lovd_isAuthorized('transcript', $nID);
// This call will make database queries if necessary.
require ROOT_PATH . 'class/object_transcripts.php';
$_DATA = new LOVD_Transcript();
$zData = $_DATA->viewEntry($nID);
$aNavigation = array();
if ($_AUTH && $_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit transcript information', 1);
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete transcript entry', 1);
}
lovd_showJGNavigation($aNavigation, 'Transcripts');
$_GET['search_transcriptid'] = $nID;
print '<BR><BR>' . "\n\n";
$_T->printTitle('Variants', 'H4');
require ROOT_PATH . 'class/object_transcript_variants.php';
$_DATA = new LOVD_TranscriptVariant($zData['geneid']);
$_DATA->sSortDefault = 'VariantOnTranscript/DNA';
$_DATA->setRowLink('VOT_for_T_VE', 'javascript:window.location.href=\'' . lovd_getInstallURL() . 'variants/{{ID}}#{{transcriptid}}\'; return false');
$_DATA->viewList('VOT_for_T_VE', array('geneid', 'transcriptid', 'id_ncbi', 'id_'));
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && !ctype_digit($_PE[1]) && !ACTION) {
// URL: /transcripts/NM_004006.2
// Try to find a transcripts by its NCBI ID and forward.
// When we have multiple hits, refer to listView.
$sID = rawurldecode($_PE[1]);
if ($nID = $_DB->query('SELECT id FROM ' . TABLE_TRANSCRIPTS . ' WHERE id_ncbi = ?', array($sID))->fetchColumn()) {
header('Location: ' . lovd_getInstallURL() . $_PE[0] . '/' . $nID);
} else {
define('PAGE_TITLE', 'View transcript');
// $sURLEnsembl = 'http://may2009.archive.ensembl.org/Homo_sapiens/Location/View?r=' . $zData['chromosome'] . ':' . ($zData['position_g_mrna_start'] - 50) . '-' . ($zData['position_g_mrna_end'] + 50) . ';data_URL=' . $sURLBedFile . rawurlencode('&name=/' . $zData['id'] . ' variants');
// //} elseif ($_CONF['refseq_build'] == 'hg19') {
// } else {
// $sURLEnsembl = 'http://www.ensembl.org/Homo_sapiens/Location/View?r=' . $zData['chromosome'] . ':' . ($zData['position_g_mrna_start'] - 50) . '-' . ($zData['position_g_mrna_end'] + 50) . ';contigviewbottom=url:' . $sURLBedFile . rawurlencode('&name=/' . $zData['id'] . ' variants');
// }
// $zData['ensembl'] = 'Show variants in the Ensembl Genome Browser (<A href="' . $sURLEnsembl . '=labels" target="_blank">full view</A>, <A href="' . $sURLEnsembl . '=normal" target="_blank">compact view</A>)';
// $zData['ncbi'] = 'Show distribution histogram of variants in the <A href="http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=' . $_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_sequences'][$zData['chromosome']] . '&v=' . ($zData['position_g_mrna_start'] - 100) . ':' . ($zData['position_g_mrna_end'] + 100) . '&content=7&url=' . $sURLBedFile . '" target="_blank">NCBI Sequence Viewer</A>';
}
}
lovd_showJGNavigation($aNavigation, 'Variants');
print ' <BR><BR>' . "\n\n" . ' <DIV id="viewentryDiv">' . "\n" . ' </DIV>' . "\n\n";
$_GET['search_id_'] = $nID;
print ' <BR><BR>' . "\n\n";
$_T->printTitle('Variant on transcripts', 'H4');
require ROOT_PATH . 'class/object_transcript_variants.php';
$_DATA = new LOVD_TranscriptVariant('', $nID);
$_DATA->setRowID('VOT_for_VOG_VE', 'VOT_{{transcriptid}}');
$_DATA->setRowLink('VOT_for_VOG_VE', 'javascript:window.location.hash = \'{{transcriptid}}\'; return false');
$_DATA->viewList('VOT_for_VOG_VE', array('id_', 'transcriptid', 'status'), true, true);
unset($_GET['search_id_']);
?>
<SCRIPT type="text/javascript">
var prevHash = '';
$( function () {
lovd_AJAX_viewEntryLoad();
setInterval(lovd_AJAX_viewEntryLoad, 250);
});
