functions.php

<?php

function query_db($con, $arr1, $arr2, $comp, &$data) {

  $result;
  $select = "d.id as ` `, t1.Genome as `Genome 1`, t2.Genome as `Genome 2`, ";
  $select .= "Average_Amino_Acid_Identity as `Average AAI`, ";
  $select .= "d.16S_rRNA as `16S rRNA`, ";
  $select .= "d.Genomic_Fluidity as `Genomic Fluidity`, ";
  $select .= "d.orthologs_criterion1 as `Orthologs (Criterion 1)`, ";
  $select .= "d.orthologs_criterion2 as `Orthologs (Criterion 2)`,";
  $select .= "ArgS, CdsA, CoaE, CpsG, DnaN, Efp, Exo, Ffh, FtsY, FusA, GlnS, GlyA, GroL, HisS, IleS, InfA, InfB, KsgA, LeuS, Map, MetG, NrdA, NusG, PepP, PheS, PheT, ProS, PyrG, RecA, RplA, RplB, RplC, RplD, RplE, RplF, RplJ, RplK, RplM, RplN, RplP, RplR, RplV, RplX, RpoA, RpoB, RpoC, RpsB, RpsC, RpsD, RpsE, RpsG, RpsH, RpsI, RpsJ, RpsK, RpsL, RpsM, RpsN, RpsO, RpsQ, RpsS,SecY, Sers, ThrS, Tmk, TopA, TrpS, TruB, TrxA, TrxB, TufB, TyrS, ValS, ";
  $query = "SELECT " . $select . " '" . $comp . "' as `Group Comparison` FROM taxonomy t1, taxonomy t2, data d USE INDEX(lookup_btree) WHERE";

  $z = 0;
  $total = count($arr2) * count($arr1);
  $mod = intval($total / 100);

  for($i = 0; $i < count($arr1); $i++) {
    for($j = 0; $j < count($arr2); $j++) {

      if($arr1[$i] != $arr2[$j]) {
        $q = $query;
        // a bit of a hack, but if we have the same arrays,we'll end up checking both combinations anyway.
        if($arr1 !== $arr2)
          $q = $query . "(t1.id=" . $arr1[$i] . " AND d.genome_id1=" . $arr1[$i] . " AND t2.id=" . $arr2[$j] . " AND d.genome_id2=" . $arr2[$j] . ") OR ";
        $q = $q . "(t1.id=" . $arr2[$j] . " AND d.genome_id1=" . $arr2[$j] . " AND t2.id=" . $arr1[$i] . " AND d.genome_id2=" . $arr1[$i] . ");";
        if($result = mysqli_query($con, $q)) {
          while($row = mysqli_fetch_array($result, MYSQL_NUM)) {
            $data[] = $row;
          }
        }
      }

      $z++;
      if($z % 10) {
        echo "<script language='javascript'>document.getElementById('" . $comp . "_load').innerHTML='" . $z . "/" . $total . "'</script>";
      }
      flush();
    }
  }
  echo "<script language='javascript'>document.getElementById('" . $comp ."_load').innerHTML='" . $total . "/" . $total . "'</script>";

  return $result;
};

?>