$val) { echo $val."

";}} } ######################################################################################## ######################################################################################## function counter() { ##This function opperates the counter and cleans-up the sessions directory global $SID, $count, $sesspath; if ($SID == 0){ ##Take the hits from the file $count $hits = file($count); ##Increment it by one $hits[0] ++; ##write the new number to the file $count $fp = fopen($count , "w"); fputs($fp , "$hits[0]"); fclose($fp); $SID = $hits[0]; ##Make directory for the new session mkdir("$sesspath$SID", 0777); } ##The variable SIDarch controls how many full session directories are kept and how many are archived $SIDarch = $SID - 10; $dir = "$sesspath/$SIDarch"; $directory = escapeshellarg($dir); exec("rm -rf $directory"); } ######################################################################################## ######################################################################################## ##This function creates a temporary file with an unverified sequence in it. This file is then used by makeconfin() as to verify that all characters are valid. This was done in this manner as to allow makeconfin work with both form data and uploaded data. function makeconfin() { #make global variables global $confin, $directions,$dirK, $dirX, $dirX0, $errors, $K, $linker, $MMTV, $nuclength, $nss, $nssarr, $numnuc, $occupancy, $seqscanfile, $seqinlength, $sesspath, $seqin, $SID, $validseq, $X, $X0; $seqinfile = "$sesspath$SID/seqin.txt"; $uploadfile = "$sesspath/$SID/uploaded.txt"; ##sequence options if($_POST['sequence'] == "seq_type") { if (isset($_POST['seqin'])) {$seqin = $_POST['seqin'];} $subseq = substr($seqin, 0, 15); $subdirections = substr($directions, 0, 15); if (($subseq == $subdirections) || ($_POST['sequence'] == "seq_default")){ $seqin = $MMTV;} else{$seqin = $_POST['seqin'];}} if($_POST['sequence'] == "seq_default") {$seqin = $MMTV;} if (($_POST['sequence'] == "seq_upload") && ($_FILES["uploadedfile"])) { uploader(); $fh0 = fopen($uploadfile, 'r'); $seqin = fread($fh0, filesize($uploadfile)); fclose($fh0); } ##For all sequence options: if (preg_match('/[^A,T,G,C,\s]/i', $seqin)) { ##if not A, T, G, C's add an error to the error array and re-print the form $errors['seqin'] = "Please fix your sequence to have only a, t, g, c, \n A, T, G, and C characters with spaces.";} $seq4prog = trim(chunk_split(strtoupper(preg_replace('/[^A,T,G,C]/i','', $seqin)), 1, "\n")); $seqinlength = (strlen($seq4prog)+1)/2; $fp = fopen($seqinfile, 'w+'); { fwrite($fp, $seq4prog ); } fclose($fp); ##energy options if ($_POST['energy'] == "energy_simple"){ $K = "$dirK/MD-B.dat"; $X = "$dirX/01kx5.min.par"; $X0 = "$dirX0/MD-B.par"; $occupancy = .70; $linker = 30; } if ($_POST['energy'] == "energy_default"){ if (isset($_POST['K_energy'])){$K = $_POST['K_energy'];} if (isset($_POST['X_energy'])){$X = $_POST['X_energy'];} if (isset($_POST['X0_energy'])){$X0 = $_POST['X0_energy'];} if (isset($_POST['occupancy_energy'])){$occupancy = $_POST['occupancy_energy'];} if (isset($_POST['linker_energy'])){$linker = $_POST['linker_energy'];} } if (($_POST['energy'] == "energy_default") || ($_POST['energy'] == "energy_simple")){ $seqinlength = (strlen(trim(chunk_split(strtoupper(preg_replace('/[^A,T,G,C]/i','', $seqin)), 1, "\n")))+1)/2; #Read nuclength from $X file $fh = fopen($X, 'r'); $nuclength = fread($fh, 5); fclose($fh); ##$numnuc = floor($occupancy*$seqinlength/($nuclength+$linker)); ##echo "\$occupancy = $occupancy \$seqinlength = $seqinlength\$nuclength = $nuclength \$linker = $linker"; ## Percent Occupancy can be < 0 => a shift ; just report as negative number add 2 b/c icm program error ## >0 && < 1 => a percentage of max; must be converted to integer ## >= 1 a number of nucleosomes if ($occupancy < 1 ) { $numnuc = floor($occupancy*$seqinlength/($nuclength+$linker)); } elseif ($occupancy < 0 ) { $numnuc = floor($numnuc) + 2 ; } elseif ($occupancy > 1 ) { $numnuc = $occupancy; } $max = ($numnuc)*($nuclength+$linker); if ((($numnuc)*($nuclength+$linker)) > $seqinlength) { $errors['2manynuc'] = "The sequence length specified is not long enough to support this many nucleosomes. Please reduce the occupancy or linker length."; } $confin = "$X0\n$X\n$K\n$sesspath$SID/seqin.txt\n$sesspath$SID/eq.out.par\n$sesspath$SID/E.dat\n$numnuc\n$linker\n"; } if ($_POST['energy'] == "nss_type"){ if (isset($_POST['linker_nss'])){$linker = $_POST['linker_nss'];} if (isset($_POST['X_nss'])){$X = $_POST['X_nss'];} if (isset($_POST['X0_nss'])){$X0 = $_POST['X0_nss'];} if (isset($_POST['K_nss'])){$K = $_POST['K_nss'];} $fh = fopen($X, 'r'); $nuclength = fread($fh, 5); fclose($fh); ##TOM Why are we not asking the user to specify a XO value? #$X0 = "$dirX0/MD-B.par"; ##TOM Why are we not asking the