$nDisabledTab = 1;
} elseif (empty($aCategories['VariantOnGenome'])) {
$nActiveTab = 1;
$nDisabledTab = 0;
}
if (!empty($aCategories['VariantOnGenome'])) {
require ROOT_PATH . 'class/object_genome_variants.php';
$_DATAvariants = new LOVD_GenomeVariant();
}
if (!empty($aCategories['Individual'])) {
require ROOT_PATH . 'class/object_individuals.php';
$_DATAindividuals = new LOVD_Individual();
}
print ' <SCRIPT type="text/javascript">' . "\n" . ' $(function() {' . "\n" . ' $("#tabs").tabs({active: ' . $nActiveTab . ', disabled: [' . $nDisabledTab . ']});' . "\n" . ' });' . "\n" . ' </SCRIPT>' . "\n" . ' <DIV id="tabs">' . "\n" . ' <UL>' . "\n" . ' <LI><A href="' . lovd_getInstallURL() . implode('/', $_PE) . '#tabs-variants">Variants</A></LI>' . "\n" . ' <LI><A href="' . lovd_getInstallURL() . implode('/', $_PE) . '#tabs-individuals">Individuals</A></LI>' . "\n" . ' </UL>' . "\n" . ' <DIV id="tabs-variants">' . "\n";
if (!empty($_DATAvariants)) {
$_DATAvariants->viewList('Variants_per_reference', $aColsToHide['VariantOnGenome'], true, true);
}
print ' </DIV>' . "\n" . ' <DIV id="tabs-individuals">' . "\n";
if (!empty($_DATAindividuals)) {
$_DATAindividuals->viewList('Individuals_per_reference', $aColsToHide['Individual'], true, true);
}
print ' </DIV>' . "\n" . ' </DIV>';
$_T->printFooter();
exit;
}
if ($bImage) {
header('Content-type: image/png');
readfile(ROOT_PATH . 'gfx/trans.png');
exit;
}
define('PAGE_TITLE', 'View data for reference: ' . $aPathElements[1]);
unset($_POST['password']);
}
} else {
// Default session values.
$_SESSION['viewlists']['Screenings_' . $nID . '_removeVariants']['checked'] = array();
}
$_T->printHeader();
$_T->printTitle();
lovd_errorPrint();
lovd_showInfoTable('The variant entries below are all variants that can be removed from this screening. Variants that are not also added to another screening can not be removed.', 'information');
$_GET['page_size'] = 10;
$_GET['search_screeningids'] = $nID;
$_GET['search_id_'] = count($aInvalidVariants) ? '!' . implode(' !', $aInvalidVariants) : '';
require ROOT_PATH . 'class/object_genome_variants.php';
$_DATA = new LOVD_GenomeVariant();
$_DATA->viewList('Screenings_' . $nID . '_removeVariants', array('id_', 'screeningids', 'chromosome'), true, false, true, false, true);
print ' <BR><BR>' . "\n\n";
// Table.
print ' <FORM id="removeVariants" action="' . CURRENT_PATH . '?' . ACTION . '" method="post">' . "\n";
// Array which will make up the form table.
$aForm = array(array('POST', '', '', '', '0%', '0', '100%'), array('', '', 'print', 'Enter your password for authorization'), array('', '', 'password', 'password', 20), array('', '', 'print', '<INPUT type="submit" value="Save variant list" onclick="lovd_AJAX_viewListSubmit(\'Screenings_' . $nID . '_removeVariants\', function () { $(\'#removeVariants\').submit(); }); return false;"> <INPUT type="submit" value="Cancel" onclick="window.location.href=\'' . lovd_getInstallURL() . ($bSubmit ? 'submit/screening/' : 'screenings/') . $nID . '\'; return false;" style="border : 1px solid #FF4422;">'));
lovd_viewForm($aForm);
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && ACTION == 'delete') {
// URL: /screenings/0000000001?delete
// Drop specific entry.
$nID = sprintf('%010d', $_PE[1]);
define('PAGE_TITLE', 'Delete screening information entry ' . $nID);
define('LOG_EVENT', 'ScreeningDelete');
$_T->printFooter();
exit;
}
if (PATH_COUNT == 3 && $_PE[1] == 'upload' && ctype_digit($_PE[2]) && !ACTION) {
// URL: /variants/upload/123451234567890
// View all genomic variant entries that were submitted in the given upload.
$nID = sprintf('%015d', $_PE[2]);
define('PAGE_TITLE', 'View genomic variants from upload #' . $nID);
$_T->printHeader();
$_T->printTitle();
lovd_requireAUTH(LEVEL_MANAGER);
require ROOT_PATH . 'class/object_genome_variants.php';
$_DATA = new LOVD_GenomeVariant();
$_GET['search_created_by'] = substr($nID, 0, 5);
$_GET['search_created_date'] = date('Y-m-d H:i:s', substr($nID, 5, 10));
$_DATA->viewList('VOG_uploads', array('allele_'), false, false, (bool) ($_AUTH['level'] >= LEVEL_MANAGER), false, true);
$_T->printFooter();
exit;
}
if (!ACTION && !empty($_PE[1]) && !ctype_digit($_PE[1])) {
// URL: /variants/DMD
// URL: /variants/DMD/unique
// URL: /variants/DMD/NM_004006.2
// URL: /variants/DMD/NM_004006.2/unique
// View all entries in a specific gene, affecting a specific transcript.
$bUnique = false;
if (isset($_PE[2]) && $_PE[2] == 'unique' || isset($_PE[3]) && $_PE[3] == 'unique') {
$bUnique = true;
}
$sGene = $_DB->query('SELECT id FROM ' . TABLE_GENES . ' WHERE id = ?', array(rawurldecode($_PE[1])))->fetchColumn();
if ($sGene) {
