$fastaFile = $myTimestamp . _ .$_FILES["fastaUpload"]["name"];

$treeFile = $myTimestamp . _ .$_FILES["treeUpload"]["name"];

$myFile = "klee_upload/$treeFile";

$fh = fopen($myFile, 'r');
$theData = fread($fh, filesize($myFile));
fclose($fh);

//Setup log file
$myLogFile = "klee_logs/log_$myTimestamp.txt";
$fhLog = fopen($myLogFile, 'w') or die("can't open file");
fwrite($fhLog, "###########LOG FILE###############\n");

$pattern = '/[A-Z]{3,5}[0-9]{3,4}-[0-9]{2}/';
//IN ORDER TO LOCATE THE INDIVIDUAL FASTA ENTRIES, THE PROGRAM SEARCHES FOR AN
//ID PATTERN.  THE DEFAULT PATTERN IS 3 TO 5 CAPITAL LETTERS FOLLOWED BY 3 OR
//4 NUMBERS FOLLOWED BY A DASH FOLLOWED BY 2 NUMBERS.  FOR EXAMPLE, "ABCD456-99"
//THIS PATTERN CAN BE CHANGED BY MODIFYING THE $pattern VARIABLE.

preg_match_all($pattern, $theData, $matches, 0);
$matches2 = $matches[0];
$countMatches = count($matches2);

fwrite($fhLog, "###############END PATTERN
MATCH############################\n");

$myFile2 = "klee_upload/$fastaFile";

$fh2 = fopen($myFile2, 'r');
$theData2 = fread($fh2, filesize($myFile2));

fwrite($fhLog, "###############END READING THE
FILE##########################\n");
$pieces = explode(">", $theData2); //pieces is an array of each chunk of the
fasta file.
$fastaCounter = 1;
foreach ($pieces as $value) {
  $mystring = substr($value, 0, strpos($value, "|")); //mystring is each code.
  $full_fasta[] = $mystring;
  $fastaCodes[$mystring] = $value; //fastaCodes is an array of fasta info with
indexes of codes from the fasta file.
  $fastaCounter++;
}
array_shift($full_fasta);

if($pieces[0] == "")
{
  array_shift($pieces);
  array_shift($full_fasta);
}

$countPieces = count($pieces);

$countfastaCodes = count($fastaCodes);

fwrite($fhLog, "There are $countPieces blocks of text in the fasta file\n");

fclose($fh2);

fwrite($fhLog, "###############END EXPLODING THE
FILE########################\n");

//SEARCH IF THERE ARE ANY CODES IN THE TREE LIST NOT IN THE FASTA FILE
$codeCounter = 0;
foreach($matches2 as $currCode)
{
  if($fastaCodes[$currCode] != "")
  {
    $analysisArray[] = $fastaCodes[$currCode];
  }
  else
  {
    fwrite($fhLog, "ERROR $currCode is NOT in the fasta file\n");
  }

  $codeCounter = $codeCounter+1;
}

//SEARCH IF THERE ARE ANY CODES IN THE FASTA FILE NOT IN THE TREE LIST
foreach($full_fasta as $currFasta)
{
  if (in_array($currFasta, $matches2)) {
  }
  else{
    fwrite($fhLog, "ERROR $currFasta is NOT in the tree list\n");
  }
}

$countanalysisArray = count($analysisArray);

fwrite($fhLog, "The output file contains $countanalysisArray blocks of
text\n");

fwrite($fhLog, "###############END GENERATING THE NEW
ORDER########################\n");

$myOutFile = "klee_results/result_$myTimestamp.fas";
$fhOut = fopen($myOutFile, 'w') or die("can't open file");
foreach($analysisArray as $analysisVal)
{
  $analysisVal = ">" . $analysisVal;
  fwrite($fhOut, $analysisVal);
}
fclose($fhOut);

fwrite($fhLog, "###############END WRITING THE NEW
FILE########################\n");

$myZipFile = "$myTimestamp.zip";

exec("zip -r klee_zips/$myZipFile $myLogFile $myOutFile");

fclose($fhLog);

$ranScript = '1';
}

function get_file_extension($file_name)
{
  return substr(strrchr($file_name,'.'),1);
}