https://github.com/carlosp420/VoSeq
Tip revision: d59e3c160fdf348b7f77698fe01119dc2d9b03cc authored by Carlos Pena on 13 February 2013, 16:39:36 UTC
1.4.2
1.4.2
Tip revision: d59e3c1
sequences.php
<?php
// #################################################################################
// #################################################################################
// Voseq sequences.php
// author(s): Carlos Peńa & Tobias Malm
// license GNU GPL v2
// source code available at https://github.com/carlosp420/VoSeq
//
// Script overview: Displays the single sequence view
// #################################################################################
// #################################################################################
// Section: Startup/includes
// #################################################################################
//check login session
include'login/auth.php';
// includes
include 'markup-functions.php';
ob_start();//Hook output buffer - disallows web printing of file info...
include 'conf.php';
ob_end_clean();//Clear output buffer//includes
include 'functions.php';
$title = "Sequences";
$yahoo_map = false;
$admin = false;
$in_includes = false;
// need dojo?
$dojo = true;
$whichDojo[] = 'ComboBox';
// #################################################################################
// Section: if no record ID -> die
// #################################################################################
// check for record ID
if (!isset($_GET['code']) || trim($_GET['code']) == '' || !isset($_GET['geneCode']) || trim($_GET['geneCode']) == '')
{
die('Missing record ID!');
}
// #################################################################################
// Section: If record ID is found - collect data from DB
// #################################################################################
// open database connection
$connection = mysql_connect($host, $user, $pass) or die ('Unable to connect!');
if( function_exists(mysql_set_charset)) {
mysql_set_charset("utf8");
}
// select database
mysql_select_db($db) or die ('Unable to select database');
// generate and execute query
$code = $_GET['code'];
$geneCode = $_GET['geneCode'];
$query = "SELECT code, family, subfamily,
tribe, genus, species,
typeSpecies, voucherImage, thumbnail, timestamp
FROM ". $p_ . "vouchers WHERE code = '$code'";
$query1 = "SELECT CHAR_LENGTH(sequences),
geneCode,
labPerson,
accession,
dateCreation,
dateModification,
sequences,
(CHAR_LENGTH(sequences) - (CHAR_LENGTH(sequences) - ((CHAR_LENGTH(sequences) - CHAR_LENGTH(REPLACE(sequences, '?', '')) + (CHAR_LENGTH(sequences) - CHAR_LENGTH(REPLACE(sequences, '-', ''))))))),
notes
FROM ". $p_ . "sequences WHERE code='$code' AND geneCode='$geneCode'";
$query2 = "SELECT primer1,
primer2,
primer3,
primer4,
primer5,
primer6
FROM ". $p_ . "primers WHERE code='$code' AND geneCode='$geneCode'";
$result = mysql_query($query) or die("Error in query: $query. " . mysql_error());
$result1 = mysql_query($query1) or die("Error in query: $query1. " . mysql_error());
$result2 = mysql_query($query2) or die("Error in query: $query2. " . mysql_error());
// get result set as object
$row = mysql_fetch_object($result);
$row1 = mysql_fetch_array($result1);
// #################################################################################
// Section: Print output
// #################################################################################
// print details
if ($row || $row1)
{
// print beginning of html page -- headers
include_once'includes/header.php';
nav();
// begin HTML page content
echo "<div id=\"content\">";
echo "<table border=\"0\" width=\"960px\"> <!-- super table -->
<tr><td valign=\"top\">";
?>
<h1><?php echo $row -> code; ?></h1>
<table width="800px" border="0"> <!-- big parent table -->
<tr><td valign="top">
<table border="0" cellspacing="10" width="240px"> <!-- table child 1-->
<tr><td>
<table width="220" cellspacing="0">
<caption>Specimen name</caption>
<tr><td class="label">Family</td><td class="field"><?php echo $row->family; ?> </td></tr>
