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package LLNL::LAVA::PrimerInfo;

use strict;
use warnings;
use Carp;

use vars qw(@ISA);

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

use LLNL::LAVA::Oligo; # Holds one of these to point back to

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

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

=head1 NAME

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

=head1 SYNOPSIS

  use LLNL::LAVA::PrimerInfo;

  # Instantiation.  Usually, this is performed by a PrimerAnalyzer so you 
  # won't need to instantiate your own.
  my $primerInfo = LLNL::LAVA::PrimerInfo->new(
    {
      "penalty" => $penalty,
      "sequence" => $sequence,
      "location" => $loaction,
      "length" => $length,
      "analyzed_primer" => $primer,
    });"

  # All non-tag functions are read-only because a PrimerInfo represents
  # an analysis result within a context, and I want to prevent accidents.
  $penatly = $primerInfo->getPenalty();
  $sequence = $primerInfo->getSequence();
  $location = $primerInfo->getLocation();
  $length = $primerInfo->getLength();
  $primer = $primerInfo->getAnalyzedPrimer();

  # 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

PrimerInfo is the vehicle for oligo analysis results.  In the simplest case,
this is just the oligo sequence and associated penalty, location, etc..  In more
complicated cases, sub-classes will help represent the position-specific decisions
and penalties of oligo analysis. 

=head1 APPENDIX

The following documentation describes the functions in this package

=cut

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

=head2 new

 Usage     : $primerInfo = LLNL::LAVA::PrimerInfo->new(
               {
                 "penalty" => $penalty,
                 "sequence" => $sequence,
                 "location" => $loaction,
                 "length" => $length,
                 "analyzed_primer" => $primer,
               });"
 Function  : Creates a new LLNL::LAVA::PrimerInfo
 Arguments : Hash ref containing:
               penalty - the oligo's penalty score from an analysis context
               sequence - the representative sequence of the oligo
               location - the oligo's location
               length - the oligo's length
               analyzed_primer - LLNL::LAVA::Oligo used to create this info
 Example   : See Usage
 Returns   : A new LLNL::LAVA::PrimerInfo

=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");
  my $sequence = optionRequired($paramHash_r, "sequence");
  my $location = optionRequired($paramHash_r, "location");
  my $length = optionRequired($paramHash_r, "length");
  my $analyzedPrimer = optionRequired($paramHash_r, "analyzed_primer");

  # Initialize via TagHolder, not expecting default information 
  my $this = $classType->SUPER::new({});

  # Handle component properties
  $this->{"d_penalty"} = $penalty;
  $this->{"d_sequence"} = $sequence;
  $this->{"d_location"} = $location;
  $this->{"d_length"} = $length;
  $this->{"d_analyzedPrimer"} = $analyzedPrimer;

  return $this;
}

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

=head2 getPenalty

 Usage     : $penalty = $primerInfo->getPenalty();
 Function  : Gets the penalty for this PrimerInfo, 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"};
}

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

=head2 getSequence

 Usage     : $sequence = $primerInfo->getSequence();
 Function  : Gets the sequence for this PrimerInfo.
 Arguments : <n/a> 
 Example   : See Usage
 Returns   : String - Primer sequence that this PrimerInfo represents

=cut

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

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

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

=head2 getLocation

 Usage     : $location = $primerInfo->getLocation();
 Function  : Gets the location for this PrimerInfo.
 Arguments : <n/a> 
 Example   : See Usage
 Returns   : Integer - the 0-indexed location this PrimerInfo is located at

=cut

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

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

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

=head2 getLength

 Usage     : $length = $primerInfo->getLength();
 Function  : Gets the length of the primer this PrimerInfo represents.
 Arguments : <n/a> 
 Example   : See Usage
 Returns   : Integer - how long the primer is that this PrimerInfo represent.

=cut

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

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

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

=head2 getAnalyzedPrimer

 Usage     : $primer = $primerInfo->getAnalyzedPrimer();
 Function  : Gets the primer that was analyzed to create this PrimerInfo
 Arguments : <n/a> 
 Example   : See Usage
 Returns   : LLNL::LAVA::Oligo - primer that was analyzed for this PrimerInfo

=cut

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

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

1; # Got one?

__END__

=head1 AUTHOR

Clinton Torres (clinton.torres@llnl.gov)

=head1 SEE ALSO

=cut