user to specify a XO value? #$K = "$dirK/MD-B.dat"; #calc $numnuc $nssarr = split("[\n\r\t ,]+", trim($nss)); $numnuc = count($nssarr); $nss = implode("\n", $nssarr); if (!empty($nss)) { $confin = "$X0\n$X\n$sesspath$SID/seqin.txt\n$nss\n-1\n$sesspath$SID/icm.par\n"; } if (empty($nss)) { $confin = "$X0\n$X\n$sesspath$SID/seqin.txt\n-1\n$sesspath$SID/icm.par\n"; } $seqscandat = "$X0\n$X\n$K\n$sesspath$SID/seqin.txt\n$sesspath$SID/eq.out.par\n$sesspath$SID/E.dat\n0\n$seqinlength\n"; $seqscanfile = "$sesspath$SID/seqscan.txt"; $fp = fopen($seqscanfile, 'w+'); { fwrite($fp, $seqscandat ); } fclose($fp); } ##write confin $fp = fopen("$sesspath$SID/confin.txt", 'w+'); { fwrite($fp, $confin ); } fclose($fp); } ######################################################################################## ######################################################################################## function uploader() { ##make global variables global $errors, $SID, $sesspath; ##Сheck that we have a file if((!empty($_FILES["uploadedfile"])) && ($_FILES['uploaded_file']['error'] == 0)) { ##Check if the file is txt and it's size is less than 1Gb $filename = basename($_FILES['uploadedfile']['name']); $ext = substr($filename, strrpos($filename, '.') + 1); if (($_FILES["uploadedfile"]) && ($_FILES["uploadedfile"]["size"] < 10000000)) { ##Determine the path to which we want to save this file $newname = "$sesspath$SID/" . "uploaded.txt"; ##Check if the file with the same name is already exists on the server if (!file_exists($newname)) { $errors['upload_absent'] = "No file was specified for the upload."; ##move the uploaded file to uploads/ } } else { $errors['upload_size'] = "Only files under 1Gb are accepted for upload"; } } else { $errors['upload_failed'] = "No file uploaded"; } } ######################################################################################## ######################################################################################## ## This function opens the nss file and confirms that all user input data is valid. function pc_validate_nss() { global $errors, $linker, $nss, $nssarr, $nuclength, $numnuc, $occupancy, $seqinlength, $sesspath, $SID; if (isset($_POST['X_nss'])){$X = $_POST['X_nss'];} ##verify entry contains only numerical entries if ($nss == ""){ $errors['nssempty'] = "If the energy function is to be bypassed at least one nucleosome start site must be specified.";} if (preg_match('/[^0-9,-\s]/i', $_POST['nss']) == TRUE) { $errors['nss'] = "Please fix your listing to have only nucleosome start sites \n (numerical entries only) separated by spaces"; }else{ ##opening file to be read as to obtain the length of the nucleosome selected. $fh = fopen($X, 'r'); $nuclength = fread($fh, 5); fclose($fh); sort($nssarr, SORT_NUMERIC); ##delete duplicate values $nss = array_unique($nssarr); $last = end($nss); $maxnss = $seqinlength - $nuclength; if ($nss['0'] <= "0"){ $errors['nsszero'] = "Nucleosome start sites must be numerical values greater or equal to '1'.";} echo "\$maxnss = $maxnss \$seqinlength = $seqinlength \$nuclength = $nuclength"; if ($last > $maxnss) { if ($seqinlength < $nuclength) { $errors['nssseq'] = "Using this X value, each nucleosome is $nuclength" . "bp in length. \nPlease specify a sequence that is greater than $nuclength" . "bp long."; } elseif ($seqinlength > $nuclength) { $errors['nssend'] = "You have requested a nucleosome start site that is less than \n $nuclength from the end of your sequence. The last nucleosome start \n sites for this sequence must be less than $maxnss"; } } $zeros = range(1, $seqinlength); ## from [0] to [n-1] in the array $nss subtract the value [i+1] from the value [i] $i=0; while($i < count($nss) -1) { $diff = $nss[$i+1] - $nss[$i]; $i++; ## if $diff is less than the $nuclength condition is false, otherwise condition is true if ($diff < $nuclength ) { $tooclose[] = $nss[$i-1]; $tooclose[] = $nss[$i]; $gtnuclength = false; $tooclose = join(', ', array_unique($tooclose)); $errors['nssclose'] = "Please fix your nucleosome start sites as to insure there \n are at least $nuclength bp between each nucleosome. The nucleosomes \n at: " . $tooclose . " are less than $nuclength bp apart."; }else $gtnuclength = true; } } } ######################################################################################## ######################################################################################## ##These functions are used to begin/end *MOST* html files created by the program. This is one area that could be cleaned up significantly and made more robust as to make the program run faster and smoother. function htmlbegin($script, $css){ echo << Interactive Chromatin Folding $script $css HTMLBEGIN; } function htmlend(){ echo << HTMLEND; } ##This function makes the Go/Reset buttons function button ($type, $value, $onclick, $style){ echo <<