.99.4
+
+=head1 AUTHOR
+
+Eric Rasche <rasche.eric@yandex.ru>
+
+=head1 COPYRIGHT AND LICENSE
+
+This software is Copyright (c) 2014 by Eric Rasche.
+
+This is free software, licensed under:
+
+  The GNU General Public License, Version 3, June 2007
+
+=cut