function evidence_qualify_impact($scores, $impact)
{
$c = str_split(evidence_compute_certainty($scores, $impact));
if ($c[0] === "-") {
return ucfirst($impact);
}
if ($c[0] === '0') {
$impact = "uncertain {$impact}";
} else {
if ($c[0] === '1') {
$impact = "likely {$impact}";
}
}
if ($c[1] === '0') {
$impact = "low clinical importance, {$impact}";
} else {
if ($c[1] === '1') {
$impact = "moderate clinical importance, {$impact}";
} else {
if ($c[1] === '2') {
$impact = "high clinical importance, {$impact}";
}
}
}
return ucfirst($impact);
}
function print_content()
{
global $config;
global $sql_where;
global $sql_having;
global $sql_occur_filter;
global $sql_orderby;
global $sql_right_join;
global $sql_params;
global $min_certainty;
global $max_certainty;
global $snap;
global $gTheTextile;
global $want_column;
$q = theDb()->query($sql = "\nSELECT s.*, v.*, g.*, fs.*,\n-- gs.summary_short AS g_summary_short,\n MAX(o.zygosity) AS max_zygosity,\n d.dataset_id AS d_dataset_id,\n g.genome_id AS g_genome_id,\n y.hitcount AS hitcount,\n vf.f AS variant_frequency\nFROM snap_{$snap} s\n{$sql_right_join}\nLEFT JOIN flat_summary fs ON s.variant_id=fs.variant_id\nLEFT JOIN variants v ON s.variant_id=v.variant_id\nLEFT JOIN variant_frequency vf ON vf.variant_id=v.variant_id\nLEFT JOIN variant_occurs o ON v.variant_id=o.variant_id AND {$sql_occur_filter}\nLEFT JOIN datasets d ON o.dataset_id=d.dataset_id\nLEFT JOIN genomes g ON d.genome_id=g.genome_id\nLEFT JOIN yahoo_boss_cache y ON s.variant_id=y.variant_id\nLEFT JOIN variant_external omim ON omim.variant_id=s.variant_id AND omim.tag='OMIM'\n-- LEFT JOIN snap_{$snap} gs ON gs.variant_id=s.variant_id AND gs.article_pmid=0 AND gs.genome_id=g.genome_id\nWHERE s.article_pmid=0 AND s.genome_id=0 AND s.disease_id=0 AND {$sql_where}\nGROUP BY v.variant_id,g.genome_id\nHAVING {$sql_having}\n{$sql_orderby}\n", $sql_params);
$colcount = 5 + count($want_column);
if (theDb()->isError($q)) {
die("DB Error: " . $q->getMessage() . "<br>" . $sql);
}
print "<TABLE class=\"report_table\" style=\"width: 100%\">\n";
print "<TR><TD colspan=\"{$colcount}\" id=\"reportpage_turner_copy\" style=\"text-align: right;\"> </TD></TR>\n";
print "<TR><TH>" . join("</TH><TH>", array("Variant", "Impact", "Inheritance pattern", "Summary", "Genomes"));
foreach ($want_column as $k => $v) {
print "</TH><TH>{$v}";
}
print "</TH></TR>\n";
$output_row = 0;
$output_page = 0;
$output_cut_off_after = 0;
$tr_attrs = "";
$genome_rows = array();
for ($row =& $q->fetchRow(); $row; $row =& $nextrow) {
$row["name"] = $row["name"] ? $row["name"] : "[" . $row["global_human_id"] . "]";
$genome_rows[$row["genome_id"]] = $row;
$nextrow =& $q->fetchRow();
if ($nextrow && $row["variant_id"] == $nextrow["variant_id"]) {
continue;
}
$certainty = evidence_compute_certainty($row["variant_quality"], $row["variant_impact"]);
$certainty = substr($certainty, 0, 1);
if ($certainty == 0 && ($min_certainty == 0 || $max_certainty == -1)) {
// need to distinguish between "insufficiently evaluated" and "uncertain"
$have_2or3 = 0;
$have_4or5 = 0;
$nonempty_scores = 0;
