4

私は次のコードでphpを使用して配列に解凍および解凍するバイナリデータ文字列を持っています（このphpページの完全なコードはこの質問の下部に含まれています）：

while ($row = mysql_fetch_array($result, MYSQL_NUM)) {
  $glycopeptide[$hits] = $row[1];
  echo $row[4];
  // $row[4] contains the binaryString
  $mz = base64_decode($row[4]);
  $unc_mz = gzuncompress($mz);
  $max = strlen($unc_mz);
  $counter = 0;
  for ($i = 0; $i < $max; $i = $i+4) {
    $temp = substr($unc_mz,$i,4);
    $temp = unpack("f",$temp);
    $mz_array[$counter] = $temp[1];
    $counter++;
  }
  $hits++;
}

mz_array（上記のコード、X-coords）には9つの未定義の値（すべて最後に）がありますが、int_array（同様のコード、Y-coords）にも9つの未定義の値（配列全体に分散されています（グループ化または開始/終了時）。

これは、ページに追加した小さなテストチャンクの例です。

テストコード：

for ($i = 0; $i < $counter; $i++) {
  echo $i;
  echo " -  ";
  echo $mz_array[$i];
  echo " - ";
  echo $int_array[$i];
  echo "<br/>";
}

出力の「選択」（欠落している値に注意してください）：

671 - 274.20001220703 - 429
672 - 274.39999389648 -
673 - 274.60000610352 - 1098
-- skipping a few lines --
10299 - 2199.8000488281 - 0
10300 - 2200 - 0
10301 - - 0
10302 - - 0

最も奇妙な部分は、完全な/元のコードに文字列を手動で入力すると（ページの下部を参照）、「echo $ row [4]」（を含む）を実行して返される文字列を手動で入力すると、未定義の値が取得されることです。次のコードのbinaryString）は、未定義の値を生成しません。

<?php
  $string = " /* Copy the string in the spoiler (on this page) here */ ";
  $int = base64_decode($string);
  $unc_int = gzuncompress($int);
  $max = strlen($unc_int);
  $counter = 0; 
  $max_int = 0;
  for ($i = 0; $i < $max; $i = $i + 4) {
     $temp= substr($unc_int,$i,4);
     $temp = unpack("f",$temp);
     $int_array[$counter] = $temp[1];
     echo $counter;
     echo " -- ";
     echo $int_array[$counter];
     echo "<br/>";
     $counter++;
  }
?>

