$Iclass = trim(readline("Name for the new interfae: "));
} else {
$path = getcwd() . DIRECTORY_SEPARATOR . $argv[1];
$class = $argv[2];
$Ipath = getcwd() . DIRECTORY_SEPARATOR . $argv[3];
$Inamespace = substr($argv[4], 0, strrpos($argv[4], "\\"));
$Iclass = substr($argv[4], strrpos($argv[4], "\\") + 1);
if (!is_file($path) || !is_readable($path)) {
errorexit(2, "Can not read from class file (parameter 1).");
}
require_once $path;
if (!class_exists($class)) {
errorexit(3, "Can not find class \"{$class}\" (parameter 2).");
}
if (is_file($Ipath)) {
errorexit(4, "Can not write to interface file (parameter 3). File exists.");
}
}
$rClass = new ReflectionClass($class);
$rMethods = $rClass->getMethods();
$interfaceContent = "<?php " . PHP_EOL;
$interfaceContent .= "namespace " . $rClass->getNamespaceName() . ";" . PHP_EOL . PHP_EOL;
$interfaceContent .= "interface " . $Iclass . "{" . PHP_EOL . PHP_EOL;
foreach ($rMethods as $rMethod) {
if ($rMethod->isPublic() && !$rMethod->isStatic()) {
$interfaceContent .= " public function ";
$interfaceContent .= $rMethod->getName() . "(";
foreach ($rMethod->getParameters() as $rParameter) {
if ($rParameter->isArray()) {
$interfaceContent .= "array ";
}
if (file_exists("work/done_{$_REQUEST['id']}")) {
// Job should be done now?
$s = stat('work/blastoutput_' . $_REQUEST['id']);
if ($s['size']) {
$xmlstr = file_get_contents('work/blastoutput_' . $_REQUEST['id']);
$xml = new SimpleXMLElement($xmlstr);
$optionsfile = file_get_contents('work/blastoptions_' . $_REQUEST['id']);
if (strpos($optionsfile, "query: ") != 0) {
$formdata = unserialize(base64_decode(substr($optionsfile, strpos($optionsfile, "query: ") + 7)));
}
}
if (!$xmlstr || !$xml) {
print file_get_contents('blast_header.template.html');
print "<span class='loading'>Sorry, something seems to have gone awry with your search\n" . " did you provide a correct fasta sequence?</span>";
print file_get_contents('blast_footer.template.html');
errorexit("Blast gave errors");
}
}
}
// Early exit functions first
// DB query track
if ($_REQUEST['op'] == 'dbs' && $_REQUEST['js'] != '' && $_REQUEST['program'] != '') {
// Should be safe to use $_REQUEST['program'] without additional washing.
// Return an object with the program (string) and dbs (array).
$result = '{ "program":"' . $_REQUEST['program'] . '", "dbs": [';
$dbs = dbs_per_prog($_REQUEST['program']);
// Build a list of all the dbs: "dbname",
$dbstring = "";
foreach ($dbs as $db) {
$dbstring = $dbstring . "\n\"{$db}\",";
}
