tripal_blast/api/blast_ui.api.inc

<?php

/**
 * @file
 * Contains more generally applicable functions as well as some meant to help developers
 * Plug-in to the BLAST UI functionality
 */

/**
 * Get a specific BlastDB.
 *
 * @param $identifiers
 *   An array of identifiers used to determine which BLAST DB to retrieve.
 *
 * @return
 *   A fully-loaded BLAST DB Node
 */
function get_blast_database($identifiers) {
  $node = FALSE;

  if (isset($identifiers['nid'])) {
    $node = node_load($identifiers['nid']);
  }
  elseif (isset($identifiers['name'])) {

    $nid = db_query('SELECT nid FROM {blastdb} WHERE name=:name', array(':name' => $identifiers['name']))->fetchField();
    $node = node_load($nid);

  } elseif (isset($identifiers['path'])) {

    $nid = db_query('SELECT nid FROM {blastdb} WHERE path LIKE :path', array(':path' => db_like($identifiers['path']) . '%'))->fetchField();
    $node = node_load($nid);

  }

  return $node;
}

/**
 * Returns a list BLAST DATABASE options
 *
 * @param $type
 *   The type of BLAST dabases to restrict the list to (ie: n: nucleotide or p: protein)
 *
 * @return
 *   An array where the nid is the key and the value is the human-readable name of the option
 */
function get_blast_database_options($type) {
  global $user;

  // Get all BlastDB nodes
  $nodes = get_blast_database_nodes();

  // Support obsolete database type n/p
  $obs_type = '';
  if ($type == 'protein') {
    $obs_type = 'p';
  }
  else {
    $obs_type = 'n';
  }

  $options = array();
  foreach ($nodes as $node) {
    if ( isset($node) && isset($node->db_dbtype) ) {
      if ( ($node->db_dbtype == $type) OR ($node->db_dbtype == $obs_type) ) {
        $options[$node->nid] = $node->db_name;
      }
    }
  }

  // Sort alphabetically
  asort($options);

  return $options;
}

/**
 * Returns all blast database nodes.
 *
 * @return
 *   An array of nodes.
 */
function get_blast_database_nodes() {
  // Use the Entity API to get a list of BLAST Nodes to load
  // We use this function in order respect node access control so that
  // administrators can use this module in combination with a node access module
  // of their choice to limit access to specific BLAST databases.
  $query = new EntityFieldQuery();
  $query->entityCondition('entity_type', 'node')
    // Restrict to BLASTDB nodes.
    ->entityCondition('bundle', 'blastdb')
    // Restrict to Published nodes.
    ->propertyCondition('status', 1)
    // Restrict to nodes the current user has permission to view.
    ->addTag('node_access');
  $entities = $query->execute();

  // Get all BlastDB nodes
  return node_load_multiple(array_keys($entities['node']));
}


/**
 * Retrieve all the information for a blast job in a standardized node-like format.
 *
 * @param $job_id
 *   The non-encoded tripal job_id.
 * @retun
 *   An object describing the blast job.
 */
function get_BLAST_job($job_id) {

  $blastjob = db_query('SELECT * FROM blastjob WHERE job_id=:id', array(':id' => $job_id))->fetchObject();

  if (!$blastjob) {
    return false;
  }

  $tripal_job = tripal_get_job($job_id);

  $job = new stdClass();
  $job->job_id = $job_id;
  $job->program = $blastjob->blast_program;
  $job->options = unserialize($blastjob->options);
  $job->date_submitted = $tripal_job->submit_date;
  $job->date_started = $tripal_job->start_time;
  $job->date_completed = $tripal_job->end_time;

  // TARGET BLAST DATABASE.
  // If a provided blast database was used then load details.
  if ($blastjob->target_blastdb ) {
    $job->blastdb = get_blast_database(array('nid' => $blastjob->target_blastdb));
  }
  // Otherwise the user uploaded their own database so provide what information we can.
  else {
    $job->blastdb = new stdClass();
    $job->blastdb->db_name = 'User Uploaded';
    $job->blastdb->db_path = $blastjob->target_file;
    $job->blastdb->linkout = new stdClass();
    $job->blastdb->linkout->none = TRUE;

    if ($job->program == 'blastp' OR $job->program == 'tblastn') {
      $job->blastdb->db_dbtype = 'protein';
    }
    else {
      $job->blastdb->db_dbtype = 'nucleotide';
    }
  }

