function readDatabase($filename)
{
// read the xml database of aminoacids
$data = implode("", file($filename));
$parser = xml_parser_create();
xml_parser_set_option($parser, XML_OPTION_CASE_FOLDING, 0);
xml_parser_set_option($parser, XML_OPTION_SKIP_WHITE, 1);
xml_parse_into_struct($parser, $data, $values, $tags);
xml_parser_free($parser);
// loop through the structures
foreach ($tags as $key => $val) {
if ($key == "molecule") {
$molranges = $val;
// each contiguous pair of array entries are the
// lower and upper range for each molecule definition
for ($i = 0; $i < count($molranges); $i += 2) {
$offset = $molranges[$i] + 1;
$len = $molranges[$i + 1] - $offset;
$tdb[] = parseMol(array_slice($values, $offset, $len));
}
} else {
continue;
}
}
return $tdb;
}
function XMLtoArray($values, $tags, $item, $parsetype = 0)
{
foreach ($tags as $key => $val) {
if ($key == $item) {
$molranges = $val;
$offset = $molranges[0];
$len = $molranges[1] - $offset;
$data = parseMol(array_slice($values, $offset, $len), $parsetype);
}
}
return $data;
}
