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mainframe.php
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<script src="http://code.jquery.com/jquery-1.10.1.min.js"></script>
<script type="text/javascript">
function toggle(input){
var x = document.getElementById(input);
if (x.style.display == "none"){
x.style.display = "block";
} else {
x.style.display = "none";
}
}
$(function() {
$("#custom_checkbox").change(function() {
$("#CustomGenome").toggle();
});
});
</script>
<div style="width:100%; align:center">
<table style="margin:0 auto;">
<tr>
<td>
<div class="bigblock">
<div class="subtitle"> <b>Co</b>mprehensive <b>Re</b>dundancy Analysis for <b>Co</b>mplete <b>P</b>roteomes </div>
<div class="general">
<form name="download" action="results.php" method="POST" enctype="multipart/form-data">
<div id="download_area">
<br><b>FASTA: </b> <input type="file" name="fastaseq"><br>
<input type='checkbox' name="exfile"> Use Example File? <p>
<b>EMAIL (optional): </b> <input type="text" name="email"></input>
<p><b>PARAMETERS</b></p>
<table>
<tr>
<td>
<table>
<tr>
<td class="setting_title">
<b>Sequence Length: </b>
<a href="javascript:toggle('Length_Description')">(?)</a>
</td>
<td>
<input type="checkbox" name="dlen"> <b>Skip</b>
</td>
</tr>
</table>
</td>
</tr>
<tr id = "Length_Description" style="display: none;width: 20em;">
<td class="descript setting">Flag sequences that are less that <b>m</b> or more than <b>n</b> amino acids long. Check <b>Skip</b> to bypass</td>
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting">
Minimum (m):
</td>
<td>
<input type="text" name="min" value="30" class="param"></input>
</td>
</tr>
<tr>
<td class="setting">
Maximum (n):
</td>
<td>
<input type="text" name="max" value="30000" class="param"></input>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting_title"><b>Intra-Sequence Complexity: </b><a href="javascript:toggle('ISC_Description')">(?)</a></td><td><input type="checkbox" name="dcomp"> <b>Skip</b> </td>
</tr>
</table>
</td>
</tr>
<tr id = "ISC_Description" style="display: none;width: 20em;">
<td class="descript setting">Flag sequences compressible at least down to <b>c</b> of the original length (repetitive structure). Check <b>Skip</b> to bypass
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting">
Complexity (c):
</td>
<td>
<input type="text" name="zj" value="0.7" class="param"></input>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting_title"><b>Inter-Sequence Redundancy: </b><a href="javascript:toggle('ISR_Description')">(?)</a></td><td> <input type="checkbox" name="dred"> <b>Skip</b> </td>
</tr>
</table>
</td>
</tr>
<tr id = 'ISR_Description' style="display: none;width: 20em;">
<td class="descript setting">Flag sequences contained with atleast <b>t</b> sequence identity within up to <b>f</b> fractional length of another sequence in this set. Check <b>Skip</b> to bypass
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting">
Identity (t):
</td>
<td>
<input type="text" name="ct" value="0.7" class="param"></input>
</td>
</tr>
<tr>
<td class="setting">
Fractional Length (f):
</td>
<td>
<input type="text" name="cl" value="0.8" class="param"></input>
</td>
</tr>
</table>
</td>
</tr>
<!--
<tr>
<td>
<table>
<tr>
<td class="setting_title"><b>Fission: </b><a href="javascript:toggle('FIS_Description')">(?)</a></td><td> <input type="checkbox" name="dfis"> Bypass? </td>
</tr>
</table>
</td>
</tr>
<tr id = 'FIS_Description' style="display: none;width: 20em;">
<td class="descript setting">Flag sequences that are potentially joinable fragments of <b>Reference Genome</b>. Check <b>Skip</b> to bypass
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting"><i>Reference Genome:</i></td>
</tr>
<tr>
<td class="setting">
<input type="checkbox" name="refgm" value="human"> Homo Sapiens
</td>
</tr>
<tr>
<td class = "setting">
<input type="checkbox" name="refgm" value="xtrop"> Xenopus Tropicalis
</td>
</tr>
<tr>
<td class="setting">
<input type="checkbox" id="custom_checkbox" name="refgm" value="custom"> Custom
</td>
</tr>
<tr id = 'CustomGenome' style="display:none;">
<td class="setting">
<input type="file" name="refgm_file">
</td>
</tr>
</table>
</td>
</tr> -->
<tr>
<td><b>Miscellaneous Settings:</b></td>
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting">
"X" tolerance (x):
</td>
<td style="width: 80px;">
<input type="text" name="xs" value="0" class="param"></input>
<a href="javascript:toggle('XS_Description')">(?)</a>
</td>
</tr>
</table>
</td>
</tr>
<tr id = 'XS_Description' style="display: none;">
<td class="descript setting">Flag sequences with regions containing more than <b>x</b> consecutive "X"s</td>
</tr>
<tr>
<td>
<table>
<tr>
<td class="setting">
Check for M at beginning of sequence?
</td>
<td class="checkbox_setting">
<input type="checkbox" name="ms"><a href="javascript:toggle('MS_Description')">(?)</a>
</td>
</tr>
</table>
</td>
</tr>
<tr id = 'MS_Description' style="display: none;">
<td class="descript setting">When checked flag sequences not beggining with "M"</td>
</tr>
</table>
<div style="height:20px;"></div>
<p></p>
<input type="submit"/>
</div>
<p>
<div style="font-size:50%;">
<b>Contact:</b><i><br>pesha (at) hms.harvard.edu <br> jonathan (at) patsenker.com</i>
</div>
</form>
</div>
</div>
</td>
</table>
</div>