function OneQuery($query_key, $text, $limit = 1, $properties = null)
{
global $config;
// clean text
$text = str_replace(':', '', $text);
$text = str_replace('"', '', $text);
// BioStor search API
$url = 'http://biostor.org/api.php?q=' . urlencode($text);
//file_put_contents('/tmp/q.txt', $url, FILE_APPEND);
$json = get($url);
//file_put_contents('/tmp/q.txt', $json, FILE_APPEND);
if ($json != '') {
$obj = json_decode($json);
if (isset($obj->rows)) {
//foreach ($obj->rows as $row)
//$row = $obj->rows[0];
for ($i = 0; $i < 3; $i++) {
$row = $obj->rows[$i];
// check
$v1 = finger_print($text);
$v2 = finger_print($row->fields->default);
$lcs = new LongestCommonSequence($v1, $v2);
$d = $lcs->score();
// echo $d;
$score = min($d / strlen($v1), $d / strlen($v2));
if ($score > 0.8) {
$hit = new stdclass();
$hit->id = str_replace('biostor/', '', $row->id);
$hit->name = $row->doc->title;
$hit->score = $score;
$hit->match = true;
$this->StoreHit($query_key, $hit);
}
}
}
}
}
function cluster($strings)
{
$result = new stdclass();
$n = count($strings);
// clean
for ($i = 0; $i < $n; $i++) {
$strings[$i] = finger_print(trim($strings[$i]));
}
$map = array();
$inv_map = array();
$count = 0;
foreach ($strings as $k => $v) {
$map[$k] = $count;
$inv_map[$count] = $k;
$count++;
}
// Create adjacency matrix and fill with 0's
$X = array();
for ($i = 0; $i < $n; $i++) {
$X[$i] = array();
for ($j = 0; $j < $n; $j++) {
$X[$i][$j] = 0;
}
}
$nodes = '';
$edges = '';
// Compare names using approximate string matching
$i = 0;
foreach ($strings as $k1 => $v1) {
$nodes .= "node {$i} [label=\"" . $v1 . "\"];\n";
if ($i < $n - 1) {
$j = 0;
foreach ($strings as $k2 => $v2) {
if ($j > $i && $j < $n) {
// Find longest common subsequence for this pair of cleaned names
$lcs = new LongestCommonSequence($v1, $v2);
$d = $lcs->score();
// Filter by longest common substring (to ensure we have a "meaningful"
// match), that is, so that we avoid subsequences that have little continuity
$str = '';
$lcstr = LongestCommonSubstring($v1, $v2, $str);
if ($lcstr >= 4) {
// Ignore matches just on date, we want more than that
if (is_numeric(trim($str))) {
} else {
// If longest common subsequence is > 70% of the length of both strings
// we accept it.
if ($d / strlen($v1) >= 0.7 || $d / strlen($v2) >= 0.7) {
$X[$map[$k1]][$map[$k2]] = 1;
$X[$map[$k2]][$map[$k1]] = 1;
$edges .= $i . " -- " . $j . " [label=\"" . $lcstr . "\"];\n";
}
}
} else {
// If just a short match is it the start if the string (e.g., an abbreviation)
$abbreviation = false;
if (strlen($v1) == $d) {
if (strpos($v2, $v1, 0) === false) {
} else {
$abbreviation = true;
}
} else {
if (strpos($v1, $v2, 0) === false) {
} else {
$abbreviation = true;
}
}
// Accept abbreviation
if ($abbreviation) {
$X[$map[$k1]][$map[$k2]] = 1;
$X[$map[$k2]][$map[$k1]] = 1;
$edges .= $i . " -- " . $j . " [label=\"" . $lcstr . "\"];\n";
}
}
}
$j++;
}
$i++;
}
}
$result->graph = "graph {\n" . $nodes . $edges . "}\n";
//echo $graph;
// Get components of adjacency matrix
$components = get_components($X);
$result->clusters = array();
foreach ($components as $component) {
$cluster = array();
foreach ($component as $k => $v) {
$member = new stdclass();
$member->id = $inv_map[$v];
$member->string = $strings[$inv_map[$v]];
$cluster[] = $member;
}
$result->clusters[] = $cluster;
}
//print_r($map);
if (0) {
print_r($c);
}
return $result;
}
$html = '<div>' . $this->left . '<br/>' . $this->right . '</div>';
return $html;
}
function printDiff($C, $X, $Y, $i, $j)
{
if ($i > 0 and $j > 0 and $X[$i - 1] == $Y[$j - 1]) {
$this->printDiff($C, $X, $Y, $i - 1, $j - 1);
//echo " " , $X{$i-1};
$this->left .= "<span style=\"background:rgb(100,255,100);color:black;\">" . $X[$i - 1] . "</span>";
$this->right .= "<span style=\"background:rgb(100,255,100);color:black;\">" . $X[$i - 1] . "</span>";
} else {
if ($j > 0 and ($i == 0 or $C[$i][$j - 1] >= $C[$i - 1][$j])) {
$this->printDiff($C, $X, $Y, $i, $j - 1);
//echo "+ " , $Y{$j-1};
$this->right .= $Y[$j - 1];
} else {
if ($i > 0 and ($j == 0 or $C[$i][$j - 1] < $C[$i - 1][$j])) {
$this->printDiff($C, $X, $Y, $i - 1, $j);
//echo "- " , $X{$i-1};
$this->left .= $X[$i - 1];
}
}
}
}
}
// test
$s1 = 'hello blue marine';
$s2 = 'yellow blue submarine';
$lcs = new LongestCommonSequence($s1, $s2);
echo $lcs->score();
echo $lcs->display();