  // FILES.
  $job->files = new stdClass();
  $job->files->query = $blastjob->query_file;
  $job->files->target = $blastjob->target_file;
  $job->files->result = new stdClass();
  $job->files->result->archive = $blastjob->result_filestub . '.asn';
  $job->files->result->xml = $blastjob->result_filestub . '.xml';
  $job->files->result->tsv = $blastjob->result_filestub . '.tsv';
  $job->files->result->html = $blastjob->result_filestub . '.html';
  $job->files->result->gff = $blastjob->result_filestub . '.gff';

  return $job;
}

/**
 * Run BLAST (should be called from the command-line)
 *
 * @param $program
 *   Which BLAST program to run (ie: 'blastn', 'tblastn', tblastx', 'blastp','blastx')
 * @param $query
 *   The full path and filename of the query FASTA file
 * @param $database
 *   The full path and filename prefix (excluding .nhr, .nin, .nsq, etc.)
 * @param $output_filestub
 *   The filename (not including path) to give the results. Should not include file type suffix
 * @param $options
 *   An array of additional option where the key is the name of the option used by
 *   BLAST (ie: 'num_alignments') and the value is relates to this particular
 *   BLAST job (ie: 250)
 */
function run_BLAST_tripal_job($program, $query, $database, $output_filestub, $options, $job_id = NULL) {

  $output_file = $output_filestub . '.asn';
  $output_file_xml = $output_filestub . '.xml';
  $output_file_tsv = $output_filestub . '.tsv';
  $output_file_html = $output_filestub . '.html';
  $output_file_gff = $output_filestub . '.gff';

  print "\nExecuting $program\n\n";
  print "Query: $query\n";
  print "Database: $database\n";
  print "Results File: $output_file\n";

  print "Options:\n";

  // Allow administrators to use an absolute path for these commands.
  // Defaults to using $PATH.
  $blast_path = variable_get('blast_path', '');
  $blast_threads = variable_get('blast_threads', 1);

  // Strip the extension off the BLAST target
  $suffix = ['.ndb', '.nhr', '.nin', '.not', '.nsq', '.ntf', '.nto',
    '.pdb', '.phr', '.pin', '.pot', '.psq', '.ptf', '.pto'];
  $database = str_replace($suffix,'',$database);

  // Check that the database exists before trying to execute the job.
  if (!(file_exists($database . '.nsq') OR file_exists($database . '.psq'))) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to find the BLAST database (ie: @db). Please ensure you have supplied the absolute path not including the file format endings.",
      array('@db' => $database),
      array('print' => TRUE)
    );
    return FALSE;
  }

  // The BLAST executeable.
  $program = $blast_path . $program;
  if (!file_exists($program)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to find the BLAST executable (ie: /usr/bin/blastn). This can be changed in the admin settings; you supplied: @command",
      array('@command' => $program),
      array('print' => TRUE)
    );
    return FALSE;
  }

  // The blast db formatter executable.
  $blast_formatter_command = $blast_path . 'blast_formatter';
  if (!file_exists($blast_formatter_command)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to find the BLAST Formatter executable (ie: /usr/bin/blast_formatter). This can be changed in the admin settings; you supplied: @command",
      array('@command' => $blast_formatter_command),
      array('print' => TRUE)
    );
    return FALSE;
  }

  // Note: all variables are escaped (adds single quotes around their values) for security reasons.
  $blast_cmd = escapeshellarg($program) . ' -query ' . escapeshellarg($query) . ' -db ' . escapeshellarg($database) . ' -out ' . escapeshellarg($output_file) . ' -outfmt=11';
  if (!empty($options)) {
    foreach ($options as $opt => $val) {
      $val = trim($val);
      if (!empty($val)) {
        print "\t$opt: $val\n";
        // We want to escape all the option values since they were supplied via
        // user input. These values should also have been checked in the
        // advanced form _validate functions but this adds an extra layer of
        // protection.
        $blast_cmd .= ' -' . escapeshellarg($opt) . ' ' . escapeshellarg($val);
      }
    }
  }