<tr><td class="label">Subfamily</td><td class="field"><?php echo $row->subfamily; ?> </td></tr>
<tr><td class="label">Tribe</td><td class="field"><?php echo $row->tribe; ?> </td></tr>
<tr><td class="label">Genus</td><td class="field"><?php echo $row->genus; ?> </td></tr>
<tr><td class="label">Species</td><td class="field"><?php echo $row->species; ?> </td></tr>
</table>
</td></tr>
<tr><td>
<table cellspacing="0" width="220">
<caption>Sequence</caption>
<tr><td class="label">Code</td><td width="80px" class="field3"><?php echo $row->code; ?> </td></tr>
<tr><td class="label">Type species</td><td class="field">
<?php if ($row->typeSpecies == '2') { echo "No"; } elseif ($row->typeSpecies == '1') { echo "Yes"; } else { echo "don't know"; } ?> </td></tr>
<tr>
<td class="label">Sequence</td><td class="field4" colspan="4"> </td>
</tr>
<tr><td class="field5" colspan="5"><textarea cols="27" rows="10" wrap="soft" readonly="yes">
<?php
$wrapped_sequence = wordwrap($row1['6'], 25, "\n", 1);
echo $wrapped_sequence;
?>
</textarea></td></tr>
<tr><td class="label">No of bp</td>
<td class="field"><?php echo $row1['0']; ?></td>
<td class="label3">Amb.</td>
<td class="field2"><?php echo $row1['7']; ?></td>
<td width="30"> </td>
</tr>
</table>
</td></tr>
</table> <!-- end table child 1 -->
</td>
<td valign="top">
<table border="0" cellspacing="10"> <!-- table child 2 -->
<tr><td valign="top">
<table width="200" cellspacing="0" border="0">
<caption>Lab Work</caption>
<tr><td class="label">Lab Person</td><td class="field"><?php echo $row1['2']; ?> </td></tr>
<tr><td class="label">Gene Code</td><td class="field3"><?php echo $row1['1']; ?> </td></tr>
<tr><td class="label">Accession</td><td class="field">
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=nucleotide&term=<?php echo $row1['3']; ?>[accn]&doptcmdl=GenBank" target="_blank"><?php echo $row1['3']; ?></a> </td></tr>
<tr><td class="label">Date Creation</td><td class="field"><?php echo $row1['4']; ?> </td></tr>
<tr><td class="label">Date Modification</td><td class="field"><?php echo $row1['5']; ?> </td></tr>
</table>
</td>
<td width="200px">
<a href="<?php echo $row->voucherImage; ?>"><img class="voucher" src="<?php echo $row->thumbnail; ?>" alt="" width="200px" /></a>
</td>
</tr>
<tr><td colspan="2">
<table width="160" cellspacing="0" border="0">
<caption>Primers Used</caption>
<tr><td class="label2">In alphabetical order</td></tr>
<?php
if (mysql_num_rows($result2) > 0)
{
while ($row2 = mysql_fetch_assoc($result2))
{
$a = array();
$i = 0;
foreach ($row2 as $val)
{
if ($val != '')
{
$a[$i] = $val;
$i++;
}
else
{
continue;
}
}
sort($a); // $a is my array containing all my used primers, print now
foreach ($a as $value)
{
echo "\n\t\t\t<tr><td align=\"right\" class=\"field\">" . $value . " </td></tr>";
}
}
}
else
{
echo "<tr><td class=\"field\"> </td></tr>";
}
?>
<td width="200px">
</td>
</tr>
<tr><td colspan="2">
<table width="160" cellspacing="0" border="0">
<caption>Notes</caption>
<tr>
<td class="label2">Notes</td>
</tr>
<tr><td class="field5">
<textarea name="notes" rows="3" cols="20"><?php echo $row1[8]; ?></textarea>
</td>
</tr>
</table>
</table>
</td></tr>
</table><!-- end table child 2 -->
</td></tr>
</table><!-- end big parent table -->
</td>
<td class="sidebar">
<?php
make_sidebar();
echo "</td>";
echo "</tr>
</table> <!-- end super table -->
</div> <!-- end content -->";
make_footer($date_timezone, $config_sitename, $version, $base_url);
}
else
{
// print beginning of html page -- headers
include_once('includes/header.php');
nav();
// begin HTML page content
echo "<div id=\"content_narrow\">";
echo "<table border=\"0\" width=\"850px\"> <!-- super table -->
<tr><td valign=\"top\">";
?>
<p>
<img src="images/warning.png" alt="" /> That record could not be located in the database.
</td>
<?php
make_sidebar(); // includes td and /td already
echo "</tr>
</table> <!-- end super table -->
</div> <!-- end content -->";
make_footer($date_timezone, $config_sitename, $version, $base_url);
}
// close database connection
mysql_close($connection);
?>
</body>
</html>
