function summary_search_results($spectrum_id, $protein_name)
{
$ops = get_operations_by_name("all(0)/process protein(*)");
foreach ($ops as $op) {
$proteinName = get_io_by_name($op['id'], "p.getName()", "protein name");
echo "<h4><a href=\"dump.php?id=" . $op['id'] . "\">" . $proteinName[0]['value'] . "</a></h4>";
$scores = get_operations_by_name("query digested peptides(*)/query digested peptide(*)/query all ptm variants(*)/QuerySequence(*)/test charge(*)/match candidate hypothesis(*)/Spectrum::ScoreSequenceVsSpectrum(*)", $op['id']);
foreach ($scores as $score) {
$seq_io = get_io_by_name($score['id'], "seq", "Sequence to match");
echo "<a href=\"dump.php?id=" . $score['id'] . "\">" . $seq_io[0]['value'] . "</a>";
#echo $seq_io[0]['value'];
#var_dump($score);
echo "<br/>";
}
// $proteinSequence = get_io_by_name($op['id'], "protein/sequence()", "protein to query");
// $str = $proteinSequence[0]['value'];
// $str2 = chunk_split($str, 10, ' ');
// $str2 = chunk_split($str2, 88);
// echo "<pre>$str2</pre><br/><br/>";
}
}
function get_operations_by_name($path, $parent_id = -1)
{
global $operation_by_name_stmt;
$names = preg_split('/\\//', $path, 2);
$current = $names[0];
$remaining = $names[1];
preg_match('/^(?P<name>.*)\\((?P<count>.*)\\)$/', $current, $matches);
$name = $matches['name'];
$count = $matches['count'];
$operation_by_name_stmt->bindParam('parent', $parent_id);
$operation_by_name_stmt->bindParam('name', $name);
$operation_by_name_stmt->execute();
$ops_array = array();
while ($op = $operation_by_name_stmt->fetch(PDO::FETCH_ASSOC)) {
$ops_array[] = $op;
}
$operation_by_name_stmt->closeCursor();
$result = array();
$i = 0;
foreach ($ops_array as $op) {
if ($count == '*' || intval($count) == $i) {
if ($remaining == '') {
$result[] = annotate($op);
} else {
$more_ops = get_operations_by_name($remaining, intval($op['id']));
$result = array_merge($result, $more_ops);
}
}
$i++;
}
return $result;
}
