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author davidmurphy
date Fri, 13 Jan 2012 07:16:13 -0500
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
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<html>
<head>
<link rel="stylesheet" type="text/css" href="logo.css" >

<title>CodonLogo - Tests </title>
<meta name="author" content="Gavin E. Crooks" >
<meta name="ID" content="$ID:" >

<style type="text/css">
td {
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.err_msg { 
    color: #900;
}

</style>
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<body style="align:center">


<table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
<tr><td >
<h1> CodonLogo: Tests</h1>

</td><td align = "right"> 
    &middot; 
  <a href="./">about</a>&nbsp;&middot;
  <a href="create.cgi">create</a>&nbsp;&middot; 
  <a href="examples.html">examples</a>&nbsp;&middot; 
  <a href="manual.html">manual</a>&nbsp;&middot; 
<br>
&nbsp;
</td></tr>

<tr><td colspan='2'>

Various tests of the CodonLogo webapp. <br >

<hr >

<dl>
<dt>Relative Entropy Test</dt>
<dd>
The entropy should be 2 bits, 1 bit, 0 bits
(The small sample correction should be turned off.) 
<br >
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" value="true" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="composition" value="comp_none" >

<input type="hidden" name="sequences" value=
">
GTTGTTGTTGTT
>
GTCGTCGTCGTC
>
GGGGGGGGGGGG
>
GGAGGAGGAGGA
" >
</form>
</dd>


<dt>Title And Labels Test</dt>
<dd>
Replace and display x-label, y-label and title. 
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" value="true" >
<input type="hidden" name="download" value="true" >

<input type="hidden" name="yaxis_label" value="The Y-axis" > 
<input type="hidden" name="xaxis_label" value="The X-axis" > 
<input type="hidden" name="logo_title" value="This is the TITLE" > 
<input type="hidden" name="sequences" value=
">
AAAGTGAAAGTGAAAGTGAAAGTG
>
AAAGCGAAAGCGAAAGCGAAAGCG
>
TGCCCTTGCCCTTGCCCTTGCCCT
>
TGCCTTTGCCTTTGCCTTTGCCTT
" >
</form>

Same, but do not show axes
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" value="true" >
<input type="hidden" name="download" value="true" >

<input type="hidden" name="yaxis_label" value="This is the Y-axis" > 
<input type="hidden" name="xaxis_label" value="This is the X-axis" > 
<input type="hidden" name="logo_title" value="This is the TITLE" > 
<input type="hidden" name="sequences" value=
">
AAAGTGAAAGTGAAAGTGAAAGTG
>
AAAGCGAAAGCGAAAGCGAAAGCG
>
TGCCCTTGCCCTTGCCCTTGCCCT
>
TGCCTTTGCCTTTGCCTTTGCCTT
" >
</form>
</dd>



<dt>Format Test</dt>
<dd>
Ensure that this logo can be created in each of the available formats
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" value="true" >
<input type="hidden" name="download" value="true" >

Format: <select name="format">
<option value="png_print">PNG</option>
<option value="png">PNG (low res.)</option>
<option value="jpeg">JPEG (low res.)</option>
<option value="eps">EPS (vector)</option>
<option value="pdf">PDF (vector)</option>
<option value="txt">data</option>
</select> 

<input type="hidden" name="sequences" value=
">
AAAGTGAAAGTGAAAGTGAAAGTG
>
AAAGCGAAAGCGAAAGCGAAAGCG
>
TGCCCTTGCCCTTGCCCTTGCCCT
>
TGCCTTTGCCTTTGCCTTTGCCTT
" >
</form>
</dd>




<dt>Test Alphabetic Order</dt>
<dd>
Each character in each stack has the same entropy. The letters
should be alphabetized, top down.
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" value="true" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="composition" value="comp_none" >
(NA)
<input type="hidden" name="sequences" value=
">
AAAGTG
>
AAAGCG
>
TGCCCT
>
TGCCTT
" >
</form>