 // Setting the value of threads by admin page
 $blast_cmd .= ' -num_threads ' . escapeshellarg($blast_threads);

  print "\nExecuting the following BLAST command:\n" . $blast_cmd . "\n";

  system($blast_cmd);

  if (!file_exists($output_file)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "BLAST did not complete successfully as is implied by the lack of output file (%file). The command run was @command",
      array('%file' => $output_file, '@command' => $blast_cmd),
      array('print' => TRUE)
    );
    return FALSE;
  }

  print "\nGenerating additional download formats...\n";

  print "\tXML\n";
  $format_cmd = escapeshellarg($blast_formatter_command) . ' -archive ' . escapeshellarg($output_file) . ' -outfmt 5 -out ' . escapeshellarg($output_file_xml);
  print "\t\tExecuting $format_cmd\n\n";
  system($format_cmd);
  if (!file_exists($output_file_xml)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to convert BLAST ASN.1 archive to XML (%archive => %file).",
      array('%archive' => $output_file, '%file' => $output_file_xml),
      array('print' => TRUE)
    );
  }

  print "\tTab-delimited\n";
  $format_cmd = escapeshellarg($blast_formatter_command) . ' -archive ' . escapeshellarg($output_file) . ' -outfmt 7 -out ' . escapeshellarg($output_file_tsv);
  print "\t\tExecuting $format_cmd\n\n";
  system($format_cmd);
  if (!file_exists($output_file_tsv)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_WARNING,
      "Unable to convert BLAST ASN.1 archive to Tabular Output (%archive => %file).",
      array('%archive' => $output_file, '%file' => $output_file_tsv),
      array('print' => TRUE)
    );
  }

  print "\tGFF\n";
  convert_tsv2gff3($output_file_tsv,$output_file_gff);

  if (!file_exists($output_file_gff)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_WARNING,
      "Unable to convert BLAST Tabular Output to GFF Output (%archive => %file).",
      array('%archive' => $output_file, '%file' => $output_file_gff),
      array('print' => TRUE)
    );
  }

  print "\tHTML (includes alignments)\n";
  $format_cmd = escapeshellarg($blast_formatter_command) . ' -archive ' . escapeshellarg($output_file) . ' -outfmt 0 -out ' . escapeshellarg($output_file_html) . ' -html';
  print "\t\tExecuting $format_cmd\n\n";
  system($format_cmd);
  if (!file_exists($output_file_tsv)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_WARNING,
      "Unable to convert BLAST ASN.1 archive to HTML Output (%archive => %file).",
      array('%archive' => $output_file, '%file' => $output_file_html),
      array('print' => TRUE)
    );
  }

  print "\nDone!\n";
}

/**
 * FASTA validating parser
 *
 * A sequence in FASTA format begins with a single-line description, followed
 * by lines of sequence data.The description line is distinguished from the
 * sequence data by a greater-than (">") symbol in the first column. The word
 * following the ">" symbol is the identifier of the sequence, and the rest of
 * the line is the description (both are optional). There should be no space
 * between the ">" and the first letter of the identifier. The sequence ends
 * if another line starting with a ">" appears which indicates the start of
 * another sequence.
 *
 * @param $type
 *   The type of sequence to be validated (ie: either nucleotide or protein).
 * @param $sequence
 *  A string of characters to be validated.
 *
 * @return
 *  Return a boolean. 1 if the sequence does not pass the format valifation stage and 0 otherwise.
 *
 */
function validate_fasta_sequence($type, $sequence) {
  //Includes IUPAC codes.
  $fastaSeqRegEx = ($type == 'nucleotide')
                   ? '/^[ATCGNUKMBVSWDYRHatcgnukmbvswdyrh\[\/\]\s\n\r]*$/'
                   : '/^[acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY\*\-\s\n\r]*$/';
  $defRegEx      = '/^>\S.*/';

