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|
Content-Type: text/html; charset=ISO-8859-1
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<!-- site meta data -->
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta name="description" content="NeXML is a file format for encoding phyloinformatic data using XML." />
<meta name="keywords" content="NeXML, XML, NEXUS, phyloinformatics, phylogenetics, phylogenies, trees, dna, rna, nucleotide, standard, continuous, amino, acid, matrix, tree, network, data" />
<meta name="author" content="Rutger Vos" />
<meta name="robots" content="index,follow" />
<meta name="verify-v1" content="mYceuNu58e0c0TNJ/gJ2NO63bxeH1nu28sZ2rtzcLoM=" />
<!-- RSS feeds -->
<link
rel="alternate"
type="application/rss+xml"
title="nexml-discuss mailing list - RSS 2.0"
href="http://mailbucket.org/nexml_discuss.xml"/>
<link
rel="alternate"
type="application/rss+xml"
title="SourceForge project summary - RSS 2.0"
href="http://sourceforge.net/export/rss2_projsummary.php?group_id=209571"/>
<link
rel="alternate"
type="application/rss+xml"
title="Wiki changes - RSS 2.0"
href="https://www.nescent.org/wg/evoinfo/index.php?title=Future_Data_Exchange_Standard&action=history&feed=rss"/>
<link
rel="alternate"
type="application/rss+xml"
title="SVN revision history - RSS 2.0"
href=""/>
<title>FAIL</title>
<link rel="stylesheet" href="/nexml/html/include/style.css" type="text/css" />
<link rel="stylesheet" href="/nexml/html/include/schema.css" type="text/css" />
<style type="text/css">
<!--
/* inclusions for validation service */
li.debug {
list-style-image: url('/nexml/html/include/bug.png');
}
li.info {
list-style-image: url('/nexml/html/include/lightbulb.png');
}
li.warn {
list-style-image: url('/nexml/html/include/error.png');
}
li.error {
list-style-image: url('/nexml/html/include/exclamation.png');
}
li.fatal {
list-style-image: url('/nexml/html/include/bomb.png');
} -->
</style>
<script type="text/javascript" src="/nexml/html/include/functions.js"></script>
<script type="text/javascript" src="/nexml/html/include/schema.js"></script>
<link rel="shortcut icon" href="/nexml/html/include/cross.png" />
</head>
<body>
<!-- This heading is only here for text browsers without css -->
<h1 class="hide">FAIL</h1>
<div id="thetop">
<a id="top" name="top"></a>
<p class="hide">
Skip to:
<a href="#sitemenu" accesskey="2">Site menu</a> |
<a href="#maincontent" accesskey="3">Main content</a>
</p>
</div>
<div id="container">
<div id="main">
<!-- main banner in the top-left -->
<div id="logo">
<h1>
[<a href="/" accesskey="4">NeXML</a>]
</h1><span id="tagline">Rich phyloinformatic data</span>
</div>
<!-- site blurb in the top-middle -->
<div id="intro">
<h2>
<a id="maincontent" name="maincontent"></a>
The future data exchange standard is here!
</h2>
<p>
NeXML is an exchange standard for representing
phyloinformatic data — inspired by the commonly used
NEXUS format, but more robust and easier to process.
