my $self = shift;
	$self->{inputs} = {};
	return;

     my $rdat = shift;
     my (%left,%right,$updir,$downdir,$var,$trunc);
     my @variables = qw(
        PRIMER_DIRECTION
        PRIMER_DIRECTION_END_STABILITY
        PRIMER_DIRECTION_EXPLAIN
        PRIMER_DIRECTION_GC_PERCENT
        PRIMER_DIRECTION_PENALTY
        PRIMER_DIRECTION_SELF_ANY
        PRIMER_DIRECTION_SELF_END
        PRIMER_DIRECTION_SEQUENCE
        PRIMER_DIRECTION_TM
         PRIMER_FIRST_BASE_INDEX
     );
          # create the hash to pass into the creation routine
          # I do it this way because the primer3 outfile variables are exactly the same for each of
          # left and right. I create two hashes- one for the left and one for the right primer.
     foreach $updir (qw(LEFT RIGHT)) {
            my %dat;
             foreach (@variables) {
               ($var = $_) =~ s/DIRECTION/$updir/e;
                    # should you truncate the name of each variable?
                    # for example, should the value be: PRIMER_RIGHT_PENALTY or PENALTY?
                    # i think it should be the second one
                    if (/^PRIMER_DIRECTION$/) {
                         $trunc = "PRIMER";
                    }
                    elsif (/^PRIMER_FIRST_BASE_INDEX/) {
                         $trunc = "FIRST_BASE_INDEX";    
				}
				else {
				     ($trunc = $_) =~ s/PRIMER_DIRECTION_//;
				}
               $dat{"-$trunc"} = $rdat->{$var};
             }
               if ($updir eq "LEFT") {
                    %left = %dat;
                    $left{-id} = $rdat->{PRIMER_SEQUENCE_ID}."-left";
               }
               else {
                    %right = %dat;
                    $right{-id} = $rdat->{PRIMER_SEQUENCE_ID}."-right";
               }
     }
     my $primer_left = new Bio::SeqFeature::Primer(%left);
     my $primer_right = new Bio::SeqFeature::Primer(%right);
     return($primer_left,$primer_right);

		# old
		# my ($self,$filename) = @_;
	my ($self,$outputs) = @_;
		# print("\$self is $self, \$outputs are $outputs\n");
		# print("in _parse_report, \$self is $self\n");
		# set this to keep track of things....
	my ($sequence_name,$line,$counter,$variable_name,$variable_value);
	my @output = split/\n/,$outputs;	
	foreach $line (@output) {
			# print("Reading line $line\n");
		next if ($line =~ /^\=/);
		if ($line =~ m/^PRIMER_SEQUENCE_ID/) {
			$line =~ m/(\S+)=(.*$)/;
			$variable_name = $1;
			$sequence_name = $2;
			$variable_value = $2;
		}
		else {
			$line =~ m/(\S+)=(.*$)/;
			$variable_name = $1;
			$variable_value = $2;
		}
			# print("$sequence_name\t$variable_name\t$variable_value\n");
		$self->{primers}{$sequence_name}{$variable_name} = $variable_value;
	} # end while <>
} # end parse_report

	     # my ($self,$filename) = @_;
		# set this to keep track of things....
	     # $self->{outfilename} = $filename;
          # to make this better for bioperl, chad should really be using catfile and things.
		# 
		# 	my $fh = new FileHandle;
		# 	open($fh,$filename) or die "I can't open the primer report ($filename) : $!\n";
		# 		# _parse_report();
		# 		# my %Primer3::primers;
		# 	my ($output,$line);
		# 	while ($line=<$fh>) {
		# 			# print("Adding $line\n");
		# 		$output .= $line;
		# 	} # end while
		# 		# print("\$output is $output\n");
	     # return $output;

	my $self = shift;
	my ($sequence,$primer,$primer_left,$primer_right,$position_left,$position_right,$boggle);
	$boggle = 1;
	foreach $primer (sort keys %{$self->{primers}}) {
		$sequence = $self->{primers}{$primer}{SEQUENCE};
		$primer_left = $self->{primers}{$primer}{PRIMER_LEFT};
		$primer_right = $self->{primers}{$primer}{PRIMER_RIGHT};
		if (!$primer_left) {
			$self->{primers}{$primer}{design_failed} = "1";
		}
		else {
			$primer_left =~ m/(.*)\,(.*)/;
			$position_left = $1+$2-1;
			$primer_right =~ m/(.*)\,(.*)/;
			$position_right = $1-$2;
			$self->{primers}{$primer}{left} = $position_left;
			$self->{primers}{$primer}{right} = $position_right;
			$self->{primers}{$primer}{amplified} = substr($sequence,$position_left,$position_right-$position_left);
		}
	}