誰かがこれが起こるかもしれない理由について何か提案やアイデアがありますか？

PS：誰かがタグgzuncompressを追加できますか？（私はそれについての評判がありません）。

編集1

例のbinaryStringを含めました（警告：巨大です！）

Y-Coords（コード内のコメント付きecho $ row [4]によって取得）：

eJztXQuQFMUZblQEQfEQUQSJYwRBSuLG + AAFHdmeRYOPS2lRgEgNvgpLhUuQkooYB5GXBLIaHwRQRwMpCqOuiciJhU4KjUoMnm98r2KUaKkXreBpSCXf3z3Lzu7Na3fn9nZhvqop2N2enu6 /// 7fPcdYjBgxYsSIESNGjBhVgvFGkqmLOWPjk77tlNs5a35AY9kdnBlPo + 3GMZ5tm87VmDULfXL / PnOwzkGfP0P7RLj2MUrAaNB0l2OtJuDzVu + 188XJnKmnYZ0a5DpZE7Fu3TVm / BOft5TZZ4yqwvwf1u + ne89ea7wM / Pke5vvI3jHfGGVA56xxEnTWKeCT / h588i5k3cEp1vyuxtQN + H / AN5 + ya9GuBf2t6zi + s2ZAHh / KC + V7BTDXoK / 15Y03uxD3zo1urmoKND4efXb17tPqgTZz0OYy / + eaB2uMHYP1UKOjVc1gDuy30TUuz3fWP82NJuy1nZyZx4GXDgO9M / acXgPd9w + mvXFrx66P + TLGNBnXBbXBB4tWwldYhvFcGmI8GbRJ1xGPhFjvPQXqvljDbZjv6jpan1pHfxcfjHyqm0Hra8vnraa + sGF68prmz4aeGtM3Y4wr3fd8I35nrxfZTU / g88YK / NbORAJ6owvG31Y49mwT / JJFXPrjYQBZSrGaAj97UMTrfFYJ4wkD9GUYtcuLBHU7Z / rzoO3dtT1OgQ0Y42neNqyFuSjrOcuamNMo7KPzecHvR45MsYtwKZfAFh7GBS9lv0LbH + BZH + 67v7KvcBEDdNrarV0hb77Ddy9VWT9AFmRfwJqtqR + 9pF8MGq / iwl7PId1bY62DQcMGB + 0hF5W1th8WIO / a7a0TsN + maDK + M9qdnynWao3H76fVAb87oN8K2 / s3XNDKfE5jzc0aW7sRNuYhkKM7bFpNt23g / XhhfBp6RtDKoW / UXmjzkaPNefg8j2Jj9UWXmgN4z7gnT0N1IuTRZ5yle4Avdzi + HWK + / 0md + eNmsLwxTsT8z8zHyMvGDOzlbujnag // cmcyOtq11c8aNDCK5Ugb1 / hvsmw5ps7GOl1dphycHs5fNS7EM26prjzJ / HTZ + rJ6tnLrnZC / 74ePczadhX0 / LZp4VWY59OcB4IdmXqALaf + JPNUAj2dUQBvql3KbhqKx6ceMZVNnjGWT1qeY / jZ00Z / xTMP2bbzkBPEudLA6ksaHfxVvf02HbaV3wfy2JJn + MeyvP + K5C8D3m5NMfRb3rfaYH + K + L / yseRXGuAT3XSHvI5tXjPk2Rz8Yi / kwl3GtiGyrxl6wff6FPr8oHK91v23D2dAX4 / NDhW1Itxvbq8DPB / jwixM9bNodBT6Yg / EO5OHoRD7t6dgr / fnekSvNBM + RYvw6fHt1n0Iakk9GMXurL / e5uz3onpYbQeMr2vvbyrd5uTgtrbXn + xJgvJeUcbGPQuiAr5IF7VoHYF4Dg2M0jSTXBvHd / NaZoDiFscuWC6Ycz / LFGN8MXA / ityXyO30bZwmsQevJ2O8j / HM3Tlh3oI / BlcWtyJ43 + uT7UFdCXn5ox418oDwlec28OYQtQDo / xF4XebkWjCdj10kkOGu8VGON + 4I3t + WfYS7P047sZv3X0j / M3pm / t1oQ9LflnwIby / g95kA0acuPIzEUdDrdzn9UIo8z0pcjWzmsHWCcgfFcX2J8akNSxsx8oA5Bvydx4Tu7Pvd59PEkxvspZy3naywN3m7dCv7ejPGbEawR2ZLTi / oZxlnDZMgJkmMjbX1DvtNheb / WmMKlv / t3XJuSrvI2vQJy7gKN6eR7ebQhmGtBgwcwH / CtiAGG3Ldh0KhpgbVd5C8KOVkEfW7p + fPGQaDbqTaPusgTiq1YS6LNkxnvS1uJ9q1ym3ctnToTzx4V0s7IYWR7X6OxK + Z3anvfWdnIhV1Idp2i2nQfHPwsYY + XQg / y8buF039 + 0EdoMhaV4w1ar2uwt6bl + b4joHbDM36bfy7VNLa9jL09H3SdmV8f62aNKX / F5zvKH0ua6g5IbiX9 + yBZKPiyWBaEhKihXBD + XtE2QIZnn0OfOzEmj1qXzFSs3zUdEDMjWkWZ24AMURt59PmSMIDOJx9O6CGv / TKssO6oBTaigfFSjILNDh7zCOJb2FBsZlHbIBscMsu4qjAm7WVvks3LniiKoUIO6W / lbUJXvIXf3uC79TDZQtZk7 / h0tWEZLvy9PskSkJ + Jh2HvPIbx4uq + RmPTntbY2tUayxyF9XlX0kLUKOX2Nvxz6yJc2DeZE7EmvfIy2lwhbbrmp3DvX / D90iSzYAfp6xwxIuhoYfdh3T7ulmLKLLTVvW2THIxL0McrnE2cN5a1cFxDxrI + 08ey759MsSOvSrF + A1OCD4WtSfo0rGz9hks9c7h / e5oDa / G2Lwgq5KjgoWbZhnyg3XH7jsS3oDOrTFdZgxw1EPAnjH7h47sm / Avj0 / Y6nGpjjOv89YJxkFx74g / rStgW4zThPwqb3PZvyRYQ + ykn20h3UezGpz6 / ZJyA / slugX2jki15LN + 9jk60wjfIwm + opA6QbBi23Z + X / KCei / 23gbMJy6V8gf / yI8v6p4dsPlcm1EnsNhEyqQH8p4 / Das0EYlH5T0soW92jJQkzbWljEiZiTqPF3Gnk3j + 39wUZ / GJsJ3 / B7 / P1zOWe2LZ9 + ej40akEGkW9iupOv6GZANxjP + sW2KW6rw + dkS2Y7sXWNT0bgg4422wu + Mn0OWLi3y36B3lCMwzy2gVXeMays + H4R // 8iOk9l7lmL + nrLiJsyR4s + P + Iy7aO9TvaTwN5w8Rr4 / aJ9QME7Ib2sSrpVcxDTYH3D9yvaN34QuwHibbsD6XSBjOSq + Ux5Fnzm + xzq0jJO5cZXiTI9hTX + J / iBLlc + 4jNGvt + XJpfjtfFmjri9Ae / hz1ufyHr91MJs5S3 + sse7Pgld + gX0HW8wgfgI9s / BxzPu5sAmdvkbD0WjDg2UX5S0S + 2A9IK / 3651iIwal2IT78JxzMKdN6LeFs22fYX / TJ / 5ecPQFHaAO8K + Nng39p8ImNsGzZj / 015WLOAjRxNhfxhUaxqDf2fgNulZZhd9hY1ivc + HbsQ / Qrq + 7 / BGgfTYP + ncVnrPa234ScWdHrfMiPItkNbsBazTX5g / 7zID6DL77BD45fNmh92oiLpLokWKH9kyxlgupzsKO6Tn4rAV + TBb6Wx0bTa5jb4A1GHvgXtBrVZ5elD8OistRTkbEzmZUl84UAyYbTVngbc9SnZdCtnkFdX1U6yLyRBMD9m0ftCPbJODcHcVGhV1eho2gfC5jweXaU43TNVlnEXDesGpYxvN6drytZwPyM + pwO14dkDc3P + TC34kyhk + 1kyLvDTmpv4PxbgB / fUm2mXxGGvaguQKyGvrWSuZlkrEQ93UpLZ / ihyx0YgOHfBuKPfA1l / mQsHX + k3HfTFzQJ41vQk6 + XVrswhVe + sABw + LijEu1c / ICdyVlLqKMOnfrP1jjRzSRpzA + 8e5Dgc2oTnD4i21jAvep2sBZE / pW4ds2L9TYbOg38x061wl9e70mfEvqr61NE3tf1CDWE0LwRcWAjSXORDvWJTMJe3AO6KqXsC + qBOtJ2Fs97HO7FcZwd / CJ + 4h9hcvK8V5S + DND18FWvhYyfwz5jnL / ZWAbmWTv5WL7F0m7K8qYPNValnPmRvhOcyLm8anBtarWG3bdWEC8vntaY4m + WLvvku31FPlhAbEaNyxaAD79U2VyUf0dF7kyMcfiOcDPMkLUzkUOet5jZT53Cvj1tnC2u / B3Ovr80vakjAV67FeRD / TaP3RPB9URUHyFfFFnzWcxWg9MgQc0lrlDY9vWaOzygSk26qgUa4Wvag6A / n8VY3fUATGKITnz31SnAfnBXnZ5RiXxQzdaboVsfBrzuU / GA8z + mqwndmlLdST6Jv + zAxQjJ5 + 4VDlrLQddMuh7scMXgm2qQ06oFJd9ycFzsKWF / 2nLA1qTxBl2 / QjFn0E / GqNoE5ADscjPyN3XySAbky0N9nuqBeNF8Ab8TLU7F7QnnzO9n50LyMnifljv4aB9z8IYhb4IvgDFtVSbF6gOkHyDWYVzI70s4oW5OjOKe1VaSxwh9FOohiVft2eMA00eLD1HquzEfbAvzfmFPEl + LsVwnXLXJN9 + RXS + SJC9 + 0PH3oIPpE5x8SVesnMAJ3Dv8 / 1uc30e + w1rSblD8W4Ar3WA / UcxXVFDGJE9VQzSr1mi / bjgfFCtgOSQyBfcHa1NRXJh1KAUW / 6Kxhou0dhJQ1Iy / nmx0HHwc5fh + zcxvtW23O7dPmaUOUjWtivYX + qxmoiHUg2bONNZj2cfw2CqowbOBcpd9L4pLmuqHTCSnZBDPs + n1uEWHvgeihj + oPOLYWuWIsEWHvjuMzp31kD78psq5Ko7EcKHKYF / jeGQa4 / KXEnY97yJ + 2wfU / gNz9TOGU7rBY2NOj3F + p2RYme / Ax97oSbrK + eBR5Z1zN6mvJf + YuEZCFFLU4ENoc + C3 / A1L7lu0twMPZPqpBqpWgbldGGLCru9I + X7pqSM77rUwUaFpj6arDXzkmPQb8ZNPjquTnFg7xRTeqVE7YzhUfsQBehcVnHMkfRLhs54Jxy + AXxFytlMWEpnKBx2TG8X / yGELKD + ldWytkPkCTvIB6l5wAYzbsy / S5Tywgr5BfTeAkdtZLabXRcUUY1UtpWzxCBZy + CM9YvzpS45H / 0hLmu0XGKGon58e8fvP7ULaPC4d33EbmTBVwei7SEydyj86Ffb62x1Yek6JweRO6mWzRcAqjvSH8d + erG9z + ELt7j7BvT1iZ0zc8TqyZ9TH / X3e1zHNj9Zc7mkGBECezHovZKegMwXccMw9lud6nfDeVbEicH2WZdSztXsSUhwz / dpVRPZD + xYVdD7JNqSsq7rLp8xU13s3NrwDWsRdG6q4pqZHIh3cFHdZ4FsqAY / Xcs9zxd1JuhcsMg5OM9jefC119ke5bXy6 + zCgPJPmW5a4RnXHXYNW1TA + mTn82jfCxcG9PcDyH4e3gm8QTKn2M6i3M / RkG9t8CmWyZiXsN8c8knUSt1Ze7y8N0DUH5R5ZqSusML ++ xt7SCyazqQYr / Hy63RcYK0riqnWGyZGkPMf7VIfRqin9yxXE2SLmp1vQ5cD8ovS52rMPFNjVgTn8mN0LoTsqpH3uO / poNxeZH5UB8D6MZfngMvV998G5BMTdl1gBfrGOoTLOqw9PDbZcIQm / uZIqPe3Ua6wjt6rGRpkY + 8NdnZnoMz30e2poPNzIl / RST + MBSFyV27IFMbYqR + j1T67sJci009jjbdo8t3ZPnk48e5RF79KvLOkBurFax3qlZxlNxbl / SBL0 / SuruMr08H1DuVvVa79ixEjRowYMWJUDeZHnFln188ZphgxYsSIESNGjBgxYsSIESNGjBgxooB473oF783vaDT11Vj2njJz7jFixOhwiL / PuDE + Mxej5vF / owjA3A ==

