1\Preamble{xhtml}
2
3% We don't want to translate font suggestions with ugly wrappers like
4% <span class="cmti-10"> for italic text
5\NoFonts
6
7% Don't output xml version tag
8\Configure{VERSION}{}
9
10\Configure{PROLOG}{DOCTYPE}
11
12% Output HTML5 doctype instead of the default for HTML4
13\Configure{DOCTYPE}{\HCode{<!doctype html>\Hnewline}}
14
15% Custom page opening
16\Configure{HTML}{\HCode{<html lang="en">\Hnewline}}{\HCode{\Hnewline</html>}}
17
18% Set custom page title
19\Configure{TITLE+}{ViennaRNA Tutorial}
20
21% Reset <head>, aka delete all default boilerplate
22%\Configure{@HEAD}{}
23
24% Setup custom <head> content
25\Configure{@HEAD}{
26  \HCode{
27    <link href="../css/bootstrap.min.css" rel="stylesheet" />\Hnewline
28    <link href="../css/bootstrap-theme.min.css" rel="stylesheet" />\Hnewline
29    <link href="../css/tbi_bootstrap.css" rel="stylesheet" />\Hnewline
30    <link href="../css/tbi_mod.css" rel="stylesheet" />\Hnewline
31  }
32}
33\Configure{@HEAD}{\HCode{<script type="text/javascript"\Hnewline
34src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"\Hnewline
35></script>\Hnewline}}
36\Configure{@HEAD}{\HCode{<style type="text/css">\Hnewline
37  .MathJax_MathML {text-indent: 0;}\Hnewline
38</style>\Hnewline}}
39
40
41\Configure{BODY}{\Tg<body role="document">}{\Tg</body>}
42\Configure{@BODY}{}
43\Configure{@BODY}{\IgnorePar\HCode{
44  <div class="container wrap">\Hnewline
45    <div class="container headwrap">\Hnewline
46        <header class="hidden-xs">\Hnewline
47          <img class="unilogo" src="../gfx/base/unilogo_small.png" alt="Univiersity of Vienna"/>\Hnewline
48          <hgroup class="head-title-lg">\Hnewline
49            <div class="title-link-lg"><a href="http://www.tbi.univie.ac.at">Theoretical Biochemistry Group</a></div>\Hnewline
50            <div class="title-link-sm"><a href="http://www.itc.univie.ac.at">Institute for Theoretical Chemistry</a></div>\Hnewline
51          </hgroup>\Hnewline
52        </header>\Hnewline
53        <nav class="navbar navbar-default navbar-tbi navbar-tbi-main center" role="navigation">\Hnewline
54          <div class="container-fluid">\Hnewline
55            <div class="navbar-header">\Hnewline
56              <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="\#navbar" aria-expanded="false" aria-controls="navbar">\Hnewline
57                <span class="sr-only">Toggle navigation</span>\Hnewline
58                <span class="icon-bar"></span>\Hnewline
59                <span class="icon-bar"></span>\Hnewline
60                <span class="icon-bar"></span>\Hnewline
61              </button>\Hnewline
62              <a class="navbar-brand visible-xs" href="/index.html"><img alt="TBI" height="24" src="../gfx/base/tbilogo.png"></a>\Hnewline
63            </div>\Hnewline
64            <div id="navbar" class="navbar-collapse collapse navbar-inner">\Hnewline
65              <ul class="nav navbar-nav navbar-tbi">\Hnewline
66                <li><a href="/index.html">TBI</a></li>\Hnewline
67                <li class="dropdown"><a href="\#" class="dropdown-toggle"\Hnewline
68                              data-toggle="dropdown"\Hnewline
69                              role="button"\Hnewline
70                              aria-haspopup="true"\Hnewline