  // For each line of the sequence.
  foreach (explode("\n", $sequence) as $line) {

    // Is this a definition line?
    if ($line[0] == '>') {
      if (!preg_match($defRegEx, $line)) {
        return FALSE;
      }
    }
    // Otherwise it's a sequence line
    else {
      if (!preg_match($fastaSeqRegEx, $line)) {
        return FALSE;
      }
    }
  }

  return TRUE;
}

/**
 * Retrieve the regex to capture the Link-out Accession from the Hit Def.
 *
 * @param $nid
 *   The node ID of the BLAST database the hit is from.
 * @param $options
 *   An array of options that can be passed to this function. Supported
 *   options include:
 *    -
 *
 * @return
 *   A PHP regex for use with preg_match to cature the Link-out Accession.
 */
function get_blastdb_linkout_regex($node, $options = array()) {

  if (empty($node->linkout->regex)) {
    switch ($node->linkout->regex_type) {
      case 'default':
        $regex = '/^(\S+).*/';
        break;
      case 'genbank':
        $regex = '/^gb\|([^\|])*\|.*/';
        break;
      case 'embl':
        $regex = '/^embl\|([^\|])*\|.*/';
        break;
      case 'swissprot':
        $regex = '/^sp\|([^\|])*\|.*/';
        break;
    }
  }
  else {
    $regex = $node->linkout->regex;
  }

  return $regex;
}

/**
 * Return a list of recent blast jobs to be displayed to the user.
 *
 * @param $programs
 *   An array of blast programs you want jobs to be displayed for (ie: blastn, blastx, tblastn, blastp)
 *
 * @return
 *   An array of recent jobs.
 */
function get_recent_blast_jobs($programs = array()) {

  $filter_jobs = !empty($programs);

  // Retrieve any recent jobs from the session variable.
  if (isset($_SESSION['blast_jobs'])) {

    $jobs = array();
    foreach ($_SESSION['blast_jobs'] as $job_secret) {
      $add = TRUE;

      $job_id = blast_ui_reveal_secret($job_secret);
      if ($job = get_BLAST_job($job_id)) {

        // @TODO: Check that the results are still available.
        // This is meant to replace the arbitrary only show jobs executed less than 48 hrs ago.

        // Remove jobs from the list that are not of the correct program.
        if ($filter_jobs AND !in_array($job->program, $programs)) {
          $add = FALSE;
        }

        if ($add) {
          $job->query_summary = format_query_headers($job->files->query);
          $jobs[] = $job;
        }
      }
    }

    return $jobs;
  }
  else {
    return array();
  }
}

/**
 * Retrieve the number of recent jobs.
 */
function get_number_of_recent_jobs() {
  if (isset($_SESSION['blast_jobs'])) {
    return sizeof($_SESSION['blast_jobs']);
  }
  return 0;
}

/**
 * Summarize a fasta file based on it's headers.
 *
 * @param $file
 *   The full path to the FASTA file.
 *
 * @return
 *   A string describing the number of sequences and often including the first query header.
 */
function format_query_headers($file) {

  $headers = array();
  exec('grep ">" ' . escapeshellarg($file), $headers);

  // Easiest case: if there is only one query header then show it.
  if (sizeof($headers) == 1 AND isset($headers[0])) {
    return ltrim($headers[0], '>');
  }
  // If we have at least one header then show that along with the count of queries.
  elseif (isset($headers[0])) {
    return sizeof($headers) . ' queries including "' . ltrim($headers[0], '>') . '"';
  }
  // If they provided a sequence with no header.
  elseif (empty($headers)) {
    return 'Unnamed Query';
  }
  // At the very least show the count of queries.
  else {
    return sizeof($headers) . ' queries';
  }

}

/**
 * Sort recent blast jobs by the date they were submitted.
 * Ascending is in order of submission.
 *
 * THIS FUNCTION SHOULD BY USED BY USORT().
 */
function sort_blast_jobs_by_date_submitted_asc($a, $b) {
  return ($a->date_submitted - $b->date_submitted);
}

