$_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'); $_T->printHeader(); $_T->printTitle(); lovd_showInfoTable('No such ID!', 'stop');
// $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); }); function lovd_AJAX_viewEntryLoad () {