1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
|
<html xmlns="http://www.w3.org/1999/xhtml"
xmlns:mrs="http://mrs.cmbi.ru.nl/mrs-web/ml"
xml:lang="en" lang="en">
<head>
<title>M6</title>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="author" content="Maarten L. Hekkelman" />
<meta name="generator" content="Japi" />
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rel="stylesheet" type="text/css" href="css/mrs-style.css" />
<script src="scripts/jquery/jquery.js" type="text/javascript">
</script>
<script src="scripts/mrs.js" type="text/javascript">
</script>
<script src="scripts/select.js" type="text/javascript">
</script>
<script src="scripts/blast.js" type="text/javascript">
</script>
</head>
<body>
<mrs:include file="header.html" />
<div id="main">
<div style="margin-bottom: 1em;">
<form id="blastForm" method="POST" action="/blast" onsubmit="BlastJobs.submit(); return false;"
class="blast_form" >
<fieldset>
<!-- <p class="reformatted">NOTE: Please check the reformatted sequence and resubmit</p>-->
<p>Enter <em>one</em> protein sequence in <em>FastA</em> format</p>
<textarea name="query" rows="5" cols="72">${query}</textarea>
<!-- <li>Or enter filename: <input type="file" name="queryFile" size="50" maxlength="80" /></li>-->
<div>
<label>Databank to search</label><select name="db" style="width:10em;">
<mrs:options collection="blastdatabanks" value="id" label="name" selected="${blastdb}" />
</select>
</div>
<div id="options">
<!-- <div><h3>Options</h3></div>-->
<div><label>Filter low complexity</label><mrs:checkbox name="filter" checked="${filter}" /></div>
<div><label>E-value cutoff</label><select name="expect"><mrs:options collection="expectRange" selected="${expect}" /></select></div>
</div>
<p class="hideOptions" style="float:left">advanced options</p>
<div id="advancedoptions" style="display:none">
<div><h3>Advanced options</h3></div>
<div><label>Word size</label><select name="wordSize">
<option value="0">Default</option>
<mrs:options collection="wordSizeRange" selected="${wordSize}" /></select>
</div>
<div><label>Scoring matrix</label><select name="matrix" onchange="updateGapValues();">
<mrs:options collection="matrices" selected="${matrix}" /></select>
</div>
<div><label>Perform gapped alignment</label><mrs:checkbox name="gapped" checked="${gapped}" onchange="gappedChanged();" /></div>
<div><label>Cost to open a gap</label><select name="gapOpen" onchange="gapOpenChanged();">
<option value="-1">Default</option>
<mrs:options collection="gapOpenRange" selected="${gapOpen}" /></select>
</div>
<div><label>Cost to extend a gap</label><select name="gapExtend" onchange="gapExtendChanged();">
<option value="-1">Default</option>
<mrs:options collection="gapExtendRange" selected="${gapExtend}" /></select>
</div>
<div><label>Limit reported hits</label><select name="reportLimit">
<mrs:options collection="reportLimitRange" selected="${reportLimit}" /></select>
</div>
</div>
<input type="hidden" name="program" value="blastp" />
<div><input type="submit" name="submit" value="Run Blast" style="float:right;" class="submit"/></div>
</fieldset>
</form>
<div style="display: inline-block; height: 20em; vertical-align: top; overflow-y: auto; overflow-x: hidden; width: 450px" >
<table cellspacing="0" id="jobList" class="status clickable list" style="width:450; padding-right:16px">
<caption>Blast results</caption>
<thead>
<tr>
<th class="c1">Nr</th>
<th class="c2">ID</th>
<th class="c3">Databank</th>
<th class="c45" colspan="2">Status</th>
</tr>
</thead>
<tbody>
<mrs:if test="${empty blastJobs}">
<tr id="nohits">
<td colspan="4">No blast results are available since no blast job has been submitted in this session.</td>
</tr>
</mrs:if>
</tbody>
</table>
</div>
</div>
<div style="clear:both;"> </div>
<div class="list" id='selectableList'>
<table cellspacing="0" id="blastResult" style="display:none; width:100%">
<caption>Blast results for</caption>
<tr>
<th colspan="2">Nr</th>
<th>ID</th>
<th>Coverage</th>
<th>Description</th>
<th>Hsps</th>
<th>BitScore</th>
<th>E-value</th>
</tr>
<tbody/>
</table>
</div>
</div>
<mrs:include file="select.html" />
</body>
</html>
|