/**
 * Sort recent blast jobs by the date they were submitted.
 * Descending is most recent first.
 *
 * THIS FUNCTION SHOULD BY USED BY USORT().
 */
function sort_blast_jobs_by_date_submitted_desc($a, $b) {
  return ($b->date_submitted - $a->date_submitted);
}

/**
 * Generate an image of HSPs for a given hit.
 *
 * history:
 *    09/23/10  Carson  created
 *    04/16/12  eksc    adapted into POPcorn code
 *    03/12/15  deepak  Adapted code into Tripal BLAST
 *    10/23/15  lacey   Fixed deepak's code to be suitable for Drupal.
 *
 * @param $acc
 *    target name
 * @param $name
 *    query name, false if none
 * @param $tsize
 *    target size
 * @param $qsize
 *    query size
 * @param $hits
 *    each hit represented in URL as: targetstart_targetend_hspstart_hspend;
 * @param $score
 *    score for each hit
 *
 * @returm
 *    A base64 encoded image representing the hit information.
 */
function generate_blast_hit_image($acc = '', $scores, $hits, $tsize, $qsize, $name, $hit_name) {
  $tok = strtok($hits, ";");
  $b_hits = Array();
  while ($tok !== false) {
    $b_hits[] = $tok;
    $tok = strtok(";");
  }

  // extract score information from score param
  $tokscr = strtok($scores, ";");
  $b_scores = Array();
  while ($tokscr !== false) {
   $b_scores[] = $tokscr;
   $tokscr = strtok(";");
  }

  // image measurements
  $height = 200 + (count($b_hits) * 16);
  $width  = 520;

  $img = imagecreatetruecolor($width, $height);

  $white      = imagecolorallocate($img, 255, 255, 255);
  $black      = imagecolorallocate($img, 0, 0, 0);
  $darkgray   = imagecolorallocate($img, 100, 100, 100);
  $strong     = imagecolorallocatealpha($img, 202, 0, 0, 15);
  $moderate   = imagecolorallocatealpha($img, 204, 102, 0, 20);
  $present    = imagecolorallocatealpha($img, 204, 204, 0, 35);
  $weak       = imagecolorallocatealpha($img, 102, 204, 0, 50);
  $gray       = imagecolorallocate($img, 190, 190, 190);
  $lightgray  = $white; //imagecolorallocate($img, 230, 230, 230);

  imagefill($img, 0, 0, $lightgray);

  // Target coordinates
  $maxlength = 300;
  $t_length = ($tsize > $qsize)
                ? $maxlength : $maxlength - 50;
  $q_length = ($qsize > $tsize)
                ? $maxlength : $maxlength - 50;

  $tnormal = $t_length / $tsize;
  $qnormal = $q_length / $qsize;

  $t_ystart = 30;
  $t_yend   = $t_ystart + 20;

  $t_xstart = 50;
  $t_xend   = $t_xstart + $t_length;
  $t_center = $t_xstart + ($t_length / 2);

  // Target labels
  $warn = '"'. $hit_name . '"';
  imagestring($img, 5, $t_xstart, $t_ystart-20, $acc.$warn, $black);
  imagestring($img, 3, 5, $t_ystart+2, "Target", $black);

  // Draw bar representing target
  imagefilledrectangle($img, $t_xstart, $t_ystart, $t_xend, $t_yend, $gray);
  imagerectangle($img, $t_xstart, $t_ystart, $t_xend, $t_yend, $darkgray);

  // query coordinates
  $q_maxheight = 250;
  $q_ystart = $t_yend + 100;
  $q_yend = $q_ystart + 20;

  $q_xstart = $t_center - $q_length / 2;
  $q_xend = $q_xstart + $q_length;

  $q_center = ($q_xend + $q_xstart) / 2;
  $q_xwidth = $q_xend - $q_xstart;

  // Query labels
  imagestring($img, 5, $q_xstart, $q_yend+2, $name, $black);
  imagestring($img, 3, $q_xstart, $q_ystart+2, 'Query', $black);

