/**
* $outfile will be overwritten with a data structure suitable for
* sortable_table.php; see that code for documentation.
* $snapfile will be overwritten with an HTML snapshot of the unsorted table;
* if null, this will be skipped.
* $resout is the file name for the table of residue analysis required for horiz
* chart. if null, this will be skipped.
* $clash is the data structure from loadClashlist()
* $rama is the data structure from loadRamachandran()
* $rota is the data structure from loadRotamer()
* $cbdev is the data structure from loadCbetaDev()
* $pperp is the data structure from loadBasePhosPerp()
* $suites is the data structure from loadSuitenameReport()
* Any of them can be set to null if the data is unavailable.
*/
function writeMulticritChart($infile, $outfile, $snapfile, $resout, $clash, $rama, $rota, $cbdev, $pperp, $suites, $bbonds, $bangles, $cablam, $omega, $outliersOnly = false, $doHtmlTable = true, $cleanupAltloc = true)
{
$startTime = time();
//{{{ Process validation data
// Make sure all residues are represented, and in the right order.
$res = listResidues($infile);
//foreach($res as $k => $v)
//{
// echo $k.$v."\n";
//}
$alts = mapAlternates($res);
//foreach($alts as $k => $v)
//{
// foreach($alts[$k] as $i => $j)
// {
// echo $k.$j."\n";
// }
//}
$Bfact = listResidueBfactors($infile);
$Bfact = $Bfact['res'];
$orderIndex = 0;
// used to maintain original PDB order on sorting.
foreach ($res as $k => $v) {
$res[$k] = array('cnit' => $v, 'order' => $orderIndex++, 'resHiB' => $Bfact[$v]);
}
$cell_color_mild = '#ffb3cc';
$cell_color_bad = '#ff76a9';
//this is used for all xxx_isbad not set otherwise
$cell_color_severe = '#ee4d4d';
if (is_array($clash)) {
$with = $clash['clashes-with'];
foreach ($clash['clashes'] as $cnit => $worst) {
$res[$cnit]['clash_val'] = $worst;
$res[$cnit]['clash'] = sprintf("%.2f", $worst) . "Å<br><small>" . $with[$cnit]['srcatom'] . " with " . $with[$cnit]['dstcnit'] . " " . $with[$cnit]['dstatom'] . "</small>";
$res[$cnit]['clash_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
if ($res[$cnit]['clash_val'] < 0.5) {
$res[$cnit]['clash_color'] = $cell_color_mild;
} elseif ($res[$cnit]['clash_val'] > 0.9) {
$res[$cnit]['clash_color'] = $cell_color_severe;
}
//$res[$cnit]['clash_color'] = '#ff3333';
//echo "clash ".$cnit."\n";
}
}
//}}}
if (is_array($rama)) {
foreach ($rama as $item) {
$res[$item['resName']]['rama_val'] = $item['scorePct'];
$phipsi = sprintf("%.1f,%.1f", $item['phi'], $item['psi']);
if (isset($item['type'])) {
if ($item['eval'] == "OUTLIER") {
$res[$item['resName']]['rama'] = "{$item['eval']} ({$item['scorePct']})%)<br><small>{$item['type']} / {$phipsi}</small>";
$res[$item['resName']]['rama_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
// ensures that all outliers sort to the top, b/c 0.2 is a Gly outlier but not a General outlier
$res[$item['resName']]['rama_val'] -= 100.0;
} elseif ($item['eval'] == "Allowed") {
$res[$item['resName']]['rama'] = "{$item['eval']} ({$item['scorePct']}%)<br><small>{$item['type']} / {$phipsi}</small>";
$res[$item['resName']]['rama_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['rama_color'] = $cell_color_mild;
// ensures that all outliers sort to the top, b/c 0.2 is a Gly outlier but not a General outlier
