myQuery("SELECT * FROM " . $this->tb . " WHERE id=" . $this->rec);
// reach the plasmid displayed
$plasmid = mysql_fetch_object($all);
if ($plasmid) {
if ($_REQUEST["action"] == "REMOVE_FILE_SEQ") {
if ($plasmid->Link_to_file != "") {
$to_rem_file = "plasmid_files/" . $plasmid->Link_to_file;
if (file_exists($to_rem_file)) {
unlink($to_rem_file);
}
}
$reqsql = "UPDATE plasmids SET sequence='', Link_to_file='' WHERE id = $this->rec";
mysql_query($reqsql);
$all = $this->myQuery("SELECT * FROM " . $this->tb . " WHERE id=" . $this->rec);
$plasmid = mysql_fetch_object($all);
}
if ($_REQUEST["action"] == "ADD_GB_GZ_FILE") {
// echo"";
// print_r($_FILES);
// echo"";
if ($_FILES["userfile"]["error"]) {
exit("ERROR, your file is probably too big, maximum upload file size is " . ini_get('upload_max_filesize') . ".
Back");
}
$userfile = $_FILES["userfile"]["tmp_name"];
$userfile_name = $_FILES["userfile"]["name"];
if (stristr($userfile_name, ".gb.gz")) {
$ext=".gb.gz";
} else if (stristr($userfile_name, ".gb")) {
$fp = fopen($userfile, "r");
$data = fread ($fp, filesize($userfile));
fclose($fp);
$zp = gzopen($userfile, "w9");
gzwrite($zp, $data);
gzclose($zp);
$userfile_name = $userfile_name . ".gz";
$ext=".gb.gz";
} else {
if(file_exists($userfile)) {
unlink($userfile);
}
exit("ERROR 1, your file MUST have the extension .gb.gz (lowercase)).
Back");
}
$dest_filename = str_replace(" ","_",substr($userfile_name, 0, strlen($userfile_name)-6)) . $ext;
$dest_filepath = "plasmid_files/" . $dest_filename;
if (file_exists($dest_filepath)) {
if (file_exists($userfile)) {
unlink($userfile);
}
exit("ERROR 2, this .gb.gz filename is already used.
Back");
}
echo "$userfile $dest_filepath
";
if (!copy($userfile, $dest_filepath)){
if (file_exists($userfile)) {
unlink($userfile);
}
exit("ERROR 3, problem copying file.
Back");
}
if(file_exists($userfile)) {
unlink($userfile);
}
$url = "/var/www/labstocks/plasmid_files/" . $dest_filename;
$handle = gzopen($url, 'r');
if ($handle) {
$content = "";
while (!gzeof($handle)) {
$buffer = gzgets($handle, 4096);
$content .= $buffer;
}
gzclose($handle);
preg_match('#ORIGIN(.*)//#sm', $content, $matches);
$seq = $matches[0];
$seq = preg_replace("#ORIGIN#", "", $seq);
$seq = preg_replace("#[^a-zA-Z]#ms", "", $seq);
$reqsql = "UPDATE plasmids SET sequence='$seq', Link_to_file='$dest_filename' WHERE id = $this->rec";
mysql_query($reqsql);
$all = $this->myQuery("SELECT * FROM " . $this->tb . " WHERE id=" . $this->rec);
$plasmid = mysql_fetch_object($all);
}
}
/*
* VIEW
*/
$in_edit_mode = $_REQUEST["PME_sys_operation"] == "Change" || $_REQUEST["PME_sys_operation"] == "PME_op_Change";
if ($plasmid->sequence) {
if ($in_edit_mode) {
$remove_gbgz_form = <<
Remove file, filename and sequence for this plasmid:
EOD;
}
$imgurl = seq2png($plasmid->sequence, PLASMAPPER_SERVER);
$plasmapper_output = <<
EOD;
$wwwblast_url = WWWBLAST_SERVER . "blast.cgi";
$resp = post_vars($wwwblast_url, array(
"DATALIB" => "plfeatstock_db",
"PROGRAM" => "blastn",
"EXPECT" => 10,
"OOF_ALIGN" => 0,
"OVERVIEW" => "on",
"ALIGNMENT_VIEW" => 0,
"DESCRIPTIONS" => 100,
"ALIGNMENTS" => 50,
"COLOR_SCHEMA" => 0,
"SEQUENCE" => $plasmid->sequence
));
$blast_output = preg_replace("/nph-viewgif.cgi/", WWWBLAST_SERVER . "nph-viewgif.cgi", $resp);
} else {
if ($in_edit_mode) {
$add_gbgz_form = <<
Add a .gb or a .gb.gz file to this plasmid
EOD;
}
}
}
$to_be_post_list_content .= <<
$remove_gbgz_form
$add_gbgz_form
$plasmapper_output
EOD;
if ($blast_output != "") {
$to_be_post_list_content .= <<
$blast_output
EOD;
}
?>