  // Draw bar representing query
  imagefilledrectangle($img, $q_xstart, $q_ystart, $q_xend, $q_yend, $gray);
  imagerectangle($img ,$q_xstart, $q_ystart, $q_xend, $q_yend, $darkgray);

  // HSP bars will start here
  $hsp_bary = $q_yend + 20;

  // Draw solids for HSP alignments
  for ($ii=count($b_hits)-1; $ii>=0; $ii--) {
    // alignment

   $cur_hit = $b_hits[$ii];
   $cur_score = intval($b_scores[$ii]);

   // set color according to score
   $cur_color = $darkgray;
   if ($cur_score > 200) {
     $cur_color = $strong;
   }
   else if ($cur_score > 80 && $cur_score <= 200) {
     $cur_color = $moderate;
   }
   else if ($cur_score > 50 && $cur_score <= 80) {
     $cur_color = $present;
   }
   else if ($cur_score > 40 && $cur_score <= 50) {
     $cur_color = $weak;
   }

   $t_start = $tnormal *  intval(strtok($cur_hit, "_")) + $t_xstart;
    $t_end = $tnormal *  intval(strtok("_")) + $t_xstart;
    $q_start = $qnormal * intval(strtok("_")) + $q_xstart;
    $q_end = $qnormal *  intval(strtok("_")) + $q_xstart;

    $hit1_array = array($t_start, $t_yend, $t_end, $t_yend, $q_end,
                        $q_ystart, $q_start, $q_ystart);

   // HSP coords
    imagefilledpolygon($img, $hit1_array, 4, $cur_color);

  }//each hit

  // Draw lines over fills for HSP alignments
  for ($ii=0; $ii<count($b_hits); $ii++) {
   // alignment

   $cur_hit = $b_hits[$ii];
   $t_start = $tnormal *  intval(strtok($cur_hit, "_")) + $t_xstart;
    $t_end = $tnormal *  intval(strtok("_")) + $t_xstart;
    $q_start = $qnormal * intval(strtok("_")) + $q_xstart;
    $q_end = $qnormal *  intval(strtok("_")) + $q_xstart;

   $hit1_array = array($t_start, $t_yend, $t_end, $t_yend, $q_end, $q_ystart,
                       $q_start, $q_ystart,);

   imagerectangle($img, $t_start, $t_ystart, $t_end, $t_yend, $black);
   imagerectangle($img, $q_start, $q_ystart, $q_end, $q_yend, $black);
   imagepolygon ($img, $hit1_array, 4, $black);

    // show HSP

   imagestring($img, 3, 2, $hsp_bary, ($acc ."HSP" . ($ii + 1)), $black);

   $cur_score = intval($b_scores[$ii]);

   // set color according to score
   $cur_color = $darkgray;
   if ($cur_score > 200) {
     $cur_color = $strong;
   }
   else if ($cur_score > 80 && $cur_score <= 200) {
     $cur_color = $moderate;
   }
   else if ($cur_score > 50 && $cur_score <= 80) {
     $cur_color = $present;
   }
   else if ($cur_score > 40 && $cur_score <= 50) {
     $cur_color = $weak;
   }

   imagefilledrectangle($img, $q_start, $hsp_bary, $q_end, $hsp_bary+10, $cur_color);
    $hsp_bary += 15;
  }//each hit

  // Draw the key

  $xchart = 390;
  $ychart = 10;
  $fontsize = 4;
  $yinc = 20;
  $ywidth = 7;
  $xinc = 10;

  imagestring($img, 5, $xchart, $ychart - 5, "Bit Scores", $black);

  imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 1) + $ywidth, ">= 200" , $black);
  imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 2) + $ywidth, "80 - 200" , $black);
  imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 3) + $ywidth, "50 - 80" , $black);
  imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 4) + $ywidth, "40 - 50" , $black);
  imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 5) + $ywidth, "< 40" , $black);

  imagefilledRectangle($img, $xchart, $ychart + ($yinc * 1) + $xinc, $xchart + $yinc, $ychart + ($yinc * 2), $strong);
  imagefilledRectangle($img, $xchart, $ychart + ($yinc * 2) + $xinc, $xchart + $yinc, $ychart + ($yinc * 3), $moderate);
  imagefilledRectangle($img, $xchart, $ychart + ($yinc * 3) + $xinc, $xchart + $yinc, $ychart + ($yinc * 4), $present);
  imagefilledRectangle($img, $xchart, $ychart + ($yinc * 4) + $xinc, $xchart + $yinc, $ychart + ($yinc * 5), $weak);
  imagefilledRectangle($img, $xchart, $ychart + ($yinc * 5) + $xinc, $xchart + $yinc, $ychart + ($yinc * 6), $darkgray);