</p>
</div>
<div class="clear"></div>
<!-- validate form -->
<div id="validateDiv">
<form
action="/nexml/validator"
enctype="multipart/form-data"
method="post"
id="validateForm">
<fieldset id="validateFieldset">
<legend class="hide">Process nexml data</legend>
<select id="validateSelect">
<option value="validator.cgi">validate</option>
<option value="nex2xml.cgi">nexus -> nexml</option>
<option value="newick2xml.cgi">newick -> nexml</option>
<option value="xml2json.cgi">nexml -> json</option>
<option value="xml2rdf.cgi">nexml -> rdf</option>
</select>
<input type="file" name="file" id="validateUpload"/>
<input type="button" onclick="submitForm()" id="validateSubmit" value="Submit"/>
</fieldset>
</form>
</div>
<!-- main heading of this page -->
<h3 class="headerstyle">FAIL</h3>
<!-- http://www.nexml.org/nexml/nex2xml -->
<div style="padding-bottom:1em;margin-top: 1em; margin-left: 10px;color: #888888">
<small>
<a href="/">~</a> /
<a href="/nexml">nexml</a> /
nex2xml </small>
</div>
<div class="linkshare credit">
<a rel="nofollow" href="http://digg.com/submit?phase=2&url=http://www.nexml.org/nexml/nex2xml">
<img class="icon" src="/nexml/html/include/digg.gif" alt="digg"/>
</a>
<a rel="nofollow" href="http://reddit.com/submit?url=http://www.nexml.org/nexml/nex2xml">
<img class="icon" src="/nexml/html/include/reddit.gif" alt="reddit"/>
</a>
<a rel="nofollow" href="http://del.icio.us/post?url=http://www.nexml.org/nexml/nex2xml">
<img class="icon" src="/nexml/html/include/delicious.gif" alt="del.icio.us"/>
</a>
<a rel="nofollow" href="http://www.facebook.com/share.php?u=http://www.nexml.org/nexml/nex2xml">
<img class="icon" src="/nexml/html/include/facebook.gif" alt="facebook"/>
</a>
<small> | Last updated: Thu Aug 25 05:35:56 EDT 2011
—</small>
</div>
<h3 class="plain">Detailed results</h3>
<p>
Below are the messages received from the parsing and validation operations (if any). They
are organized as debugging messages (<img class="icon" src="/nexml/html/include/bug.png"/>),
informational (<img class="icon" src="/nexml/html/include/lightbulb.png"/>),
warnings (<img class="icon" src="/nexml/html/include/error.png"/>), errors
(<img class="icon" src="/nexml/html/include/exclamation.png"/>) and fatal
exceptions (<img class="icon" src="/nexml/html/include/bomb.png"/>):
</p>
<ul>
<li class="info validator">
going to parse nexus data </li>
<li class="info validator">
going to split nexus data on lines </li>
<li class="info validator">
going to split lines on tokens </li>
<li class="info validator">
going to split non-quoted/commented fragments on whitespace </li>
<li class="info validator">
tokenized and split data, going to parse blocks </li>
<li class="info validator">
found nexus token </li>
<li class="info validator">
starting taxa block </li>
<li class="info validator">
number of taxa: 6 </li>
<li class="info validator">
starting taxlabels </li>
<li class="info validator">
starting characters block </li>
<li class="info validator">
number of characters: 45 </li>
<li class="info validator">
datatype: dna </li>
<li class="info validator">
missing character: ? </li>
<li class="info validator">
gap character: - </li>
<li class="info validator">
block has title 'dna_forty_five' </li>
<li class="info validator">
charlabels: labone labtwo labthree labfour labfive labsix labseven </li>
<li class="info validator">
adding matrix metadata </li>
<li class="fatal validator">
Can't call method "set_name" on an undefined value at perl/lib/Bio/Phylo/Matrices/Matrix.pm line 431, <DATA> line 1.
</li>
</ul>
<h3 class="plain">Submitted contents</h3>
<p>
Below are the contents (if any) that were submitted to this query:
</p>
<div style="width:470px;overflow:auto;margin-left:2em;padding-bottom:1em">
<a name="line1"></a>
<div title="1" style="white-space:pre;font-family:courier"><span style="color:silver">1</span> #nexus
</div>
<a name="line2"></a>
<div title="2" style="white-space:pre;font-family:courier"><span style="color:silver">2</span>
</div>
<a name="line3"></a>
<div title="3" style="white-space:pre;font-family:courier"><span style="color:silver">3</span> begin taxa;
</div>
<a name="line4"></a>
<div title="4" style="white-space:pre;font-family:courier"><span style="color:silver">4</span> dimensions ntax=6;
</div>
<a name="line5"></a>
<div title="5" style="white-space:pre;font-family:courier"><span style="color:silver">5</span> taxlabels
</div>
<a name="line6"></a>
<div title="6" style="white-space:pre;font-family:courier"><span style="color:silver">6</span> 'P. fimbriata'
</div>
<a name="line7"></a>
<div title="7" style="white-space:pre;font-family:courier"><span style="color:silver">7</span> 'P. robusta'
</div>
<a name="line8"></a>
<div title="8" style="white-space:pre;font-family:courier"><span style="color:silver">8</span> 'P. americana'
</div>
<a name="line9"></a>
<div title="9" style="white-space:pre;font-family:courier"><span style="color:silver">9</span> 'P. myriophylla'
</div>
<a name="line10"></a>
<div title="10" style="white-space:pre;font-family:courier"><span style="color:silver">10</span> 'P. polygama'
</div>
<a name="line11"></a>
<div title="11" style="white-space:pre;font-family:courier"><span style="color:silver">11</span> 'P. macrophylla'
</div>
<a name="line12"></a>
<div title="12" style="white-space:pre;font-family:courier"><span style="color:silver">12</span> ;
</div>
<a name="line13"></a>
<div title="13" style="white-space:pre;font-family:courier"><span style="color:silver">13</span> blockid bogus;
</div>
<a name="line14"></a>
<div title="14" style="white-space:pre;font-family:courier"><span style="color:silver">14</span> end;
</div>
<a name="line15"></a>
<div title="15" style="white-space:pre;font-family:courier"><span style="color:silver">15</span>
</div>
<a name="line16"></a>
<div title="16" style="white-space:pre;font-family:courier"><span style="color:silver">16</span> [!
