$sGene = '';
} else {
$sGene = $_DB->query('SELECT id FROM ' . TABLE_GENES . ' WHERE id = ?', array(rawurldecode($_PE[1])))->fetchColumn();
$_GET['search_geneid'] = '="' . $sGene . '"';
lovd_isAuthorized('gene', $sGene);
}
define('PAGE_TITLE', 'View all transcripts' . ($sGene ? ' of gene ' . $sGene : ''));
$_T->printHeader();
$_T->printTitle();
if ($sGene) {
lovd_printGeneHeader();
}
require ROOT_PATH . 'class/object_transcripts.php';
$_DATA = new LOVD_Transcript();
$_DATA->sSortDefault = $sGene ? 'variants' : 'geneid';
$_DATA->viewList('Transcripts', $sGene ? 'geneid' : '', false, false, (bool) ($_AUTH['level'] >= LEVEL_CURATOR));
if ($sGene) {
lovd_printGeneFooter();
}
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && !ACTION) {
// URL: /transcripts/00001
// View specific entry.
$nID = sprintf('%08d', $_PE[1]);
define('PAGE_TITLE', 'View transcript #' . $nID);
$_T->printHeader();
$_T->printTitle();
// Load appropriate user level for this transcript.
lovd_isAuthorized('transcript', $nID);
$aNavigation[$_PE[0] . '/' . $sID . '?empty'] = array('menu_empty.png', 'Empty this gene database', (bool) $zData['variants']);
$aNavigation[$_PE[0] . '/' . $sID . '/graphs'] = array('menu_graphs.png', 'View graphs about this gene database', 1);
$aNavigation[$_PE[0] . '/' . $sID . '/columns'] = array('menu_columns.png', 'View enabled variant columns', 1);
$aNavigation[$_PE[0] . '/' . $sID . '/columns?order'] = array('menu_columns.png', 'Re-order enabled variant columns', 1);
$aNavigation['columns/VariantOnTranscript'] = array('menu_columns.png', 'View all available variant columns', 1);
$aNavigation['download/all/gene/' . $sID] = array('menu_save.png', 'Download all this gene\'s data', 1);
$aNavigation['javascript:lovd_openWindow(\'' . lovd_getInstallURL() . 'scripts/refseq_parser.php?step=1&symbol=' . $sID . '\', \'refseq_parser\', 900, 500);'] = array('menu_scripts.png', 'Create human-readable refseq file', $zData['refseq_UD'] && count($zData['transcripts']));
}
lovd_showJGNavigation($aNavigation, 'Genes');
$_GET['search_geneid'] = '="' . $sID . '"';
print '<BR><BR>' . "\n\n";
$_T->printTitle('Active transcripts', 'H4');
require ROOT_PATH . 'class/object_transcripts.php';
$_DATA = new LOVD_Transcript();
$_DATA->setSortDefault('variants');
$_DATA->viewList('Transcripts_for_G_VE', 'geneid', true, true);
// Disclaimer.
if ($zData['disclaimer']) {
print '<BR>' . "\n\n" . ' <TABLE border="0" cellpadding="0" cellspacing="1" width="950" class="data">' . "\n" . ' <TR>' . "\n" . ' <TH class="S15">Copyright & disclaimer</TH></TR>' . "\n" . ' <TR class="S11">' . "\n" . ' <TD>' . $zData['disclaimer_text_'] . '</TD></TR></TABLE><BR>' . "\n\n";
}
lovd_printGeneFooter();
$_T->printFooter();
exit;
}
if (PATH_COUNT == 1 && ACTION == 'create') {
// URL: /genes?create
// Create a new entry.
define('PAGE_TITLE', 'Create a new gene information entry');
define('LOG_EVENT', 'GeneCreate');
// Require manager clearance.
lovd_requireAUTH(LEVEL_MANAGER);
