<form id="{$row['tag_id']}_frm">
<input type="hidden" name="url" value="{$root_path}/annotate_marker.php?db={$database}&batch_id={$batch_id}&tag_id={$row['tag_id']}" />
<input type="input" size=15 name="ext_id" value="" />
<a onclick="annotate_marker('{$row['tag_id']}')">save</a>|<a onclick="toggle_annotation('{$row['tag_id']}')">cancel</a>
</form>
</div>
</div>
</td>
EOQ;
if (count($snps) == 0) {
print " <td>No</td>\n";
} else {
print " <td>Yes <span class=\"s\">[" . count($snps) . "nuc]</span></td>\n";
}
$s = print_snps($row['tag_id'], $row['seq'], $row['seq'], $snps, true);
$ratio = explode(";", $row['ratio']);
$ratio_parsed = "";
$i = 0;
foreach ($ratio as $r) {
if (strlen($r) == 0) {
continue;
}
preg_match("/([a-z]+):(\\d+)\\((\\d+\\.?\\d*%)\\)/", $r, $matches);
for ($j = 0; $j < strlen($matches[1]); $j++) {
$color = $color_map[$matches[1][$j]];
$ratio_parsed .= "<span style=\"color: {$color}; font-weight: bold\">" . $matches[1][$j] . "</span>";
}
$ratio_parsed .= ": {$matches['2']}";
if ($matches[3] > 0) {
$ratio_parsed .= " ({$matches['3']})";
if ($row['relationship'] == "model") {
$model = $row['seq'];
} else {
if ($row['relationship'] == "secondary") {
array_push($secondary, array('s' => $row['seq'], 'id' => $row['seq_id']));
} else {
if (!isset($stacks[$row['sub_id']])) {
$stacks[$row['sub_id']] = array();
}
array_push($stacks[$row['sub_id']], array('s' => $row['seq'], 'id' => $row['seq_id']));
}
}
}
}
$con_len = strlen($consensus);
$c = print_snps($tags[$i], $consensus, $consensus, $snps, false);
$c = addslashes($c);
$scale = print_scale($con_len);
$scale = addslashes($scale);
$json_str .= "{" . "\"sample_id\": \"{$sample_id}\"," . "\"sample_name\": \"{$file}\"," . "\"tag_id\": \"{$tag_id}\"," . "\"consensus\": \"{$c}\"," . "\"model\": \"{$model}\"," . "\"scale\": \"{$scale}\"," . "\"primary\": [";
foreach ($stacks as $sub_id => $stack) {
$s = print_snps_errs($consensus, $stack[0]['s'], $snps, $cat_snps);
$s = addslashes($s);
$json_str .= "{" . "\"seq\": \"{$s}\"," . "\"ids\": [";
foreach ($stack as $seq) {
$json_str .= "\"{$seq['id']}\",";
}
if (count($stack) > 0) {
$json_str = substr($json_str, 0, -1);
}
$json_str .= "]" . "},";