</div>
<a name="line17"></a>
<div title="17" style="white-space:pre;font-family:courier"><span style="color:silver">17</span> *************
</div>
<a name="line18"></a>
<div title="18" style="white-space:pre;font-family:courier"><span style="color:silver">18</span> * dna *
</div>
<a name="line19"></a>
<div title="19" style="white-space:pre;font-family:courier"><span style="color:silver">19</span> *************
</div>
<a name="line20"></a>
<div title="20" style="white-space:pre;font-family:courier"><span style="color:silver">20</span> ]
</div>
<a name="line21"></a>
<div title="21" style="white-space:pre;font-family:courier"><span style="color:silver">21</span> begin characters;
</div>
<a name="line22"></a>
<div title="22" style="white-space:pre;font-family:courier"><span style="color:silver">22</span> dimensions nchar=45;
</div>
<a name="line23"></a>
<div title="23" style="white-space:pre;font-family:courier"><span style="color:silver">23</span> format datatype=dna missing=? gap=-;
</div>
<a name="line24"></a>
<div title="24" style="white-space:pre;font-family:courier"><span style="color:silver">24</span> title dna_forty_five;
</div>
<a name="line25"></a>
<div title="25" style="white-space:pre;font-family:courier"><span style="color:silver">25</span> CHARLABELS labone labtwo labthree labfour labfive labsix labseven;
</div>
<a name="line26"></a>
<div title="26" style="white-space:pre;font-family:courier"><span style="color:silver">26</span>
</div>
<a name="line27"></a>
<div title="27" style="white-space:pre;font-family:courier"><span style="color:silver">27</span> matrix
</div>
<a name="line28"></a>
<div title="28" style="white-space:pre;font-family:courier"><span style="color:silver">28</span> P._fimbriata {a, G}cctcggcttaacgaacctcggcttaacgaacctcggcttaacga
</div>
<a name="line29"></a>
<div title="29" style="white-space:pre;font-family:courier"><span style="color:silver">29</span> P._robusta (a, , C)cctcggcttaaccaacctcggcttaacgaacctcggcttaacga
</div>
<a name="line30"></a>
<div title="30" style="white-space:pre;font-family:courier"><span style="color:silver">30</span> P._americana rcgtcgctttca---acgtcgctttcaccaacgtcgctttcacca
</div>
<a name="line31"></a>
<div title="31" style="white-space:pre;font-family:courier"><span style="color:silver">31</span> P._myriophylla acgtcgctttca---acgtcgctttcaccaacgtc?ctttcacca
</div>
<a name="line32"></a>
<div title="32" style="white-space:pre;font-family:courier"><span style="color:silver">32</span> P._polygama acgtcgctctcaccaacgtcgctttcaccaacgtc?ctttcacca
</div>
<a name="line33"></a>
<div title="33" style="white-space:pre;font-family:courier"><span style="color:silver">33</span> P._macrophylla acgtcgctctcaccaacgtcgctttcaccaacgtcgctttcacca
</div>
<a name="line34"></a>
<div title="34" style="white-space:pre;font-family:courier"><span style="color:silver">34</span> ;
</div>
<a name="line35"></a>
<div title="35" style="white-space:pre;font-family:courier"><span style="color:silver">35</span> end;
</div>
<a name="line36"></a>
<div title="36" style="white-space:pre;font-family:courier"><span style="color:silver">36</span> BEGIN SETS;
</div>
<a name="line37"></a>
<div title="37" style="white-space:pre;font-family:courier"><span style="color:silver">37</span> CHARSET csone (STANDARD CHARACTERS='dna forty five') = 1-3;
</div>
<a name="line38"></a>
<div title="38" style="white-space:pre;font-family:courier"><span style="color:silver">38</span> CHARSET cstwo (CHARACTERS='dna forty five' STANDARD) = csone;
