$_T->printFooter();
exit;
}
// Check which tab is active and which must be disabled. Depending on available data
$nActiveTab = 0;
$nDisabledTab = null;
if (empty($aCategories['Individual'])) {
$nActiveTab = 0;
$nDisabledTab = 1;
} elseif (empty($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>';
$_T->printFooter();
// Because we're sending the data back to the form, I need to unset the password fields!
unset($_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);
}
print '</TABLE>';
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && ACTION == 'map') {
// URL: /variants/0000000001?map
// Map a variant to additional transcript.
$nID = sprintf('%010d', $_PE[1]);
define('PAGE_TITLE', 'Map variant entry #' . $nID);
define('LOG_EVENT', 'VariantMap');
// Require manager clearance.
lovd_isAuthorized('variant', $nID);
lovd_requireAUTH(LEVEL_OWNER);
require ROOT_PATH . 'class/object_genome_variants.php';
$_DATA = new LOVD_GenomeVariant();
$zData = $_DATA->loadEntry($nID);
// Load all transcript ID's that are currently present in the database connected to this variant.
$aCurrentTranscripts = $_DB->query('SELECT t.id, t.geneid FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) WHERE vot.id = ? ORDER BY t.geneid', array($nID))->fetchAllCombine();
require ROOT_PATH . 'inc-lib-form.php';
if (POST) {
lovd_errorClean();
// Preventing notices...
// $_POST['transcripts'] stores the IDs of the transcripts that are supposed to go in TABLE_VARIANTS_ON_TRANSCRIPTS.
if (empty($_POST['transcripts']) || !is_array($_POST['transcripts'])) {
$_POST['transcripts'] = array();
} else {
// Verify all given IDs; they need to exist in the database, and they need to be on the same chromosome.
$aTranscripts = $_DB->query('SELECT t.id, t.geneid FROM ' . TABLE_TRANSCRIPTS . ' AS t LEFT OUTER JOIN ' . TABLE_GENES . ' AS g ON (t.geneid = g.id) WHERE g.chromosome = ? AND t.id IN (?' . str_repeat(', ?', count($_POST['transcripts']) - 1) . ')', array_merge(array($zData['chromosome']), $_POST['transcripts']))->fetchAllCombine();
foreach ($_POST['transcripts'] as $nTranscript) {
if (!isset($aTranscripts[$nTranscript])) {