コード例 #1
0
ファイル: visualize.php プロジェクト: smlewis/MolProbity
/**
* $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) . "&Aring;<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']) . "&Aring;";
                $res[$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", $item['dev']) . "&Aring;";
                }
            }
        }
    }
    //}}}
    if (is_array($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']) {
                    $reasons[] = "&delta; & &epsilon; outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
                } elseif ($item['deltaOut']) {
                    $reasons[] = "&delta; outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
                } elseif ($item['epsilonOut']) {
                    $reasons[] = "&epsilon; outlier <br><small>(P-perp distance implies {$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'];
            $bin = "&delta;-1&delta;&gamma; {$item['bin']}";
            if ($bin == '&delta;-1&delta;&gamma; trig') {
                $bin = "&delta;-1&delta;&gamma; none (triaged  {$item['triage']}  )";
                $res[$cnit]['suites_val'] = -1;
                // sorts to very top
            } elseif ($bin == '&delta;-1&delta;&gamma; inc ') {
                $bin = '&delta;-1&delta;&gamma; 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]) . " &sigma;</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]) . " &sigma;</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)) {
            $header1[] = array('html' => "<b>Clash &gt; 0.4&Aring;</b>", 'sort' => -1);
        }
        if (is_array($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)) {
            $header1[] = array('html' => "<b>C&beta; deviation</b>", 'sort' => -1);
        }
        if (is_array($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() - $startTime)." seconds\n";
    }
}
コード例 #2
0
ファイル: analyze.php プロジェクト: smlewis/MolProbity
/**
* Composites the results of the find___Outliers() functions into a simple,
* non-redundant list of 9-char residues names (keys)
* and counts of outliers (values).
*/
function findAllOutliers($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;
}