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<?php
//
// Copyright 2010-2016, Julian Catchen <jcatchen@illinois.edu>
//
// This file is part of Stacks.
//
// Stacks is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// Stacks is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Stacks. If not, see <http://www.gnu.org/licenses/>.
//
require_once("header.php");
if (isset($_GET['db']))
$database = $_GET['db'];
else if (isset($_POST['db']))
$database = $_POST['db'];
if (isset($_GET['tag_id']))
$tag_id = $_GET['tag_id'];
else if (isset($_POST['tag_id']))
$tag_id = $_POST['tag_id'];
else
$tag_id = 0;
if (isset($_GET['batch_id']))
$batch_id = $_GET['batch_id'];
else if (isset($_POST['batch_id']))
$batch_id = $_POST['batch_id'];
else
$batch_id = 0;
// Connect to the database
$db = db_connect($database);
// Save these variables for automatic URL formation later on.
$display = array();
$display['db'] = $database;
$display['tag_id'] = $tag_id;
$display['batch_id'] = $batch_id;
//
// Prepare the possible select lists we will want to construct
//
$marker_types = array('ab/--' => array('aa', 'bb', '-'),
'--/ab' => array('aa', 'bb', '-'),
'ab/aa' => array('aa', 'ab', '-'),
'aa/ab' => array('aa', 'ab', '-'),
'ab/ab' => array('aa', 'ab', 'bb', '-'),
'ab/ac' => array('aa', 'ab', 'ac', 'bc', '-'),
'ab/cd' => array('aa', 'bb', 'cc', 'dd', 'ac', 'ad', 'bc', 'bd', '-'),
'aa/bb' => array('aa', 'bb', 'ab', '-'),
'ab/cc' => array('aa', 'bb', 'ab', 'ac', 'bc', 'cc', '-'),
'cc/ab' => array('aa', 'bb', 'ab', 'ac', 'bc', 'cc', '-'));
//
// Prepare some SQL queries
//
$query =
"SELECT count(samples.id) as count FROM samples WHERE batch_id=?";
if (!($db['samp_sth'] = $db['dbh']->prepare($query)))
write_db_error($db['dbh'], __FILE__, __LINE__);
$query =
"SELECT marker, catalog_genotypes.sample_id, file, " .
"catalog_genotypes.genotype, genotype_corrections.genotype as corrected " .
"FROM catalog_genotypes " .
"LEFT JOIN genotype_corrections ON " .
"(genotype_corrections.catalog_id=catalog_genotypes.catalog_id AND " .
"genotype_corrections.sample_id=catalog_genotypes.sample_id AND " .
"genotype_corrections.batch_id=catalog_genotypes.batch_id) " .
"JOIN samples ON (catalog_genotypes.sample_id=samples.id) " .
"JOIN catalog_index ON (catalog_genotypes.catalog_id=catalog_index.tag_id AND " .
"catalog_genotypes.batch_id=catalog_index.batch_id) " .
"WHERE catalog_genotypes.batch_id=? and catalog_genotypes.catalog_id=? " .
"ORDER BY catalog_genotypes.sample_id";
if (!($db['geno_sth'] = $db['dbh']->prepare($query)))
write_db_error($db['dbh'], __FILE__, __LINE__);
$page_title = "Catalog Genotype Viewer";
write_compact_header($page_title);
//
// Get number of samples so we can determine how many rows to display
// in the genotype table.
//
if (!$db['samp_sth']->bind_param("i", $batch_id))
write_db_error($db['samp_sth'], __FILE__, __LINE__);
if (!$db['samp_sth']->execute())
write_db_error($db['samp_sth'], __FILE__, __LINE__);
$res = $db['samp_sth']->get_result();
$row = $res->fetch_assoc();
$num_samples = $row['count'];
$num_cols = 10;
$num_rows = ceil($num_samples / $num_cols);
$gtypes = array();
if (!$db['geno_sth']->bind_param("ii", $batch_id, $tag_id))
write_db_error($db['geno_sth'], __FILE__, __LINE__);
if (!$db['geno_sth']->execute())
write_db_error($db['geno_sth'], __FILE__, __LINE__);
$res = $db['geno_sth']->get_result();
if ($res->num_rows == 0) {
print
"<h4 style=\"margin-left: auto; margin-right: auto; text-align: center;\">" .
"This marker has no genotypes, probably because this tag does not have enough mappable progeny.</h4>\n";
write_compact_footer();
return;
}
while ($row = $res->fetch_assoc()) {
$gtypes[$row['sample_id']] = array('file' => $row['file'],
'genotype' => $row['genotype'],
'corrected' => $row['corrected'],
'marker' => $row['marker']);
}
print
"<form id=\"genotypes\" name=\"genotypes\" method=\"post\" action=\"$root_path/correct_genotypes.php\">\n" .
"<input type=\"hidden\" name=\"op\" id=\"op\" value=\"\" />\n" .
"<input type=\"hidden\" name=\"batch_id\" value=\"$batch_id\" />\n" .
"<input type=\"hidden\" name=\"tag_id\" value=\"$tag_id\" />\n" .
"<input type=\"hidden\" name=\"db\" value=\"$database\" />\n" .
"<table class=\"genotypes\">\n" .
"<tr>\n";
$i = 0;
foreach ($gtypes as $sample_id => $sample) {
$i++;
$id = "gtype_" . $batch_id . "_" . $tag_id . "_" . $sample_id;
if (strlen($sample['corrected']) > 0) {
$sel = generate_element_select($id, $marker_types[$sample['marker']], strtolower($sample['corrected']), "");
$genotype = "<span class=\"corrected\">$sample[corrected]</span>";
} else {
$sel = generate_element_select($id, $marker_types[$sample['marker']], strtolower($sample['genotype']), "");
$genotype = $sample['genotype'];
}
print
" <td>" .
"<span class=\"title\">" . ucfirst(str_replace("_", " ", $sample['file'])) . "</span><br />" .
"<a onclick=\"toggle_sel('{$id}_div')\">" . $genotype . "</a>\n" .
" <div id=\"{$id}_div\" style=\"display: none;\">\n" .
$sel .
" </div>" .
"</td>\n";
if ($i % $num_cols == 0)
print
"</tr>\n" .
"<tr>\n";
}
while ($i % $num_cols != 0) {
print " <td></td>\n";
$i++;
}
echo <<< EOQ
</tr>
<tr>
<td colspan="$num_cols" style="text-align: right;">
<input type="button" value="Reset" onclick="set_operation('genotypes', 'reset')" />
<input type="button" value="Submit" onclick="set_operation('genotypes', 'correct')" />
</td>
</tr>
</table>
</form>
EOQ;
write_compact_footer();
?>
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