$category_index = -1;
$scores = str_split(str_pad($row["variant_quality"], 6, "-"));
foreach ($scores as $score) {
if ($score != "-") {
++$nonempty_scores;
}
}
if ($nonempty_scores < 4 || $scores[2] == "-" && $scores[3] == "-" || $scores[4] == "-" && $scores[5] == "-") {
$certainty = -1;
}
}
if ($min_certainty > $certainty || $max_certainty < $certainty) {
$genome_rows = array();
continue;
}
++$output_row;
if ($output_row % $config["ROWSPERPAGE"] == 1) {
++$output_page;
$tr_attrs = " class=\"reportpage reportpage_{$output_page}\"";
if ($output_page > 1) {
$tr_attrs = " class=\"reportpage reportpage_{$output_page} csshide\"";
}
}
if ($output_page > $config["MAXPAGES"]) {
if (!$output_cut_off_after) {
$output_cut_off_after = $output_row - 1;
}
$genome_rows = array();
continue;
}
$variant_name_display = evidence_get_variant_name($row, " ", true);
$variant_name_link = evidence_get_variant_name($row, "-", true);
$rowspan = count($genome_rows);
if ($rowspan < 1) {
$rowspan = 1;
}
$rowspan = "rowspan=\"{$rowspan}\"";
$impact = ereg_replace("^likely ", "l.", $row["variant_impact"]);
if ($certainty == -1) {
$impact = "insufficiently evaluated / uncertain {$impact}";
} else {
if ($certainty == 1) {
$impact = "likely {$impact}";
} else {
if ($certainty <= 0) {
$impact = "uncertain {$impact}";
}
}
}
if (strlen($row["variant_frequency"])) {
$impact .= sprintf(", f=%.3f", $row["variant_frequency"]);
}
$summary_short = $gTheTextile->textileRestricted($row["summary_short"]);
if ($row["hitcount"] > 0) {
$s = $row["hitcount"] == 1 ? "" : "s";
$summary_short .= "<P>({$row['hitcount']} web hit{$s})</P>";
}
printf("<TR{$tr_attrs}><TD {$rowspan}>%s</TD><TD {$rowspan}>%s</TD><TD {$rowspan}>%s</TD><TD {$rowspan}>%s</TD>", "<A href=\"{$variant_name_link}\">{$variant_name_display}</A>", $impact, $row["variant_dominance"], $summary_short);
$rownum = 0;
foreach ($genome_rows as $id => $row) {
if (++$rownum > 1) {
print "</TR>\n<TR{$tr_attrs}>";
}
if (!$row["g_genome_id"]) {
print "<TD></TD>";
} else {
print "<TD width=\"15%\"><A href=\"{$variant_name_link}#g{$id}\">" . htmlspecialchars($row["name"]) . "</A>";
if ($row["max_zygosity"] == 'homozygous') {
print " (hom)";
}
print "</TD>";
}
if ($rownum == 1) {
foreach ($want_column as $k => $v) {
printf("<TD {$rowspan}>%s</TD>", $row[$k]);
}
}
}
print "</TR>\n";
$genome_rows = array();
}
if ($output_page > 1) {
print "<TR><TD colspan=\"{$colcount}\" id=\"reportpage_turner\" style=\"text-align: right;\">Page: ";
for ($p = 1; $p <= $output_page && $p <= $config["MAXPAGES"]; $p++) {
print "<A class=\"reportpage_turnbutton\" href=\"#\" onclick=\"reportpage_goto({$p});\">{$p}</A> ";
}
print "<BR /><STRONG>Total results: {$output_row}</STRONG>";
if ($output_cut_off_after) {
print "<BR />(Only displaying first {$output_cut_off_after} results)";
}
print "</TD></TR>\n";
print "<SCRIPT type=\"text/javascript\"><!--\n";
print "reportpage_init();\n";
print "\n// -->\n</SCRIPT>";
} else {
print "<TR><TD colspan=\"{$colcount}\" style=\"text-align: right;\"><STRONG>Total results: {$output_row}</STRONG></TD></TR>";
}
print "</TABLE>\n";
}