". $url . "
";
$cookie = tempnam ("/tmp", "CURLCOOKIE");
$ch = curl_init();
curl_setopt( $ch, CURLOPT_USERAGENT, "Mozilla/5.0 (Windows; U; Windows NT 5.1; rv:1.7.3) Gecko/20041001 Firefox/0.10.1" );
curl_setopt( $ch, CURLOPT_URL, $url );
curl_setopt( $ch, CURLOPT_COOKIEJAR, $cookie );
curl_setopt( $ch, CURLOPT_FOLLOWLOCATION, true );
curl_setopt( $ch, CURLOPT_ENCODING, "" );
curl_setopt( $ch, CURLOPT_RETURNTRANSFER, true );
curl_setopt( $ch, CURLOPT_AUTOREFERER, true );
curl_setopt( $ch, CURLOPT_SSL_VERIFYPEER, false ); # required for https urls
curl_setopt( $ch, CURLOPT_CONNECTTIMEOUT, $timeout );
curl_setopt( $ch, CURLOPT_TIMEOUT, $timeout );
curl_setopt( $ch, CURLOPT_MAXREDIRS, 10 );
$content = curl_exec( $ch );
$response = curl_getinfo( $ch );
curl_close ( $ch );
return array($content, $response);
}
function AllPermutations($InArray, $InProcessedArray = array())
{
$ReturnArray = array();
foreach($InArray as $Key=>$value)
{
$CopyArray = $InProcessedArray;
$CopyArray[$Key] = $value;
$TempArray = array_diff_key($InArray, $CopyArray);
if (count($TempArray) == 0)
{
$ReturnArray[] = $CopyArray;
}
else
{
$ReturnArray = array_merge($ReturnArray, AllPermutations($TempArray, $CopyArray));
}
}
return $ReturnArray;
}
function permutations($arr,$n)
{
$res = array();
foreach ($arr as $w)
{
if ($n==1) $res[] = $w;
else
{
$perms = permutations($arr,$n-1);
foreach ($perms as $p)
{
$res[] = $w." ".$p;
}
}
}
return $res;
}
if($_REQUEST){
if($_REQUEST['dosearchonwords']){
$wordlist = json_decode($_REQUEST['wordlistJSON']);
}else
if($_REQUEST['action']== "step1"){
$wordcombolist = array();
$searchwords = $_REQUEST['wordMatches'];
echo "You are searching for ". sizeof($searchwords) . " different words:";
foreach($searchwords as $value){
echo $value . "----";
}
echo "
";
//print_r(AllPermutations($searchwords));
$finalcombolist = array();
for($i = 1; $i <= sizeof($searchwords); $i++){
$finalcombolist[] = permutations($searchwords, $i);
}
foreach($finalcombolist as $key=> $value){
//echo "Number of words: " . ($key + 1 ). "
";
foreach($value as $combokey => $combovalue){
//echo $combovalue . ", ";
array_push($wordcombolist, $combovalue);
}
echo "
";
}
?>
Select which words you would like to search for:
$yvalue){
array_push($yesFind, $allwordcombos[$yvalue]);
}
foreach($_REQUEST['no'] as $nkey => $nvalue){
array_push($noFind, $allwordcombos[$nvalue]);
}
echo "Getting UniProt data...";
$url = str_replace( "&", "&", urldecode(trim("http://www.uniprot.org/uniprot/?query=" . $_REQUEST['proteinToSearch'].'&sort=score&offset=0&limit=250&format=rss')) );
$url = preg_replace("/\s+/", "%20", $url);
echo "Accessing ". $url . "
";
$cookie = tempnam ("/tmp", "CURLCOOKIE");
$ch = curl_init();
curl_setopt( $ch, CURLOPT_USERAGENT, "Mozilla/5.0 (Windows; U; Windows NT 5.1; rv:1.7.3) Gecko/20041001 Firefox/0.10.1" );
curl_setopt( $ch, CURLOPT_URL, $url );
curl_setopt( $ch, CURLOPT_COOKIEJAR, $cookie );
curl_setopt( $ch, CURLOPT_FOLLOWLOCATION, true );
curl_setopt( $ch, CURLOPT_ENCODING, "" );
curl_setopt( $ch, CURLOPT_RETURNTRANSFER, true );
curl_setopt( $ch, CURLOPT_AUTOREFERER, true );
curl_setopt( $ch, CURLOPT_SSL_VERIFYPEER, false ); # required for https urls
curl_setopt( $ch, CURLOPT_CONNECTTIMEOUT, $timeout );
curl_setopt( $ch, CURLOPT_TIMEOUT, $timeout );
curl_setopt( $ch, CURLOPT_MAXREDIRS, 10 );
$content = curl_exec( $ch );
$response = curl_getinfo( $ch );
curl_close ( $ch );
$xmlresponse = simplexml_load_string($content);
//var_dump($xmlresponse);
$objects = new SimpleXMLElement($content);
foreach($objects->channel->item as $listkey => $listitem){
var_dump($listitem);
$findmatches = preg_split("/,/", $_REQUEST['matchingwords']);
//echo "looking in wikipedia entries for any of the matches:" . var_dump($findmatches);
echo "
".$listitem->link;
$uniprotdata = getWebUrl($listitem->link);
foreach($yesFind as $yeskey => $yeswordtofind){
echo "Looking for: " . preg_replace("/\s+/", " & ", $yeswordtofind) . "
";
}
foreach($noFind as $nokey => $nowordtofind){
echo "Looking to see if not present : " . preg_replace("/\s+/", " & ",$nowordtofind) . "
";
}
/*
foreach($findmatches as $key => $match){
if(preg_match("/"."/", $match, $uniprotdata[1])){
echo $match . "..Found
";
}else{
echo $match . "..Not Found
";
}
}
*/
//var_dump($uniprotdata);
echo "
";
}
exit();
}
?>