//$res[$item['resName']]['rama_val'] -= 100.0;
$res[$item['resName']]['rama_val'] -= 50.0;
} else {
$res[$item['resName']]['rama'] = "{$item['eval']} ({$item['scorePct']}%)<br><small>{$item['type']} / {$phipsi}</small>";
}
}
}
}
//}}}
if (is_array($rota)) {
foreach ($rota as $item) {
$res[$item['resName']]['rota_val'] = $item['scorePct'];
#if($item['scorePct'] <= 1.0)
if ($item['eval'] == 'OUTLIER') {
$res[$item['resName']]['rota'] = "{$item['eval']} ({$item['scorePct']}%)<br><small>chi angles: " . formatChiAngles($item) . "</small>";
$res[$item['resName']]['rota_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['rota_val'] -= 100.0;
//sorting hack
} elseif ($item['eval'] == 'Allowed') {
$res[$item['resName']]['rota'] = "{$item['eval']} ({$item['scorePct']}%) <i>{$item['rotamer']}</i><br><small>chi angles: " . formatChiAngles($item) . "</small>";
$res[$item['resName']]['rota_color'] = $cell_color_mild;
$res[$item['resName']]['rota_val'] -= 50.0;
//sorting hack
} else {
$res[$item['resName']]['rota'] = "{$item['eval']} ({$item['scorePct']}%) <i>{$item['rotamer']}</i><br><small>chi angles: " . formatChiAngles($item) . "</small>";
}
}
}
//}}}
if (is_array($cablam)) {
//note: sorting keys off of cablam_val
foreach ($cablam as $item) {
$outlierType = trim($item['outlierType']);
if ($outlierType == "CaBLAM Outlier") {
$res[$item['resName']]['cablam'] = "{$item['outlierType']} ({$item['cablamScore']}%)<br><small>{$item['secStruc']}</small>";
$res[$item['resName']]['cablam_val'] = "{$item['cablamScore']}";
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['cablam_isbad'] = true;
//$res[$item['resName']]['cablam_color'] = '#ff6699';
} elseif ($outlierType == "CaBLAM Disfavored") {
$res[$item['resName']]['cablam'] = "{$item['outlierType']} ({$item['cablamScore']}%)<br><small>{$item['secStruc']}</small>";
$res[$item['resName']]['cablam_val'] = "{$item['cablamScore']}";
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['cablam_isbad'] = true;
$res[$item['resName']]['cablam_color'] = $cell_color_mild;
} elseif ($outlierType == "CA Geom Outlier") {
$res[$item['resName']]['cablam'] = "{$item['outlierType']} ({$item['caGeomScore']}%)";
$res[$item['resName']]['cablam_val'] = "{$item['caGeomScore']}";
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['cablam_isbad'] = true;
//$res[$item['resName']]['cablam_color'] = '#999999';//dark grey
$res[$item['resName']]['cablam_color'] = $cell_color_severe;
} else {
$secStruc = ltrim(trim($item['secStruc']), 'try');
$res[$item['resName']]['cablam'] = "Favored ({$item['cablamScore']}%)<br><small>{$secStruc}</small>";
$res[$item['resName']]['cablam_val'] = "{$item['cablamScore']}";
}
}
}
//}}}
if (is_array($cbdev)) {
foreach ($cbdev as $item) {
$res[$item['resName']]['cbdev_val'] = $item['dev'];
if ($item['dev'] >= 0.25) {
$res[$item['resName']]['cbdev'] = sprintf("%.2f", $item['dev']) . "Å";
$res[$item['resName']]['cbdev_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
if ($item['dev'] >= 0.7) {
$res[$item['resName']]['cbdev_color'] = $cell_color_severe;
}
} else {
if ($res[$item['resName']]['cbdev'] == null) {
//for fixing a bug where an ok alt conf dev would get reported instead of the bad dev.