  // Now, we have a completed image resource and need to change it to an actual image
  // that can be displayed. This is done using imagepng() but unfortuatly that function
  // either saves the image to a file or outputs it directly to the screen. Thus, we use
  // the following code to capture it and base64 encode it.
  ob_start(); // Start buffering the output
  imagepng($img, null, 0, PNG_NO_FILTER);
  $b64_img = base64_encode(ob_get_contents()); // Get what we've just outputted and base64 it
  imagedestroy($img);
  ob_end_clean();

  return $b64_img;
}

/**
 * Convert tsv blast output to gff output file.
 *
 * Created by Sofia Robb
 * 09/15/2016
 * counter bugfix 10/27/2016
 *
 * The subject (hit) will be the source feature.
 * The query will be the target.
 *
 * @todo: find a more efficient way since currently the first loop stores all the blast
 *   results into an array and then the second loop prints them.
 *
 * @param $blast_tsv
 *  The name of the blast tsv output file.
 * @param $blast_gff
 *  The name of the blast gff output file.
 */
function convert_tsv2gff3($blast_tsv,$blast_gff){

  // Open a new file for writting the gff.
  $gff = fopen($blast_gff,"w");
  fwrite($gff,"##gff-version 3\n");

  // Open the TSV file to read from.
  $tsv = fopen($blast_tsv, "r") or die("Unable to open tsv file!");

  // For each line in the TSV file...
  // Need to go thru each line of tsv to find the first and last hsp of a hit.
  $last_s = NULL;
  $hsp = NULL;
  $HitResult=array();

  while(!feof($tsv)) {
    $line = fgets($tsv);
    $line = rtrim($line);

    // Skip the line if it's empty.
    if (preg_match('/^#/',$line) or preg_match('/^\s*$/',$line)){
      continue;
    }

    ## for keeping track of new queries and hits

    // Each line has the following parts:
    //  0: query id,
    //  1: subject id,
    //  2: % identity,
    //  3: alignment length,
    //  4: mismatches,
    //  5: gap opens,
    //  6: q. start,
    //  7: q. end,
    //  8: s. start,
    //  9: s. end,
    // 10: evalue,
    // 11: bit score
    $parts = preg_split('/\t/', $line);

    // Assign the important parts of the line to readable variables.
    $s = $parts[1];
    $q = $parts[0];
    $ss = $parts[8];
    $se = $parts[9];
    $qs = $parts[6];
    $qe = $parts[7];
    $e = $parts[10];


    // if this is a new hit print the last and
    // empty the $HitResult array and
    // reset hsp counter
    if ($last_s != NULL and $s != $last_s ) {
      printGFF_parent_children($gff,$HitResult);
      $HitResult = array();
      $hsp=0;
    }

    // every line is a new hsp
    $hsp++;

    // determine query strand to use in match_part line, no need to store, just print
    $q_strand = '+';
    if ($qs > $qe) {
        list($qs,$qe) = array($qe,$qs);
        $q_strand = '-';
    }

    // determine subject (hit) strand to use in match line, needs to be stored
    $HitResult["$s,$q"]['strand']='+';
    list($start,$end) = array($ss,$se);
    if($ss > $se) {
       list($start,$end) = array($se,$ss);
       $HitResult["$s,$q"]['strand']='-';
     }

    // store smallest start
     if (!array_key_exists('SS',$HitResult["$s,$q"]) or $ss < $HitResult["$s,$q"]['SS']) {
       $HitResult["$s,$q"]['SS'] = $ss;
     }

