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package LLNL::LAVA::PrimerSetInfo;

use strict;
use vars qw(@ISA);
use Carp;

use LLNL::LAVA::Constants ":standard";
use LLNL::LAVA::Options ":standard";

use LLNL::LAVA::TagHolder; # is-a
@ISA = ("LLNL::LAVA::TagHolder");

# POD-formatted documentation
#-------------------------------------------------------------------------------

=head1 NAME

LLNL::LAVA::PrimerSetInfo - The basic functionality of PrimerSetInfo, which 
represents an analysis result of a PrimerSet within a specific context.

=head1 SYNOPSIS

  use LLNL::LAVA::PrimerSetInfo;

  # Instantiation.  Usually, this is performed by a PrimerAnalyzer so you 
  # won't need to instantiate your own.
  # Instantiation will also usually be of a more specific sub-class such
  # as LLNL::LAVA::PrimerSetInfo::PCRPair
  my $primerInfo = LLNL::LAVA::PrimerSetInfo->new(
    {
      "penalty" => $penalty,
    });"

  # All non-tag functions are read-only because a PrimerSetInfo represents
  # an analysis result within a context, and I want to prevent accidents.
  $penatly = $primerInfo->getPenalty();

  # Tag use
  $primerInfo->setTag("useful_tag_name", $value);
  $exists = $primerInfo->getTagExists("useful_tag_name");
  $value = $primerInfo->getTag("useful_tag_name");
   
=head1 EXAMPLES

See synopsis.

=head1 DESCRIPTION

PrimerSetInfo is the vehicle for primer set analysis results.  

=head1 APPENDIX

The following documentation describes the functions in this package

=cut

#-------------------------------------------------------------------------------

=head2 new

 Usage     : $primerInfo = LLNL::LAVA::PrimerSetInfo->new(
               {
                 "penalty" => $penalty,
               });"
 Function  : Creates a new LLNL::LAVA::PrimerSetInfo
 Arguments : Hash ref containing:
               penalty - the PrimerSet's penalty score from an analysis context
 Example   : See Usage
 Returns   : A new LLNL::LAVA::PrimerSetInfo

=cut

sub new
{
  my ($classType, $paramHash_r) = @_;

  if(!defined $paramHash_r)
  {
    confess("programming error - first parameter is a required hash ref");
  }
  if(ref($paramHash_r) ne "HASH")
  {
    confess("programming error - first parameter must be a hash reference");
  } 

  # Read the properties
  my $penalty = optionRequired($paramHash_r, "penalty");

  # Initialize via TagHolder
  my $this = $classType->SUPER::new({});

  # Handle component properties
  $this->{"d_penalty"} = $penalty;

  return $this;
}

#-------------------------------------------------------------------------------

=head2 getPenalty

 Usage     : $penalty = $primerInfo->getPenalty();
 Function  : Gets the penalty for this PrimerSetInfo, built from a specific
             analysis context.
 Arguments : <n/a> 
 Example   : See Usage
 Returns   : Float - in the simplest case, this can be the Primer3 penalty

=cut

sub getPenalty
{
  my ($this) = @_;

  return $this->{"d_penalty"};
}

1; # Got one?

__END__

=head1 AUTHOR

Clinton Torres (clinton.torres@llnl.gov)

=head1 SEE ALSO

=cut