$res[$item['resName']]['cbdev'] = sprintf("%.2f", $item['dev']) . "Å";
}
}
}
}
//}}}
if (is_array($omega)) {
foreach ($omega as $item) {
if ($item['conf'] == 'Cis') {
$res[$item['resName']]['any_isbad'] = true;
if ($item['type'] == 'General') {
$res[$item['resName']]['omega'] = "{$item['conf']} nonPRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "1";
//for column sort
$res[$item['resName']]['omega_isbad'] = true;
} elseif ($item['type'] == 'Pro') {
$res[$item['resName']]['omega'] = "{$item['conf']} PRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "2";
//for column sort
}
} elseif ($item['conf'] == 'Twisted') {
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['omega_isbad'] = true;
if ($item['type'] == 'General') {
$res[$item['resName']]['omega'] = "{$item['conf']} nonPRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "1";
} elseif ($item['type'] == 'Pro') {
$res[$item['resName']]['omega'] = "{$item['conf']} PRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "1";
}
//for column sort
}
}
}
//}}}
if (is_array($pperp)) {
foreach ($pperp as $item) {
if ($item['outlier']) {
//echo "pperp ".$item['resName']."\n";
$reasons = array();
if ($item['deltaOut'] && $item['epsilonOut']) {
$reasons[] = "δ & ε outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
} elseif ($item['deltaOut']) {
$reasons[] = "δ outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
} elseif ($item['epsilonOut']) {
$reasons[] = "ε outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
}
$res[$item['resName']]['pperp_val'] = 1;
// no way to quantify this
$res[$item['resName']]['pperp'] = "suspect sugar pucker - " . implode(", ", $reasons) . "";
$res[$item['resName']]['pperp_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
}
}
}
//}}}
if (is_array($suites)) {
foreach ($suites as $cnit => $item) {
$res[$cnit]['suites_val'] = $item['suiteness'];
$bin = "δ-1δγ {$item['bin']}";
if ($bin == 'δ-1δγ trig') {
$bin = "δ-1δγ none (triaged {$item['triage']} )";
$res[$cnit]['suites_val'] = -1;
// sorts to very top
} elseif ($bin == 'δ-1δγ inc ') {
$bin = 'δ-1δγ none (incomplete)';
$res[$cnit]['suites_val'] = 0.0001;
// sorts just below all outliers
} elseif (preg_match('/7D dist/', $item['triage'])) {
$bin = "{$bin} ( {$item['triage']} )";
}
//echo $cnit."\n";
if ($item['isOutlier']) {
$res[$cnit]['suites'] = "OUTLIER<br><small>{$bin}</small>";
$res[$cnit]['suites_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
} elseif ($item['bin'] == 'inc ') {
$res[$cnit]['suites'] = "conformer: {$item['conformer']}<br><small>{$bin}</small>";
} else {
$res[$cnit]['suites'] = "conformer: {$item['conformer']}<br><small>{$bin}, suiteness = " . sprintf("%.2f", $item[suiteness]) . "</small>";
}
}
}
//}}}
if (is_array($bbonds)) {
//{{{
foreach ($bbonds as $cnit => $item) {
if ($item['isOutlier']) {
$res[$cnit]['bbonds_val'] = abs($item['sigma']);
$res[$cnit]['bbonds'] = "{$item['count']} OUTLIER(S)<br><small>worst is {$item['measure']}: " . sprintf("%.1f", $item[sigma]) . " σ</small>";
$res[$cnit]['bbonds_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
if ($res[$cnit]['bbonds_val'] >= 10) {
$res[$cnit]['bbonds_color'] = $cell_color_severe;
}
}
}
}
//}}}
if (is_array($bangles)) {
//{{{
foreach ($bangles as $cnit => $item) {
if ($item['isOutlier']) {
$res[$cnit]['bangles_val'] = abs($item['sigma']);
$res[$cnit]['bangles'] = "{$item['count']} OUTLIER(S)<br><small>worst is {$item['measure']}: " . sprintf("%.1f", $item[sigma]) . " σ</small>";
$res[$cnit]['bangles_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
if ($res[$cnit]['bangles_val'] >= 10) {
$res[$cnit]['bangles_color'] = $cell_color_severe;
}
}
}
}
//}}}
//}}} Process validation data
//echo "Processing validation data took ".(time() - $startTime)." seconds\n";
//{{{check for alternates