    // store largest end
     if (!array_key_exists('SE',$HitResult["$s,$q"]) or $se > $HitResult["$s,$q"]['SE']) {
       $HitResult["$s,$q"]['SE'] = $se;
     }

     // store best evalue
     if (!array_key_exists('E',$HitResult["$s,$q"]) or $e < $HitResult["$s,$q"]['E']) {
       $HitResult["$s,$q"]['E'] = $e;
     }

     // generate the match_part line for each hsp
     $HitResult["$s,$q"]['HSPs'][] = join("\t", array($s, "BLASTRESULT" , "match_part" , $start , $end , $e , $HitResult["$s,$q"]['strand'] , '.' , "ID=$s.$q.$hsp;Parent=$s.$q;Target=$q $qs $qe $q_strand"));
     $last_s = $s;
  } // end tsv file while

  // print hit and hsp for the last hit
  printGFF_parent_children($gff,$HitResult);

  // Close the files.
  fclose($tsv);
  fclose($gff);
}

/**
 *   printGFF_parent_children
 *   prints the GFF parent feature and all of its children features
 *
 *
 *  @param $blast_feature_array
 *  an array of the all the child features which is used to generate the smallest and largest coordinates for the parent
 *
 *
 */
function printGFF_parent_children ($gff,$blast_feature_array){
  foreach ($blast_feature_array as $sq => $value ) {
    list ($s,$q) = preg_split('/,/' , $sq);
    $evalue =  $blast_feature_array["$s,$q"]['E'];
    $parent =  join ("\t", array($s, "BLASTRESULT" , "match" , $blast_feature_array["$s,$q"]['SS'] , $blast_feature_array["$s,$q"]['SE'] , $blast_feature_array["$s,$q"]['E'] , $blast_feature_array["$s,$q"]['strand'] , '.' , "ID=$s.$q;Name=$q($evalue)")) . "\n";
    $child = join ("\n",$blast_feature_array["$s,$q"]['HSPs']) . "\n";
    fwrite($gff,$parent);
    fwrite($gff,$child);
  }
}

/**
 * Get text from cvitjs conf file, if possible.
 *
 * @param $genome_target
 *   The section of the config to return. Should consist of "data."+[blastdb name].
 *
 * @return
 *   A string containing the entire contents of the cvitjs configuration file. FALSE otherwise.
 */
function blast_ui_get_cvit_conf_text($genome_target = FALSE) {

  // Retrieve the full path and filename of the conf.
  $cvit_conf = blast_ui_get_cvit_conf();
  if ($cvit_conf) {

    // Retrieve the contents of the file.
    $contents = '';
    if (file_exists($cvit_conf)) {
      $contents = file_get_contents($cvit_conf);
    }

    // If no genome target was provided then return the full file.
    if ($contents && $genome_target == FALSE) {
      return $contents;
    }

    // If a genome target was provided, then only return that section.
    if ($genome_target) {
      $section = array();
      $in_section = FALSE;

      // For each line of the configuration file...
      $section_header = '['.$genome_target.']';
      $lines = preg_split('/\r\n|\n|\r/', trim($contents));
      foreach($lines as $l) {

        // Are we in the section for this genome target?
        if (trim($l) == $section_header) {
          $in_section = TRUE; }

        // Id so and we haven't fallen out of it through an empty line,
        // then add it to saved section for returning.
        if ($in_section) {
          if (trim($l) == '') { break; }
          $section[] = trim($l);
        }
      }

      // If we found the section, then return it ;-).
      if (!empty($section)) {
        return implode("\n", $section);
      }
    }
  }

  return false;
}


/**
 * Get path to cvitjs conf file.
 *
 * @return
 *  The path to the CViTjs codebase.
 */
function blast_ui_get_cvit_conf($cvitjs_location = NULL) {
  if (!$cvitjs_location) {
    $cvitjs_location = libraries_get_path('cvitjs') . DIRECTORY_SEPARATOR;
  }

  $cvit_conf_path = $cvitjs_location . 'cvit.conf';

  return $cvit_conf_path;
}