php uncompress&unpack给出包含一些(10309中的9个)未定义值
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我有一个二进制数据字符串,我解压缩并使用
PHP解压缩到一个数组中,代码如下(此问题的底部包含此php页面的完整代码)：
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++;
}
$hits++;
}
我发现mz_array(上面的代码,X-coords)都有9个未定义的值(全部在最后),但是int_array(类似的代码,Y-coords)也有9个未定义的值(分布在整个数组中)分组或在开头/结尾). 以下是我添加到页面中的小测试块的示例： 测试代码： for ($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,如果我手动输入完整/原始代码中的字符串(参见页面底部),我得到未定义的值,而如果我手动输入通过执行“echo $row [4]”(包含)返回的字符串下面的代码中的binaryString)它不会产生任何未定义的值. <?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,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,为什么会出现这种情况？ PS：有人可以添加标签gzuncompress吗？ (我没有它的声誉). 编辑1 我已经包含了一个示例binaryString(警告：巨大！) Y-Coords(由代码中的注释echo $row [4]检索)： ???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 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X7pqSM77rUwUaFpj6arDXzkmPQb8ZNPjquTnFg7xRTeqVE7YzhUfsQBehcVnHMkfRLhs54Jxy AXxFytlMWEpnKBx2TG8X / yGELKD ldWytkPkCTvIB6l5wAYzbsy / S5Tywgr5BfTeAkdtZLabXRcUUY1UtpWzxCBZy CM9YvzpS45H / 0hLmu0XGKGon58e8fvP7ULaPC4d33EbmTBVwei7SEydyj86Ffb62x1Yek6JweRO6mWzRcAqjvSH8d erG9z ELt7j7BvT1iZ0zc8TqyZ9TH / X3e1zHNj9Zc7mkGBECezHovZKegMwXccMw9lud6nfDeVbEicH2WZdSztXsSUhwz / dpVRPZD xYVdD7JNqSsq7rLp8xU13s3NrwDWsRdG6q4pqZHIh3cFHdZ4FsqAY / Xcs9zxd1JuhcsMg5OM9jefC119ke5bXy 6 zCgPJPmW5a4RnXHXYNW1TA mTn82jfCxcG9PcDyH4e3gm8QTKn2M6i3M / RkG9t8CmWyZiXsN8c8knUSt1Ze7y8N0DUH5R5ZqSusML xt7SCyazqQYr / Hy63RcYK0riqnWGyZGkPMf7VIfRqin9yxXE2SLmp1vQ5cD8ovS52rMPFNjVgTn8mN0LoTsqpH3uO / poNxeZH5UB8D6MZfngMvV998G5BMTdl1gBfrGOoTLOqw9PDbZcIQm / uZIqPe3Ua6wjt6rGRpkY 8NdnZnoMz30e2poPNzIl / RST MBSFyV27IFMbYqR j1T67sJci009jjbdo8t3ZPnk48e5RF79KvLOkBurFax3qlZxlNxbl / SBL0 / SuruMr08H1DuVvVa79ixEjRowYMWJUDeZHnFln188ZphgxYsSIESNGjBgxYsSIESNGjBgxooB473oF783vaDT11Vj2njJz7jFixOhwiL /慧普德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,4);
$temp = unpack("f",$temp);
$mz_array[$counter] = $temp[1];
$counter++;
}
$hits++;
}
$query = sprintf("select precursor.mzValue,binaryDataArray.arrayData from glycoPeptide,precursor where run.glycoPeptide = glycoPeptide.id AND spectrum.run = run.id AND precursor.run = run.id AND binaryDataArray.spectrum = spectrum.id AND precursor.id = spectrum.precursor AND spectrum.spectrum like 'intensity' AND precursor.mzValue like '%s' and glycoPeptide.protein like '%s' and run.glycoSite like '%s' and run.glycoType like '%s' ORDER by glycoPeptide.protein,(string)$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,$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,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>
解决方法
这很复杂：
$max = strlen($unc_mz);
$counter = 0;
for ($i = 0; $i < $max; $i = $i+4) {
$temp = substr($unc_mz,$temp);
$mz_array[$counter] = $temp[1];
$counter++;
}
改用它： $mz_array = array_values(unpack("f*",$unc_mz));
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