foreach ($res as $cnit => $current) {
$altloc = substr($cnit, 7, 1);
if ($altloc != ' ') {
$b_key = substr($cnit, 0, 7) . ' ' . substr($cnit, 8, 3);
if (isset($res[$b_key])) {
//{{{clash
if (!isset($res[$cnit]['clash'])) {
$res[$cnit]['clash_val'] = $res[$b_key]['clash_val'];
$res[$cnit]['clash'] = $res[$b_key]['clash'];
$res[$cnit]['clash_isbad'] = $res[$b_key]['clash_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
//}}}
//{{{rama
if (!isset($res[$cnit]['rama'])) {
$res[$cnit]['rama_val'] = $res[$b_key]['rama_val'];
$res[$cnit]['rama'] = $res[$b_key]['rama'];
if (isset($res[$b_key]['rama_isbad'])) {
$res[$cnit]['rama_isbad'] = $res[$b_key]['rama_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{rota
if (!isset($res[$cnit]['rota'])) {
$res[$cnit]['rota_val'] = $res[$b_key]['rota_val'];
$res[$cnit]['rota'] = $res[$b_key]['rota'];
if (isset($res[$b_key]['rota_isbad'])) {
$res[$cnit]['rota_isbad'] = $res[$b_key]['rota_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{cbdev
if (!isset($res[$cnit]['cbdev_val'])) {
$res[$cnit]['cbdev_val'] = $res[$b_key]['cbdev_val'];
$res[$cnit]['cbdev'] = $res[$b_key]['cbdev'];
if (isset($res[$b_key]['rama_isbad'])) {
$res[$cnit]['cbdev_isbad'] = $res[$b_key]['cbdev_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{pperp
if (!isset($res[$cnit]['pperp'])) {
if (isset($res[$b_key]['pperp'])) {
$res[$cnit]['pperp_val'] = $res[$b_key]['pperp_val'];
$res[$cnit]['pperp'] = $res[$b_key]['pperp'];
$res[$cnit]['pperp_isbad'] = $res[$b_key]['pperp_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{suites
if (!isset($res[$cnit]['suites'])) {
$res[$cnit]['suites_val'] = $res[$b_key]['suites_val'];
$res[$cnit]['suites'] = $res[$b_key]['suites'];
if (isset($res[$b_key]['suites_isbad'])) {
$res[$cnit]['suites_isbad'] = $res[$b_key]['suites_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{bbonds
if (!isset($res[$cnit]['bbonds'])) {
if (isset($res[$b_key]['bbonds_isbad'])) {
$res[$cnit]['bbonds_val'] = $res[$b_key]['bbonds_val'];
$res[$cnit]['bbonds'] = $res[$b_key]['bbonds'];
$res[$cnit]['bbonds_isbad'] = $res[$b_key]['bbonds_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{bangles
if (!isset($res[$cnit]['bangles'])) {
if (isset($res[$b_key]['bangles_isbad'])) {
$res[$cnit]['bangles_val'] = $res[$b_key]['bangles_val'];
$res[$cnit]['bangles'] = $res[$b_key]['bangles'];
$res[$cnit]['bangles_isbad'] = $res[$b_key]['bangles_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{omega
if (isset($res[$cnit]['omega'])) {
if (isset($res[$b_key]['omega_isbad'])) {
$res[$cnit]['omega_val'] = $res[$b_key]['omega_val'];
$res[$cnit]['omega'] = $res[$b_key]['omega'];
$res[$cnit]['omega_isbad'] = $res[$b_key]['omega_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{Bfactor
if (isset($res[$b_key]['resHiB'])) {
$res[$cnit]['resHiB'] = max($res[$cnit]['resHiB'], $res[$b_key]['resHiB']);
}
//}}}
//{{{CaBLAM
if (isset($res[$cnit]['cablam'])) {
if (isset($res[$b_key]['cablam_isbad'])) {
$res[$cnit]['cablam_val'] = $res[$b_key]['cablam_val'];
$res[$cnit]['cablam'] = $res[$b_key]['cablam'];
$res[$cnit]['cablam_isbad'] = $res[$b_key]['cablam_isbad'];
}
}
//}}}
}
}
}
//}}}
//remove redundant ' ' entries for residues with alternates
if ($cleanupAltloc) {
foreach ($alts as $cnit => $alt) {
foreach ($alts[$cnit] as $i => $j) {
$b_key = substr($cnit, 0, 7) . ' ' . substr($cnit, 8, 3);
unset($res[$b_key]);
}
}
}
//foreach ($bbonds as $cnit => $alt)
//{
// echo $bbonds[$cnit]['resName']."\n";
//}
// $res needs to be saved in raw_data for the horoizontal chart
if ($resout) {
$out = fopen($resout, 'wb');
fwrite($out, mpSerialize($res));
fclose($out);
}
// Set up output data structure
$table = array('prequel' => '', 'headers' => array(), 'rows' => array(), 'footers' => array(), 'sequel' => '');
$startTime = time();