<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" value="true" > (AA)
<input type="hidden" name="download" value="true" >
<input type="hidden" name="sequences" value=
">
CA
>
CA
>
VA
>
VG
>
KG
>
KG
" >
</form>
</dd>



<dt>One Single Column</dt>
<dd>
Should not die just because there is only 1 stack.
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="sequences" value=
">
A
>
A
>
G
>
G
>
G
>
G
" >
</form>
</dd>


<dt> Small Sample Correction Test</dt>
<dd>
The samples per column decrease from 32 (left) to 1 (right).
Before the small sample correction the relative entropy of each stack
is 2 bits. 
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<select name="composition" >
<option value = "comp_none" >No adjustment for composition</option>
<option value = "comp_auto" >auto</option>
</select>

<input type="hidden" name="sequences" value=
">
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
>
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-
>
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--
>
GGGGGGGGGGGGGGGGGGGGGGGGGGGGG---
>
GGGGGGGGGGGGGGGGGGGGGGGGGGGG----
>
GGGGGGGGGGGGGGGGGGGGGGGGGGG-----
>
GGGGGGGGGGGGGGGGGGGGGGGGGG------
>
GGGGGGGGGGGGGGGGGGGGGGGGG-------
>
GGGGGGGGGGGGGGGGGGGGGGGG--------
>
GGGGGGGGGGGGGGGGGGGGGGG---------
>
GGGGGGGGGGGGGGGGGGGGGG----------
>
GGGGGGGGGGGGGGGGGGGGG-----------
>
GGGGGGGGGGGGGGGGGGGG------------
>
GGGGGGGGGGGGGGGGGGG-------------
>
GGGGGGGGGGGGGGGGGG--------------
>
GGGGGGGGGGGGGGGG----------------
>
GGGGGGGGGGGGGGG-----------------
>
GGGGGGGGGGGGGG------------------
>
GGGGGGGGGGGGG-------------------
>
GGGGGGGGGGGG--------------------
>
GGGGGGGGGGG---------------------
>
GGGGGGGGGG----------------------
>
GGGGGGGGG-----------------------
>
GGGGGGGG------------------------
>
GGGGGGG-------------------------
>
GGGGGG--------------------------
>
GGGGG---------------------------
>
GGGG----------------------------
>
GGG-----------------------------
>
GG------------------------------
>
G-------------------------------
" >
</form>
</dd>



<dt> Test Graceful Failure</dt>
<dd>
Each of these tests should result in a polite and informative error message.
<form method="post" action="create.cgi">
<input type="submit" name="cmd_create" value="Fail: No sequence data" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="show_errorbars" checked="checked" >
<input type="hidden" name="sequences" value="" >
</form>

<form method="post" action="create.cgi">
<input type="submit" name="cmd_create" value="Fail: Malformed sequences" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" checked="checked" >
<input type="hidden" name="sequences" value="
asdajksgh
>
GGGGGGGGGGGGGG------------------
>
GGGGGGGGGGGGG-------------------
>
" >
</form>

<form method="post" action="create.cgi">
<input type="submit" name="cmd_create" value="Fail: Unknown format" >
<input type="hidden" name="format" value="NO_SUCH_FORMAT" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" checked="checked" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="sequences" value=">
GGGGGGGGGGGGGG------------------
>
GGGGGGGGGGGGG-------------------
>
" >
</form>

<form method="post" action="create.cgi">
<input type="submit" name="cmd_create" value="Fail: Malformed data" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="download" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
<input type="hidden" name="show_errorbars" checked="checked" >
<input type="hidden" name="sequences" value=">
GGGGGGGGGGGGGG------------------
>
GGGGGGGGGGGGG------------------
>
" >
</form>