完全なコード：

<?php
  require 'phplot/phplot.php';
      $type = $_GET['type'];
      $gp = $_GET['gp'];
      $site = $_GET['site'];
      $prec = $_GET['prec'];
      $link = mysql_connect("localhost","reader","") or die (mysql_error());
      mysql_select_db('leidenGlycoPeptide') or die ();
      $query = sprintf("select precursor.mzValue, glycoPeptide.protein, binaryDataArray.arrayLength, binaryDataArray.encodedLength, binaryDataArray.arrayData, precursor.chargeState, run.pepMass, run.PepSeq from glycoPeptide, spectrum, binaryDataArray, run, precursor where run.glycoPeptide = glycoPeptide.id AND spectrum.run = run.id AND precursor.run = run.id AND binaryDataArray.spectrum = spectrum.id AND precursor.id = spectrum.precursor AND spectrum.spectrum like 'm/z' AND precursor.mzValue like '%s' and glycoPeptide.protein like '%s' and run.glycoSite like '%s' and run.glycoType like '%s' ORDER by glycoPeptide.protein, spectrum.spectrum",(string)$prec, (string)$gp, (string)$site, (string)$type);
      $result = mysql_query($query);
      $hits = 0;
      while ($row = mysql_fetch_array($result, MYSQL_NUM)) {
        $charge = $row[5];
        $pepmass = $row[6];
        $pepseq = $row[7];
        $glycopeptide[$hits] = $row[1];
        /* Manually entering string here also gives undefined values */
        /* $mz = " I was not able to include the mz string due to message size limit "; */
        $mz = base64_decode($row[4]);
        $unc_mz = gzuncompress($mz);
        $max = strlen($unc_mz);
        $counter = 0;
        for ($i = 0; $i < $max; $i = $i+4) {
          $temp = substr($unc_mz,$i,4);
          $temp = unpack("f",$temp);
          $mz_array[$counter] = $temp[1];
          $counter++;
        }
        $hits++;
      }
      $query = sprintf("select precursor.mzValue, glycoPeptide.protein, binaryDataArray.arrayLength, binaryDataArray.encodedLength, binaryDataArray.arrayData from glycoPeptide, spectrum, binaryDataArray, run, precursor where run.glycoPeptide = glycoPeptide.id AND spectrum.run = run.id AND precursor.run = run.id AND binaryDataArray.spectrum = spectrum.id AND precursor.id = spectrum.precursor AND spectrum.spectrum like 'intensity' AND precursor.mzValue like '%s' and glycoPeptide.protein like '%s' and run.glycoSite like '%s' and run.glycoType like '%s' ORDER by glycoPeptide.protein, spectrum.spectrum",(string)$prec, (string)$gp, (string)$site, (string)$type);
      $result = mysql_query($query);
      while ($row = mysql_fetch_array($result, MYSQL_NUM)) {
        /* Manually entering string here also gives undefined values */
        /* $int = " Copy the string from above in here "; */
        $int = base64_decode($row[4]);
        /* The result from this is the above binaryString */
        /* echo $row[4]; */ 
        $unc_int = gzuncompress($int);
        $max = strlen($unc_int);
        $counter = 0;
        $max_int = 0;
        for ($i = 0; $i < $max; $i = $i + 4) {
          $temp= substr($unc_int,$i,4);
          $temp = unpack("f",$temp);
          $int_array[$counter] = $temp[1];
          $counter++;
          if ($temp[1] > $max_int) {
            $max_int = $temp[1];
            $counter++;
          }
        }
      }
      /* The following chunk is just to test the arrays */
      for ($i = 0; $i < $counter; $i++) {
        echo $i;
        echo " -  ";
        echo $mz_array[$i];
        echo " - ";
        echo $int_array[$i];
        echo "<br/>";
      }
      for ($i = 0; $i < $counter; $i++) {
        $plot_data[$i] = array('',$mz_array[$i],$int_array[$i]);
      }
      // Plot the regular spectrum
      $width = 1024;
      $height = 768;
      $plot = new PHPlot($width,$height);
      $plot->SetMarginsPixels(NULL,NULL,NULL,35);
      $plot->SetPrintImage(False);
      $plot->SetPlotType('thinbarline');
      //$plot->SetXTitle('m/z Values');
      $plot->SetXTickAnchor('400');
      $plot->SetDataColors('red');
      $plot->SetXTickIncrement('200');
      $plot->SetXDataLabelPos('none');
      $plot->SetYTitle('Intensity');
      $plot->SetYTickAnchor('0');
      //Might need to define this dynamically with nested if/else loops
      $plot->SetYTickIncrement('100000');
      $plot->SetDataType('data-data');
      $plot->SetDataValues($plot_data);
      $plot->SetTitle('Fragmentation Spectrum');
      //$plot->DrawGraph();