//{{{ Table prequel and headers
// Do summary chart
$pdbstats = pdbstat($infile);
$table['prequel'] = makeSummaryStatsTable($pdbstats['resolution'], $clash, $rama, $rota, $cbdev, $pperp, $suites, $bbonds, $bangles, $cablam, $omega);
if ($doHtmlTable) {
$header1 = array();
$header1[] = array('html' => "<b>#</b>", 'sort' => 1);
$header1[] = array('html' => "<b>Alt</b>", 'sort' => 1);
$header1[] = array('html' => "<b>Res</b>", 'sort' => 1);
$header1[] = array('html' => "<b>High B</b>", 'sort' => -1);
if (is_array($clash)) {
$header1[] = array('html' => "<b>Clash > 0.4Å</b>", 'sort' => -1);
}
if (is_array($rama)) {
$header1[] = array('html' => "<b>Ramachandran</b>", 'sort' => 1);
}
if (is_array($rota)) {
$header1[] = array('html' => "<b>Rotamer</b>", 'sort' => 1);
}
if (is_array($cbdev)) {
$header1[] = array('html' => "<b>Cβ deviation</b>", 'sort' => -1);
}
if (is_array($cablam)) {
$header1[] = array('html' => "<b>CaBLAM</b>", 'sort' => 1);
}
if (is_array($pperp)) {
$header1[] = array('html' => "<b>Base-P perp. dist.</b>", 'sort' => -1);
}
if (is_array($suites)) {
$header1[] = array('html' => "<b>RNA suite conf.</b>", 'sort' => 1);
}
if (is_array($bbonds)) {
$header1[] = array('html' => "<b>Bond lengths</b>", 'sort' => -1);
}
if (is_array($bangles)) {
$header1[] = array('html' => "<b>Bond angles</b>", 'sort' => -1);
}
if (is_array($omega)) {
$header1[] = array('html' => "<b>Cis Peptides</b>", 'sort' => 1);
}
$header2 = array();
$header2[] = array('html' => "");
$header2[] = array('html' => "");
$header2[] = array('html' => "");
$header2[] = array('html' => sprintf("Avg: %.2f", array_sum($Bfact) / count($Bfact)));
if (is_array($clash)) {
$header2[] = array('html' => "Clashscore: {$clash['scoreAll']}");
}
if (is_array($rama)) {
$header2[] = array('html' => "Outliers: " . count(findRamaOutliers($rama)) . " of " . findAltTotal($rama));
}
if (is_array($rota)) {
$header2[] = array('html' => "Poor rotamers: " . count(findRotaOutliers($rota)) . " of " . findAltTotal($rota));
}
if (is_array($cbdev)) {
$header2[] = array('html' => "Outliers: " . count(findCbetaOutliers($cbdev)) . " of " . findAltTotal($cbdev));
}
if (is_array($cablam)) {
$header2[] = array('html' => "Outliers: " . count(findCablamOutliers($cablam)) . " of " . findAltTotal($cablam));
}
if (is_array($pperp)) {
$header2[] = array('html' => "Outliers: " . count(findBasePhosPerpOutliers($pperp)) . " of " . findAltTotal($pperp));
}
if (is_array($suites)) {
$header2[] = array('html' => "Outliers: " . count(findSuitenameOutliers($suites)) . " of " . findAltTotal($suites));
}
if (is_array($bbonds)) {
$header2[] = array('html' => "Outliers: " . count(findGeomOutliers($bbonds)) . " of " . findAltTotal($bbonds));
}
if (is_array($bangles)) {
$header2[] = array('html' => "Outliers: " . count(findGeomOutliers($bangles)) . " of " . findAltTotal($bangles));
}
if (is_array($omega)) {
$header2[] = array('html' => "Non-Trans: " . count(findOmegaOutliers($omega)) . " of " . findAltTotal($omega));
}
$table['headers'] = array($header1, $header2);
}
//}}} Table prequel and headers
//echo "Table prequel and headers took ".(time() - $startTime)." seconds\n";
$startTime = time();
//{{{ Table body
if ($doHtmlTable) {
$rows = array();
foreach ($res as $cnit => $eval) {
if ($outliersOnly && !$eval['any_isbad']) {
continue;
}
if (!$_SESSION['useSEGID']) {
$cni = substr($cnit, 0, 7);
$alt = substr($cnit, 7, 1);
$type = substr($cnit, 8, 3);
} else {
$cni = substr($cnit, 0, 9);
$alt = substr($cnit, 9, 1);
$type = substr($cnit, 10, 3);
}
//$cni = "'".$cni."'";
$row = array();
//$row[] = array('html' => $cnit, 'sort_val' => $eval['order']+0);
$row[] = array('html' => $cni, 'sort_val' => $eval['order'] + 0);
$row[] = array('html' => $alt, 'sort_val' => $alt);
$row[] = array('html' => $type, 'sort_val' => $type);
