#!/usr/bin/perl

use strict;
use Data::Dumper;
use constant SUCCESS => 0;
use constant ERROR => -1;
use XML::Simple;


my $results;
my $sequence;
my $target;

# Hard coding input file
my %args = getParams();

my $probe_file = new XML::Simple();
my $probes = $probe_file->XMLin($args{hybrid_file}, keyattr => {});


open(INFILE, $args{file});
open(OUTFILE, ">".$args{outfile});

while (<INFILE>)
{
  if ($_ =~ /Comment/)
    {
      last;
    }
}


for (my $i=0; $i<2; $i++)
{ $_ = <INFILE>; }

printXMLheader (*OUTFILE);

PROBE_NAME: while (<INFILE>)
{

      if ($_ =~ /<TD WIDTH=72/)
      {
              ($target) = ($_ =~ m/quot;(.).*?&quot/);
                 
	      for (my $i=0; $i < 7; $i++)
	      { $_ = <INFILE>; }

	      ($results) = ($_ =~ m/<FONT.*?>(.+)<\/FONT>/);
               $results = uc($results);

	      for (my $i=0; $i<11; $i++)
	      { $_ = <INFILE>; }
	      ($sequence) = ($_ =~ m/<FONT.*?>([ATGC]{0,40})<\/FONT>/);

              addResults( *OUTFILE, $probes, $target, $results, $sequence);

	      for (my $i=0; $i < 4; $i++)
	      { $_ = <INFILE>; }
      }

}
close (INFILE);

printXMLfooter (*OUTFILE);



sub addResults
{
   local *OUTFILE = shift;

   my $probes   = shift;      
   my $target   = shift;
   my $all_results  = shift;
   my $sequence = shift;

   if (($target == $args{target}) && ($args{probesize} == length($sequence)))
   {
      for (my $i=0; $i<@{$probes->{probe}}; $i++)
      {
    
        if ($sequence eq $probes->{probe}->[$i]->{sequence})
        { 
            printProbeHeader ( *OUTFILE, $probes->{probe}->[$i] );
            for (my $j=0; $j<@{$probes->{probe}->[$i]->{results}}; $j++)
            {
               my $species_name = $probes->{probe}->[$i]->{results}->[$j]->{species};
               my $species_sequence = $probes->{probe}->[$i]->{results}->[$j]->{species2_align};
               my $species_result = determineResult($all_results, $species_name, $species_sequence);
               printProbeResults ( *OUTFILE, $probes->{probe}->[$i]->{results}->[$j], $species_result); 
            }
            printProbeFooter ( *OUTFILE, $probes->{probe}->[$i] );
            last;
         }
      }
   }
   return;
}





sub determineResult
{
  my $all_results = shift;
  my $species     = shift;
  my $sequence    = shift;
  my $result = "";


  # Species Lookup to get Character code. 

  my %species_lookup = ( "HUMAN"  => "H", 
                         "BABOON" => "B", 
                         "CHIMP"  => "M", 
                         "CAT"    => "K", 
                         "DOG"    => "D", 
                         "COW"    => "C", 
                         "PIG"    => "P", 
                         "MOUSE"  => "F" ); 


  # If the species doesn't have a sequence, then the XML read will set the sequence to
  # be a hash.  If no sequence, then the result will be "".
  
  $species = uc($species);
  if (ref($sequence) ne "HASH")
  {
       $result = "FAIL";
       my $species_code = $species_lookup{$species};
       $result = "PASS" if ($all_results =~ m/$species_code/);
       $result = "" if ($species_code eq "");
  }
  return $result; 
  
}





sub getParams {
    my %opts;
    my $errstr = "";
    use Getopt::Long;
    use Data::Dumper;
 
    GetOptions(\%opts, 'file=s', 'target=i', 'probesize=i', 'inputfile=s', 'output=s', 'help');
    if (!defined($opts{help}))
    {
      if (!defined($opts{file}))
      {
        $errstr .= "ERROR : No probes sources defined.\n";
      }
  
      if (!defined($opts{target}))
      {
        $errstr .= "ERROR : No target specified\n";
      }
    }
    else
    { 
      $errstr = " ";
    }


    if ($errstr) {
        print <<"END_USAGE";
Description:
This script will take a html formated file containing probe results 
and add the results to the hybridization file.

Usage: 
add_results_to_hybridization.pl -file <filename> -target <target> -inputfile <filename> -probesize <size> [-output <filename>]

-file   <filename>  Name of file that contains lab results
-target             Number of target to process
-inputfile          Name of file that contains XML computational hyrbidizaiton results
-probesize          Size of probes in hybridizefile
-output             Output XML, that contains the lab results (default : add_results.out)

END_USAGE
        print "\n$errstr" if ($errstr);
        die("\n");
    }
    return (
            file => $opts{file},
            target => $opts{target},
            hybrid_file => $opts{inputfile},
            probesize => $opts{probesize} || 36,
            outfile => $opts{output} || "add_results.out"
           );
}


sub printXMLheader
{
  local *OUTFILE = shift;
  print OUTFILE "<?xml version='1.0' encoding='ISO-8859-1' ?>\n";
  print OUTFILE "<hybridization>\n";
  return;
}

sub printXMLfooter
{
  local *OUTFILE = shift;
  print OUTFILE "\n\n";
  print OUTFILE "</hybridization>\n";
  return;
}

sub printProbeHeader
{
  local *OUTFILE = shift;
  my $probe = shift;

  print OUTFILE "\n\n";
  print OUTFILE "   <probe>\n";
  print OUTFILE "      <source>".$probe->{source}."</source>\n";
  print OUTFILE "      <sequence>".$probe->{sequence}."</sequence>\n";
  print OUTFILE "      <start>".$probe->{start}."</start>\n";
  print OUTFILE "      <stop>".$probe->{stop}."</stop>\n";

  return;
}



sub printProbeFooter
{
  local *OUTFILE = shift;
  my $probe = shift;
  print OUTFILE "   </probe>\n";
  return;
}


sub printProbeResults
{
   local *OUTFILE = shift;
   my $probe = shift;
   my $result = shift;

   my $species1_align = "";
   my $species2_align = "";
   my $alignment_mask = "";

   $species1_align = $probe->{species1_align} if (!ref($probe->{species1_align}));
   $species2_align = $probe->{species2_align} if (!ref($probe->{species2_align}));
   $alignment_mask = $probe->{alignment_mask} if (!ref($probe->{alignment_mask}));

   print OUTFILE "      <results>\n";
   print OUTFILE "         <species>".$probe->{species}."</species>\n";
   print OUTFILE "         <start>".$probe->{start}."</start>\n";
   print OUTFILE "         <stop>".$probe->{stop}."</stop>\n";
   print OUTFILE "         <species1_align>".$species1_align."</species1_align>\n";
   print OUTFILE "         <alignment_mask>".$alignment_mask."</alignment_mask>\n";
   print OUTFILE "         <species2_align>".$species2_align."</species2_align>\n";
   print OUTFILE "         <result>$result</result>\n";
   print OUTFILE "      </results>\n";

   return;
}