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<?php
//
// Copyright 2015-2016, 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");
$database = isset($_GET['db']) ? $_GET['db'] : "";
$tag_id = isset($_GET['tag_id']) ? $_GET['tag_id'] : 0;
$batch_id = isset($_GET['batch_id']) ? $_GET['batch_id'] : 0;
$batch_type = isset($_GET['type']) ? $_GET['type'] : "map";
// 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 some SQL queries
//
$query =
"SELECT pop_id, pop_name FROM populations " .
"WHERE batch_id=?";
if (!($db['pop_sth'] = $db['dbh']->prepare($query)))
write_db_error($db['dbh'], __FILE__, __LINE__);
$query =
"SELECT pop_id, bp, n, hapcnt, gene_div, hap_div FROM hapstats " .
"WHERE batch_id=? AND tag_id=?";
if (!($db['stats_sth'] = $db['dbh']->prepare($query)))
write_db_error($db['dbh'], __FILE__, __LINE__);
//
// Fetch population names if available.
//
$pop_names = array();
if ($batch_type == "population") {
if (!$db['pop_sth']->bind_param("i", $batch_id))
write_db_error($db['pop_sth'], __FILE__, __LINE__);
if (!$db['pop_sth']->execute())
write_db_error($db['pop_sth'], __FILE__, __LINE__);
$res = $db['pop_sth']->get_result();
while ($row = $res->fetch_assoc())
$pop_names[$row['pop_id']] = $row['pop_name'];
}
if (!$db['stats_sth']->bind_param("ii", $batch_id, $tag_id))
write_db_error($db['stats_sth'], __FILE__, __LINE__);
if (!$db['stats_sth']->execute())
write_db_error($db['stats_sth'], __FILE__, __LINE__);
$res = $db['stats_sth']->get_result();
$stats = array();
while ($row = $res->fetch_assoc()) {
$a = array('bp' => $row['bp'],
'n' => $row['n'],
'hapcnt' => $row['hapcnt'],
'gene_div' => $row['gene_div'],
'hap_div' => $row['hap_div'],
'pop_id' => $row['pop_id']);
$stats[$row['pop_id']] = $a;
}
ksort($stats);
$json_str =
"{" .
"\"path\": \"$root_path\"," .
"\"batch_id\": \"$batch_id\"," .
"\"db\": \"$database\"," .
"\"id\": \"$tag_id\"," .
"\"type\": \"$batch_type\",";
$json_str .= "\"hapstats\": [";
foreach ($stats as $pop_id => $stat)
if (!isset($pop_names[$pop_id]))
$pop_names[$pop_id] = $pop_id;
$rows = 0;
foreach ($stats as $pop_id => $s) {
$gdiv = $s['gene_div'] > 0 ? sprintf("%.3f", $s['gene_div']) : $s['gene_div'];
$hdiv = $s['hap_div'] > 0 ? sprintf("%.3f", $s['hap_div']) : $s['hap_div'];
$json_str .=
"{" .
"\"pop_id\": \"" . $pop_names[$pop_id] . "\"," .
"\"bp\": \"$s[bp]\"," .
"\"n\": \"$s[n]\"," .
"\"hapcnt\": \"$s[hapcnt]\"," .
"\"genediv\": \"$gdiv\"," .
"\"hapdiv\": \"$hdiv\"" .
"},";
$rows++;
}
if ($rows > 0)
$json_str = substr($json_str, 0, -1);
$json_str .=
"]}";
echo $json_str;
?>
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