$row[] = array('html' => $eval['resHiB'], 'sort_val' => $eval['resHiB'] + 0);
foreach (array('clash', 'rama', 'rota', 'cbdev', 'cablam', 'pperp', 'suites', 'bbonds', 'bangles', 'omega') as $type) {
if (is_array(${$type})) {
$cell = array();
if (isset($eval[$type])) {
$cell['html'] = $eval[$type];
} else {
$cell['html'] = "-";
}
if (isset($eval[$type . '_color'])) {
$cell['color'] = $eval[$type . '_color'];
} elseif (isset($eval[$type . '_isbad'])) {
$cell['color'] = $cell_color_bad;
}
if (isset($eval[$type . '_val'])) {
$cell['sort_val'] = $eval[$type . '_val'] + 0;
}
$row[] = $cell;
}
}
/*
if(is_array($clash))
$row[] = array('html' => (isset($eval['clash']) ? $eval['clash'] : "-"), 'sort_val' => $eval['clash_val']+0);
if(is_array($rama))
$row[] = array('html' => (isset($eval['rama']) ? $eval['rama'] : "-"), 'sort_val' => $eval['rama_val']+0);
if(is_array($rota))
$row[] = array('html' => (isset($eval['rota']) ? $eval['rota'] : "-"), 'sort_val' => $eval['rota_val']+0);
if(is_array($cbdev))
$row[] = array('html' => (isset($eval['cbdev']) ? $eval['cbdev'] : "-"), 'sort_val' => $eval['cbdev_val']+0);
if(is_array($pperp))
$row[] = array('html' => (isset($eval['pperp']) ? $eval['pperp'] : "-"), 'sort_val' => $eval['pperp_val']+0);
*/
$rows[] = $row;
}
$table['rows'] = $rows;
}
//}}} Table body
//echo "Table body took ".(time() - $startTime)." seconds\n";
$startTime = time();
$out = fopen($outfile, 'wb');
fwrite($out, mpSerialize($table));
fclose($out);
//echo "Serializing table took ".(time() - $startTime)." seconds\n";
// serialize() and unserialize() screw up floating point numbers sometimes.
// Not only is there a change in precision, but sometimes numbers become INF
// in some versions of PHP 4, like those shipped with Mac OS X.
//
#$tmpfile = $_SESSION['dataDir'].'/'.MP_DIR_RAWDATA.'/table_dump';
#$out = fopen($tmpfile.'1', 'wb');
#fwrite($out, var_export($table, true));
#fclose($out);
#$time = time();
# $out = fopen($tmpfile.'2', 'wb');
# fwrite($out, var_export(unserialize(serialize($table)), true));
# fclose($out);
#echo "Dump+load time for serialize: ".(time() - $time)." seconds\n";
#$time = time();
# $out = fopen($tmpfile.'3', 'wb');
# fwrite($out, var_export(eval("return ".var_export($table, true).";"), true));
# fclose($out);
#echo "Dump+load time for var_export: ".(time() - $time)." seconds\n";
# WAY TOO SLOW (all in PHP, no C code):
#$time = time();
# $json = new Services_JSON();
# $out = fopen($tmpfile.'4', 'wb');
# fwrite($out, var_export($json->decode($json->encode($table)), true));
# fclose($out);
#echo "Dump+load time for JSON: ".(time() - $time)." seconds\n";
if ($snapfile) {
$startTime = time();
$out = fopen($snapfile, 'wb');
//fwrite($out, formatSortableTable($table, 'DUMMY_URL'));
fwrite($out, formatSortableTableJS($table));
fclose($out);
//echo "Formatting sortable table took ".(time() - $startTime)." seconds\n";
}
}
/**
* Composites the results of the find___Outliers() functions into a simple,
* non-redundant list of 9-char residues names (keys)
* and counts of outliers (values).
*/
function findAllOutliers($clash, $rama, $rota, $cbdev, $pperp)
{
$worst = array();
#$worst = array_merge($worst, findClashOutliers($clash));
#$worst = array_merge($worst, findRamaOutliers($rama));
#$worst = array_merge($worst, findRotaOutliers($rota));
#$worst = array_merge($worst, findCbetaOutliers($cbdev));
#$worst = array_merge($worst, findBasePhosPerpOutliers($pperp));
foreach (array(findClashOutliers($clash), findRamaOutliers($rama), findRotaOutliers($rota), findCbetaOutliers($cbdev), findBasePhosPerpOutliers($pperp)) as $criterion) {
if (is_array($criterion)) {
foreach ($criterion as $cnit => $dummy) {
$worst[$cnit] += 1;
}
}
}
ksort($worst);
// Put the residues into a sensible order
#return array_keys($worst);
return $worst;
}