Php uncompress & unpack gives an array containing multiple values ​​(9 in 10309) undefined

Question

I have a binary string of data that I decompress and decompress into an array using php with the following code (full code for this php page is included at the bottom of this question):

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++; } 

I found that mz_array (the above code, X-coordinates) has 9 undefined values ​​(all at the end), but that int_array (the same Y-coordinate code) also has 9 undefined values ​​(distributed throughout the array (not grouped or in beginning / end).

Here is an example of a small piece of testing that I added to my page:

Test code:

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

"Selecting" the output signal (note the missing values):

 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 

The strangest part is that if I manually enter the lines in the full / source code (see the bottom of the page), I get undefined values, and if I manually enter the line that is returned by executing "echo $ row [4]" ( contains binaryString) in the following code, it does not give undefined values.

 <?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++; } ?> 

Does anyone have any suggestions or ideas why this might happen?

PS: Can someone add the gzuncompress tag? (I have no reputation).

EDIT 1

I have included the binaryString example (WARNING: Huge!)

Y-Coords (retrieved from echo $ row [4] comments in code):

eJztXQuQFMUZblQEQfEQUQSJYwRBSuLG + AAFHdmeRYOPS2lRgEgNvgpLhUuQkooYB5GXBLIaHwRQRwMpCqOuiciJhU4KjUoMnm98r2KUaKkXreBpSCXf3z3Lzu7Na3fn9nZhvqop2N2enu6 /// 7fPcdYjBgxYsSIESNGjBhVgvFGkqmLOWPjk77tlNs5a35AY9kdnBlPo + 3GMZ5tm87VmDULfXL / PnOwzkGfP0P7RLj2MUrAaNB0l2OtJuDzVu + 188XJnKmnYZ0a5DpZE7Fu3TVm / BOft5TZZ4yqwvwf1u + ne89ea7wM / Pke5vvI3jHfGGVA56xxEnTWKeCT / h588i5k3cEp1vyuxtQN + H / an 5 + ya9GuBf2t6zi + s2ZAHh / KC + V7BTDXoK / 15Y03uxD3zo1urmoKND4efXb17tPqgTZz0OYy / + eaB2uMHYP1UKOjVc1gDuy30TUuz3fWP82NJuy1nZyZx4GXDgO9M / acXgPd9w + mvXFrx66P + TLGNBnXBbXBB4tWwldYhvFcGmI8GbRJ1xGPhFjvPQXqvljDbZjv6jpan1pHfxcfjHyqm0Hra8vnraa + sGF68prmz4aeGtM3Y4wr3fd8I35nrxfZTU / g88YK / NbORAJ6owvG31Y49mwT / JJFXPrjYQBZSrGaAj97UMTrfFYJ4wkD9GUYtcuLBHU7Z / rzoO3dtT1OgQ0Y42neNqyFuSjrOcuamNMo7KPzecHvR45MsYtwKZfAFh7GBS9lv0LbH + BZH + 67v7KvcBEDdNrarV0hb77Ddy9VWT9AFmRfwJqtqR + 9pF8MGq / iwl7PId1bY62DQcMGB + 0hF5W1th8WIO / a7a0TsN + maDK + M9qdnynWao3H76fVAb87oN8K2 / s3XNDKfE5jzc0aW7sRNuYhkKM7bFpNt23g / 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Full code:

 <?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> 

Answer 1

I incremented one of the indices where I didn’t have to, $ counter ++ inside if ($ temp [1]> $ max_int) {// stuff} threw the index when a new maximum value was found.

The new code for int_array now looks like this (using the Sectus trick and 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); } 

Also apply the following syntax (if you do not want to use the Sectus trick):

 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]; } } } 

I would like to thank everyone who also broke their heads.

Answer 2

It is very difficult:

 $max = strlen($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++; } 

use this instead:

 $mz_array = array_values(unpack("f*", $unc_mz));