71                              aria-expanded="false">RNA Software <span class="caret"></span></a>\Hnewline
72                  <ul class="dropdown-menu">\Hnewline
73                    <li><a href="../">ViennaRNA Package</a></li>\Hnewline
74                    <li><a href="../Barriers">Barriers</a></li>\Hnewline
75                    <li><a href="../Treekin">Treekin</a></li>\Hnewline
76                    <li><a href="../bar_map">barMap</a></li>\Hnewline
77                    <li><a href="../BHG">Basin Hopping Graph</a></li>\Hnewline
78                    <li><a href="http://www.tbi.univie.ac.at/software/rnawolf/rnawolf.html">RNAwolf</a></li>\Hnewline
79                    <li><a href="https://www.tbi.univie.ac.at/~wash/RNAz/">RNAz</a></li>\Hnewline
80                    <li><a href="../Alidot">AliDot</a></li>\Hnewline
81                  </ul>\Hnewline
82                </li>\Hnewline
83                <li><a href="../">ViennaRNA</a></li>\Hnewline
84                <li><a href="../documentation.html">Documentation</a></li>\Hnewline
85                <li class="selected"><a href="\#">Tutorial</a></li>\Hnewline
86                <li><a href="../changelog.html">Changelog</a></li>\Hnewline
87              </ul>\Hnewline
88            </div><!--/.nav-collapse -->\Hnewline
89          </div>\Hnewline
90        </nav>\Hnewline
91    </div>\Hnewline
92    <!-- Main Content Container  -->\Hnewline
93    <div class="container contentwrap" role="main">\Hnewline
94      <div class="container-main">\Hnewline
95        <!-- BREADCRUMB BAR -->\Hnewline
96        <div class="row wai">\Hnewline
97            <div class="col-xs-12 col-sm-6 breadcrumbs">\Hnewline
98              <span class="caption">You are here:</span>\Hnewline
99              <ol class="breadcrumb">\Hnewline
100                <li><a href="/">TBI</a></li>\Hnewline
101                <li><a href="/software">Software</a></li>\Hnewline
102                <li><a href="../index.html">ViennaRNA</a></li>\Hnewline
103                <li class="active"><a href="tutorial.html">Tutorial</a></li>\Hnewline
104              </ol>\Hnewline
105            </div>\Hnewline
106            <div class="col-xs-12 col-sm-6 appearance">\Hnewline
107              <span class="caption">Font size: </span>\Hnewline
108              <a class="incfont" href="\#"><img src="../gfx/base/font_inc.gif" alt="Increase font size"></a>\Hnewline
109              <a class="decfont" href="\#"><img src="../gfx/base/font_dec.gif" alt="Decrease font size"></a>\Hnewline
110              <a class="highcontrast" href="\#"><img src="../gfx/base/contrast.gif" alt="Switch style sheet from default to highcontrast and back"></a>\Hnewline
111            </div>\Hnewline
112        </div><!-- /.row -->\Hnewline
113        <div class="row row-offcanvas row-offcanvas-right">\Hnewline
114          <div class="col-xs-12 col-sm-9">\Hnewline
115            <article>\Hnewline
116              <p class="pull-right visible-xs">\Hnewline
117                <button type="button" class="btn btn-primary btn-xs" data-toggle="offcanvas">Toggle sidebar</button>\Hnewline
118              </p>\Hnewline
119  }
120}
121\Configure{@/BODY}{
122  \HCode{\IgnorePar
123            </article>\Hnewline
124          </div><!-- /.row -->\Hnewline\Hnewline