      mysql_close($link);
    ?>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
   "http://www.w3.org/TR/html4/loose.dtd">
<html>
  <head>
    <title>Query result page</title>
    <script src="jquery-1.9.1.min.js"></script>
  </head>
  <script>
    var gp = '<?php echo htmlspecialchars($_GET['gp']); ?>';
    $(document).ready(function() {
      $('.button').click(function() {
        window.open('http://www.uniprot.org/uniprot/?query='+gp+'+AND+organism:human&sort=score');
      });
      $('.XY').click(function() {
        var mz_array = <?php echo json_encode($mz_array) ?>;
        var int_array = <?php echo json_encode($int_array) ?>;
        var table = 
          "<table border=\"1\">"
            +"<tr>"
              +"<th>m/z</th>"
              +"<th>intensity<t/h>"
            +"</tr>";
        var max = <?php echo $counter ?>;
        for (var i = 0; i < max; i++) {
        table += "<tr>"
                   +"<td>"+mz_array[i]+"</td>"
                   +"<td>"+int_array[i]+"</td>"
                 +"</tr>";
        }
        table += "</table>";
        var disp = window.open();
        $(disp.document.body).html(table); 
      });
    });
  </script>
  <body>
    <p>The displayed spectrum belongs to <?php echo $gp ?> with a precursor [M+H] of <?php echo (($prec*$charge)-($charge+1)); ?>.<br>
    The peptide belonging to this glycopeptide has a mass of <?php echo $pepmass ?> and sequence: <?php echo $pepseq ?>.<br>
    <button class="button">Uniprot search</button> <button class="XY">Display XY data</button></p>
    <img src="<?php echo $plot->EncodeImage();?>" alt="Plot Image">
  </body>
</html>
4

2 に答える 2

1

それは非常に複雑です：

$max = strlen($unc_mz);
  $counter = 0;
  for ($i = 0; $i < $max; $i = $i+4) {
    $temp = substr($unc_mz,$i,4);
    $temp = unpack("f",$temp);
    $mz_array[$counter] = $temp[1];
    $counter++;
  }

代わりにこれを使用してください：

$mz_array = array_values(unpack("f*", $unc_mz));
于 2013-02-20T04:44:53.903 に答える
0

あるべきではないインデックスの1つをインクリメントしていましたが、if（$ temp [1]> $ max_int）{//stuff}内の$counter ++は、新しい最大値を検出するとインデックスをバンプしていました。

int_arrayの新しいコードは次のようになります（Sectusのトリックとmax（array）を使用）。

while ($row = mysql_fetch_array($result, MYSQL_NUM)) {
  $int = base64_decode($row[4]);
  $unc_int = gzuncompress($int);
  $int_array = array_values(unpack("f*",$unc_int));
  $max_int = max($int_array);
}

次の構文も有効です（Sectusのトリックを使用したくない場合）。

while ($row = mysql_fetch_array($result, MYSQL_NUM)) {
  $int = base64_decode($row[4]);
  $unc_int = gzuncompress($int);
  $max = strlen($unc_int);
  $counter = 0; 
  $max_int = 0;
  for ($i = 0; $i < $max; $i = $i + 4) {
    $temp= substr($unc_int,$i,4);
    $temp = unpack("f",$temp);
    $int_array[$counter] = $temp[1];
    $counter++;
    if ($temp[1] > $max_int) {
      $max_int = $temp[1];
    } 
  } 
}

これにも頭を悩ませてくれた皆さんに感謝します。

于 2013-02-20T09:43:04.803 に答える