</div>
<a name="line39"></a>
<div title="39" style="white-space:pre;font-family:courier"><span style="color:silver">39</span> CHARSET csthree = 5 labfour cstwo;
</div>
<a name="line40"></a>
<div title="40" style="white-space:pre;font-family:courier"><span style="color:silver">40</span> CHARSET csfour = 4 labone - . \ 3 7;
</div>
<a name="line41"></a>
<div title="41" style="white-space:pre;font-family:courier"><span style="color:silver">41</span> CHARSET csfive = 44 43 csthree 41 10 - 16 \2 18 40 42 45;
</div>
<a name="line42"></a>
<div title="42" style="white-space:pre;font-family:courier"><span style="color:silver">42</span> CHARSET cssix (CHARACTERS='dna forty five') = labseven csthree csfour 6;
</div>
<a name="line43"></a>
<div title="43" style="white-space:pre;font-family:courier"><span style="color:silver">43</span> end;
</div>
<a name="line44"></a>
<div title="44" style="white-space:pre;font-family:courier"><span style="color:silver">44</span>
</div>
<a name="line45"></a>
<div title="45" style="white-space:pre;font-family:courier"><span style="color:silver">45</span>
</div>
<a name="line46"></a>
<div title="46" style="white-space:pre;font-family:courier"><span style="color:silver">46</span> BEGIN ASSUMPTIONS;
</div>
<a name="line47"></a>
<div title="47" style="white-space:pre;font-family:courier"><span style="color:silver">47</span>
</div>
<a name="line48"></a>
<div title="48" style="white-space:pre;font-family:courier"><span style="color:silver">48</span> EXSET csone (STANDARD CHARACTERS='dna forty five') = 1-3;
</div>
<a name="line49"></a>
<div title="49" style="white-space:pre;font-family:courier"><span style="color:silver">49</span> EXSET cstwo (CHARACTERS='dna forty five' STANDARD) = csone;
</div>
<a name="line50"></a>
<div title="50" style="white-space:pre;font-family:courier"><span style="color:silver">50</span> EXSET csthree = 5 labfour cstwo;
</div>
<a name="line51"></a>
<div title="51" style="white-space:pre;font-family:courier"><span style="color:silver">51</span> EXSET * csfour = 4 labone - . \ 3 7;
</div>
<a name="line52"></a>
<div title="52" style="white-space:pre;font-family:courier"><span style="color:silver">52</span> EXSET csfive = 44 43 csthree 41 10 - 16 \2 18 40 42 45;
</div>
<a name="line53"></a>
<div title="53" style="white-space:pre;font-family:courier"><span style="color:silver">53</span> EXSET cssix (CHARACTERS='dna forty five') = labseven csthree csfour 6;
</div>
<a name="line54"></a>
<div title="54" style="white-space:pre;font-family:courier"><span style="color:silver">54</span> end;
</div>
</div> </div>
<div id="sidebar">
<!-- top-right site navigation menu -->
<h2 class="quicklinks">
<a id="quicklinks" name="quicklinks"></a>Quick links:
</h2>
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<h3>
External links
</h3>
<ul>
<li class="external">
<a href="http://sourceforge.net/projects/nexml/" rel="nofollow">SF.net project</a>
</li>
<li class="external">
<a href="http://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard" rel="nofollow">EvoInfo wiki</a>
</li>
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<a href="http://www.evolutionaryontology.org/" rel="nofollow">CDAO</a>
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Site design: © <a href="http://andreasviklund.com/" class="credit">Andreas Viklund</a>
of <a href="http://jokkmokk.biz/" title="ITUS Jokkmokk">Jokkmokk</a>.
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