125          <!-- SIDEBAR -->\Hnewline
126          <div class="col-xs-6 col-sm-3 sidebar-offcanvas" id="sidebar" role="navigation">\Hnewline\Hnewline
127        <aside>\Hnewline
128          <nav id="sidebarNav" role="navigation">\Hnewline
129            __SIDENAVLIST__\Hnewline
130          </nav>\Hnewline
131        </aside>\Hnewline
132          </div><!--/.sidebar-offcanvas-->\Hnewline
133        </div><!-- /.row-offcanvas -->\Hnewline
134        <div class="topwrap hidden"><a class="top hidden" href="\#">Top</a></div>\Hnewline
135      </div>\Hnewline
136    </div>\Hnewline
137  </div> <!-- /.wrap -->\Hnewline\Hnewline
138  <footer>\Hnewline
139    <p class="legalstuff">\Hnewline
140        <a href="/legal.html">Legal Details</a>\Hnewline
141    </p>\Hnewline
142  </footer>\Hnewline\Hnewline
143  <!-- Bootstrap core JavaScript\Hnewline
144  ================================================== -->\Hnewline
145  <!-- Placed at the end of the document so the pages load faster -->\Hnewline\Hnewline
146  <!-- jQuery (necessary for Bootstrap's JavaScript plugins) -->\Hnewline
147  <script src="../js/jquery.min.js"></script>\Hnewline\Hnewline
148  <!-- Include all compiled plugins (below), or include individual files as needed -->\Hnewline
149  <script src="../js/bootstrap.min.js"></script>\Hnewline
150  <script src="../js/offcanvas.js"></script>\Hnewline\Hnewline
151  <script src="../js/jquery.cookie.js" type="text/javascript"></script>\Hnewline
152  <script src="../js/tbi_base.js" type="text/javascript"></script>\Hnewline
153  <script src="../js/tbi_bootstrap.js" type="text/javascript"></script>
154  }
155}
156
157% Translate \textbf, \textit, \texttt, and \emph directives into
158% <b>, <em>, <code>, and <em>
159\Configure{textbf}{\ifvmode\ShowPar\fi\HCode{<b>}}{\HCode{</b>}}
160\Configure{textit}{\ifvmode\ShowPar\fi\HCode{<i>}}{\HCode{</i>}}
161\Configure{texttt}{\ifvmode\ShowPar\fi\HCode{<code>}}{\HCode{</code>}}
162\Configure{emph}{\ifvmode\ShowPar\fi\HCode{<em>}}{\HCode{</em>}}
163
164
165% Translate verbatim and lstlisting blocks into <pre> elements
166\ScriptEnv{verbatim}
167  {\IgnorePar\EndP\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{<pre class="commands">}\NoFonts}
168  {\egroup\IgnorePar\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{</pre>}\egroup\EndNoFonts}
169%\ScriptEnv{Verbatim}
170%  {}
171%  {}
172\ScriptEnv{lstlisting}
173  {\IgnorePar\EndP\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{<pre><code>}\NoFonts}
174  {\egroup\IgnorePar\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{</code></pre>}\egroup\EndNoFonts}
175
176%\HAssign\fancyvrbNo=0
177\Configure{fancyvrb}
178    {\IgnorePar \EndP \gHAssign\fancyvrbCnt 0 }
179    {\EndP}
180    {\gHAdvance\fancyvrbCnt by 1 \ifnum \fancyvrbCnt > 1 \HCode{<br />}\fi}
181    {}
182    {}{}
183
184\ConfigureEnv{VerbatimExample}
185  {\IgnorePar\EndP\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{<div class="tbi-example"><p><samp>}\NoFonts}
186  {\egroup\IgnorePar\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{</samp></p></div>}\egroup\EndNoFonts}
187  {}
188  {}
189
190\ConfigureEnv{VerbatimTask}
191  {\IgnorePar\EndP\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{<div class="tbi-example tbi-task"><p><samp>}\NoFonts}