</dd>



<dt> Logos Sizes</dt>
<dd>
Same sequences, three different sizes.
<form method="post" action="create.cgi">
<input type="submit" name="cmd_edit" value="Edit" >
<input type="hidden" name="download" value="true" >
<input type="submit" name="cmd_create" value="Create" >
<input type="hidden" name="show_yaxis" value="true" >
<input type="hidden" name="show_xaxis" value="true" >
<input type="hidden" name="show_fineprint" value="true" >
Size: 
<select name="size" >
<option  selected="selected" >small</option>
<option >medium</option>
<option  >large</option>
</select> 


<input type="hidden" name="sequences" value=
">aldB -18->4
attcgtgatagctgtcgtaaag
>ansB 103->125
ttttgttacctgcctctaactt
>araB1 109->131
aagtgtgacgccgtgcaaataa
>araB2 147->169 
tgccgtgattatagacactttt
>cdd 1 107->129
atttgcgatgcgtcgcgcattt
>cdd 2 57->79
taatgagattcagatcacatat
>crp 1 115->137
taatgtgacgtcctttgcatac
>crp 2
gaaggcgacctgggtcatgctg
>cya 151->173 
aggtgttaaattgatcacgttt
>cytR 1 125->147
cgatgcgaggcggatcgaaaaa
>cytR 2 106->128
aaattcaatattcatcacactt
>dadAX 1 95->117
agatgtgagccagctcaccata
>dadAX 2 32->54
agatgtgattagattattattc
>deoP2 1 75->97
aattgtgatgtgtatcgaagtg
>deoP2 2 128->150 
ttatttgaaccagatcgcatta
>fur 136->158
aaatgtaagctgtgccacgttt
>gal 56->78
aagtgtgacatggaataaatta
>glpACB (glpTQ) 1 54->76  
ttgtttgatttcgcgcatattc
>glpACB (glpTQ) 2 94->116
aaacgtgatttcatgcgtcatt
>glpACB (glpTQ) 144->166 
atgtgtgcggcaattcacattt
>glpD (glpE) 95->117 
taatgttatacatatcactcta
>glpFK 1 120->142
ttttatgacgaggcacacacat
>glpFK 2 95->117
aagttcgatatttctcgttttt
>gut (srlA) 72->94
ttttgcgatcaaaataacactt
>ilvB 87->109
aaacgtgatcaacccctcaatt
>lac 1 (lacZ) 88->110
taatgtgagttagctcactcat
>lac 2 (lacZ) 16->38 
aattgtgagcggataacaattt
>malEpKp1 110->132
ttgtgtgatctctgttacagaa
>malEpKp2 139->161
TAAtgtggagatgcgcacaTAA
>malEpKp3 173->195
TTTtgcaagcaacatcacgAAA
>malEpKp4 205->227
GACctcggtttagttcacaGAA
>malT 121->143
aattgtgacacagtgcaaattc
>melR 52->74
aaccgtgctcccactcgcagtc
>mtl 302->324
TCTTGTGATTCAGATCACAAAG
>nag 156->178
ttttgtgagttttgtcaccaaa
>nupG2 97->119
aaatgttatccacatcacaatt
>nupG1 47->69
ttatttgccacaggtaacaaaa
>ompA 166->188
atgcctgacggagttcacactt
>ompR 161->183
taacgtgatcatatcaacagaa
>ptsH A 316->338
Ttttgtggcctgcttcaaactt
>ptsH B 188->210
ttttatgatttggttcaattct
>rhaS (rhaB) 161->183 
aattgtgaacatcatcacgttc
>rot 1 (ppiA) 182->204 
ttttgtgatctgtttaaatgtt
>rot 2 (ppiA) 129->151
agaggtgattttgatcacggaa
>tdcA 60->82
atttgtgagtggtcgcacatat
>tnaL 73->95
gattgtgattcgattcacattt
>tsx 2 146->168
gtgtgtaaacgtgaacgcaatc
>tsx 1 107->129
aactgtgaaacgaaacatattt
>uxuAB 165->187
TCTTGTGATGTGGTTAACCAAT
" >
</form>
</dd>




</dl>



</td></tr>




</table>

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