	my ($self,%args) = @_;
	my ($currkey,$renamed,$sequence_id,$value);
	if (!$args{-PRIMER_SEQUENCE_ID}) {
		print("You cannot add an element to the primer3 infile without specifying the PRIMER_SEQUENCE_ID. Sorry.\n");
	}
	else {
		$sequence_id = $args{-PRIMER_SEQUENCE_ID};
		foreach $currkey (keys %args) {
			# print("\$currkey is $currkey\n");
			next if ($currkey eq "-PRIMER_SEQUENCE_ID");
			($renamed = $currkey) =~ s/-//;
				# print("Adding $renamed to the hash under $sequence_id\n");
			$value = $args{$currkey};
				# print("\$value is $value\n");
			if ($renamed eq "SEQUENCE") { $value =~ s/\n//g; }
			$self->{infile}{$sequence_id}{$renamed} = $value;
		}
	}

	my $self = shift;
	my $dumper = new Dumpvalue;
	$dumper->dumpValue($self);
} # end dump_hash

	my $self = shift;
	my $dumper = new Dumpvalue;
	$dumper->dumpValue($self->{infile});
}



1;
__END__

	my $primer = $_[1];
	my $error = $Primer3::primers{$primer}{PRIMER_ERROR};
	if ($error) { return $error; }
	else { return "Some error that primer3 didn't define.\n"; }

	my ($self) = @_;
} # end get_amplified_region

	my $self = shift;
	return sort keys %{$self->{primers}};
} # end get keys

     my($class,@args) = @_;
     my $self = $class->SUPER::new(@args);
     my($filename) = $self->_rearrange([qw(FILE)],@args);
     if (!$filename) {
          print("Ahh grasshopper, you are planning to create a primer3 infile\n");
          return $self;
     }
     $self->{filename} = $filename;
          # check to see that the file exists
          # I think that catfile should be used here.
     if (!-f $filename) {
          print("That file doesn't exist. Bah.\n");
     }
     $self->_initialize_io( -file => $filename );
     return $self;

     my $self = shift;
     my $fh = $self->_fh();
     my ($line,%primer);
          # first, read in the next set of primers
     while ($line = $self->_readline()) {
          chomp ($line);
          last if ($line =~ /^=/);
          $line =~ m/(^.*)\=(.*$)/;
          $primer{$1} = $2; 
     }
               # then, get the primers as SeqFeature::Primer objects
     
     my ($left,$right) = &_create_primer_features(\%primer);
               # then, create the sequence to place them on
     my $sequence = Bio::Seq->new(-seq => $primer{SEQUENCE},
                                         -id => $primer{PRIMER_SEQUENCE_ID});
     # print("Sequence is ".$primer{SEQUENCE}." and id is ".$primer{PRIMER_SEQUENCE_ID}."\n");
     my $primedseq = new Bio::Seq::PrimedSeq(
                                           -target_sequence => $sequence,
                                           -left_primer => $left,
                                           -right_primer => $right,
                                           -primer_sequence_id => $primer{PRIMER_SEQUENCE_ID},
                                           -primer_comment => $primer{PRIMER_COMMENT},
                                           -target => $primer{TARGET},
                                           -primer_product_size_range => $primer{PRIMER_PRODUCT_SIZE_RANGE},
                                           -primer_file_flag => $primer{PRIMER_FILE_FLAG},
                                           -primer_liberal_base => $primer{PRIMER_LIBERAL_BASE},
                                           -primer_num_return => $primer{PRIMER_NUM_RETURN},
                                           -primer_first_base_index => $primer{PRIMER_FIRST_BASE_INDEX},
                                           -primer_explain_flag => $primer{PRIMER_EXPLAIN_FLAG},
                                           -primer_pair_compl_any => $primer{PRIMER_PAIR_COMPL_ANY},
                                           -primer_pair_compl_end => $primer{PRIMER_PAIR_COMPL_END},
                                           -primer_product_size => $primer{PRIMER_PRODUCT_SIZE}
                                        );
     return $primedseq;

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