<tocpart> HEADER; require_once "XML_PullParser.inc"; $files = array(); $file = "synopsis.xml"; $xml_outfile = "XML_PullParser_contents.xml"; $html_outfile = "html_contents.html"; $handle = openOutputFile($xml_outfile); $html_handle = openOutputFile($html_outfile); writeHeader($handle); writeText($html_handle, $HTML_Header); echo "<A href = \"article2html.php?fn=synopsis.xml\">Synopsis</A><br>\n"; writeEntry($handle, "synopsis.xml", "Synopsis"); writeHTMLEntry($html_handle, "synopsis.xml", "Synopsis"); while ($file = toc($file)) { } writeFooter($handle, $xml_outfile); writeHTMLFooter($html_handle, $html_outfile); function toc($file) { global $handle, $html_handle; global $files; $tags = array("para"); $child_tags = array("ulink"); $parser = new XML_PullParser($file, $tags, $child_tags); $next_url = ""; $prev_url = ""; while ($token = $parser->XML_PullParser_getToken()) { if ($link = $parser->XML_PullParser_getElement('ulink')) { while ($link = $parser->XML_PullParser_nextElement()) {
<?php include 'html/header.html'; require_once 'db_functions.php'; require_once 'qtl_functions.php'; require_once 'utils.php'; require_once 'fill_related_projects.php'; fill_compara_array(); connectToQtlDBs(array('Ratte')); global $compara_array; $db = $compara_array['Ratte']['connection']; useDB('eqtl_stockholm_eae_logplier', $db); //useDB('eqtl_rostock_eae', $db); $loci = array('c1.loc1', 'c1.loc10', 'c1.loc100', 'c1.loc101', 'c1.loc102', 'c1.loc103', 'c1.loc104', 'c1.loc105', 'c1.loc106', 'c1.loc107', 'c1.loc108', 'c1.loc109', 'c1.loc11', 'c1.loc110', 'c1.loc111', 'c1.loc112', 'c1.loc113', 'c1.loc114', 'c1.loc115'); //$loci = array('c9.loc48', 'c9.loc43', 'c9.loc40' , 'c9.loc39'); loci2stable_ids_new($loci, $db); loci2stable_ids_new($loci, $db); $t = tic(); print_r(loci2stable_ids_new($loci, $db)); print "<br>"; print "<br>"; toc($t, 'opt'); print "<br>"; print "<br>"; $t = tic(); print_r(loci2stable_ids($loci, $db)); print "<br>"; print "<br>"; toc($t, 'normal'); include 'html/footer.html';
$intervalEnd[$i] = bp2cM($regionChr[$i], (int) $regionEnd[$i], $experiment1['species']); } $chromosomsEx1 = $regionChr; $ex1 = get_loci_from_sql($database1, $experiment1['connection'], 'userinterval', $chromosomsEx1, $confidence_int, $group2region, $intervalStart, $intervalEnd); if (!empty($ex1)) { // converts $ex1 in 2 arrays: $groups1 = groupnr -> ('loci' -> lociOfGroup, 'start', 'end', 'Chr') $mapEx1 = index -> (locus,groupNr) list($groups1, $mapEx1) = $ex1; } else { echo '<INPUT TYPE=BUTTON VALUE="back" onClick="history.back()">'; echo '<br />'; fatal_error('nothing found for the given region(-s)'); } // generates an arrays with index -> locinames // $loci_ex1 = array_map('current',$mapEx1); $chromosomsEx2 = getChromosomes($compara, $experiment2['ensembl_species']); //filter compara chromosoms for existing chromosoms in QTL-database $chromosomsEx2 = filter_chromos($experiment2['connection'], array_flip($chromosomsEx2)); $chromosomsEx2 = array_flip($chromosomsEx2); $ex2 = get_loci_from_sql($database2, $experiment2['connection'], 'wholeGenome', $chromosomsEx2, $confidence_int, $group2region2); // converts $ex2 in 2 arrays: $groups2 = groupnr -> ('loci' -> lociOfGroup, 'start', 'end') $mapEx2 = index -> (locus,groupNr) list($groups2, $mapEx2) = $ex2; // generates an arrays with index -> locinames // $loci_ex2 = array_map('current',$mapEx2); // SYNTENY $genome_db_ids = getGenomeDBIDs($compara, array($experiment1['ensembl_species'], $experiment2['ensembl_species'])); $dbs = array($database1, $database2); $groupSynteny_ex12ex2 = getSyntenyGroups(array($experiment1['connection'], $experiment2['connection']), $compara, $groups1, $groups2, $species_names, $genome_db_ids, $dbs); // display ----------------------- include 'display_table.php'; toc($start, 'Synteny search'); require_once "../eqtl/footer.php";
function runTest($func, $name, $octave) { $func($octave); echo $name . str_repeat(" ", 10 - strlen($name)) . toc() . "\n"; }