4

我有一个二进制数据字符串，我使用 php 使用以下代码解压缩并解压到一个数组中（此 php 页面的完整代码包含在此问题的底部）：

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++;
}

我发现 mz_array （上面的代码，X-coords）都有 9 个未定义的值（全部在末尾），但是 int_array（类似的代码，Y-coords）也有 9 个未定义的值（分布在整个数组中（不是分组或在开头/结尾）。

这是我添加到页面中的一个小测试块的示例：

测试代码：

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

输出的“选择”（注意缺失值）：

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

最奇怪的部分是，如果我在完整/原始代码中手动输入字符串（见页面底部），我会得到未定义的值，而如果我手动输入通过执行“echo $row[4]”返回的字符串（包含binaryString) 在下面的代码中它不会产生未定义的值。

<?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++;
  }
?>

有没有人有任何建议或想法为什么会发生这种情况？

PS：有人可以添加标签 gzuncompress 吗？（我没有这方面的声誉）。

编辑 1

我已经包含了一个示例 binaryString （警告：巨大！）

Y 坐标（由代码中注释的 echo $row[4] 检索）：

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​​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 SJC9+0PH3oIPpE5x8SVesnMAJ3Dv8/1uc30e+w1rSblD8W4Ar3WA/UcxXVFDGJE9VQzSr1mi/bjgfFCtgOSQyBfcHa1NRXJh1KAUW/6Kxhou0dhJQ1Iy/nmxw6bsBNA7JJbPxXwvzNv8+i7w0HHwc5fh+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==

完整代码：

<?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 回答 2

1

这很复杂：

$max = strlen($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++;
  }

改用这个：

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

我正在增加我不应该拥有的索引之一，if ($temp[1] > $max_int) { // stuff } 中的 $counter++ 在检测到新的最大值时会碰撞索引。

int_array 的新代码现在看起来像这样（使用 Sectus 的技巧和 max(array)）：

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);
}

以下语法也是有效的（如果您不想使用 Sectus 的技巧）：

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];
    } 
  } 
}

我还要感谢所有为此烦恼的人。

于 2013-02-20T09:43:04.803 回答