192  {\egroup\IgnorePar\nobreak\vfil\penalty0\vfilneg\vtop\bgroup\HCode{</samp></p></div>}\egroup\EndNoFonts}
193  {}
194  {}
195
196\Configure{newline}{\HCode{<br>}}
197%\Configure{Link}
198%  {a} % replaces a
199%  {href=} % replaces href=
200%  {name=} % replaces name=
201%  {}  % replaces '#'
202
203% Do not set `indent`/`noindent` classes on paragraphs
204\Configure{HtmlPar}
205{\EndP\Tg<p>}
206{\EndP\Tg<p>}
207{\HCode{</p>\Hnewline}}
208{\HCode{</p>\Hnewline}}
209
210\Configure{section}
211   {\EndP\IgnorePar\Tg<section id="sec\thesection">}
212   {\EndP\Tg</section>}
213   {\Tg<h2>}
214   {\Tg</h2>\ShowPar}
215
216\Configure{subsection}
217   {\EndP\IgnorePar\Tg<div id="sec\thesubsection">}
218   {\EndP\Tg</div>}
219   {\Tg<h3>}
220   {\Tg</h3>\ShowPar}
221
222\Configure{subsubsection}
223   {\EndP\IgnorePar\Tg<div id="sec\thesubsubsection">}
224   {\EndP\Tg</div>}
225   {\Tg<b>}
226   {\HCode{</b><br>}\ShowPar}
227
228\ConfigureList{itemize}
229  {\EndP\HCode{<ul class="list-group">}\let\endItem=\empty}
230  {\ifvmode \IgnorePar\fi  \EndP\HCode{</li></ul>}\ShowPar}
231  {\endItem \def\endItem{\EndP\Tg</li>}\HCode{<li class="list-group-item">} \DeleteMark}
232  {}
233
234\ConfigureList{enumerate}
235  {\EndP\HCode{<ol class="list-group">}\let\endItem=\empty}
236  {\ifvmode \IgnorePar\fi  \EndP\HCode{</li></ol>}\ShowPar}
237  {\endItem \def\endItem{\EndP\Tg</li>}\HCode{<li class="list-group-item">} \DeleteMark}
238  {}
239
240\Configure{graphics*}
241    {eps}
242    {\Needs{"convert -trim +repage -density 200x200 -geometry 25\% -transparent '\#FFFFFF' \csname Gin@base\endcsname.eps \csname Gin@base\endcsname.png"}
243    \Picture[pict]{\csname Gin@base\endcsname.png}}
244\Configure{graphics*}
245    {ps}
246    {\Needs{"convert -trim +repage -density 200x200 -geometry 25\% -transparent '\#FFFFFF' \csname Gin@base\endcsname.ps \csname Gin@base\endcsname.png"}
247    \Picture[pict]{\csname Gin@base\endcsname.png}}
248
249%\Configure{tabular}
250%   {\HCode{<table class='table'>}}
251%   {\HCode{</tbody></table>}}
252%   {\ifnum \HRow=1 \HCode{<thead><tr>} \else \HCode{<tr>} \fi}
253%   {\ifnum \HRow=1 \HCode{</tr><tbody>} \else \HCode{</tr>} \fi}
254%   {\ifnum \HRow=1 \HCode{<th>} \else \HCode{<td colspan="\HMultispan">} \fi}
255%   {\ifnum \HRow=1 \HCode{</th>} \else \HCode{</td>} \fi}
256%
257\Configure{hline} {}
258
259\ConfigureEnv{titlepage} {\HCode{<div class='titlepage'>}} {\HCode{</div>}} {} {}
260
261\begin{document}
262
263\Configure{tableofcontents}
264  {}
265  {\tocNesting{0}}
266  {}
267  {}
268  {}
269\HAssign\IdTOC=0
270\HAssign\IdTOCsub=0
271
272\ConfigureToc{section}
273      {}
274      {\tocNesting{1}\HAssign \IdTOCsub=0 \HAdvance \IdTOC by 1 \HCode{<li class="has-subnav"><a href="\#sec\IdTOC">}}
275      {}
276      {\HCode{</a>}}
277
278\ConfigureToc{subsection}
279      {}
280      {\tocNesting{2}\HAdvance \IdTOCsub by 1 \HCode{<li><a href="\#sec\IdTOC.\IdTOCsub">}}
281      {}
282      {\HCode{</a>}}
283
284\ConfigureToc{subsubsection}{}{}{}{}
285
286\Configure{TocLink}{#4}
287
288%\ConfigureToc{section}
289%      {}
290%      {\gHAdvance \IdTOC by 1 \HCode{Items[\IdTOC]=["}}
291%      {}
292%      {\HCode{"]\Hnewline}}
293
294%\Configure{TocLink}{\HCode{"\##2","#4"}}
295
296%\ConfigureToc{section}
297%  {\HCode{<li>}}
298%  {}
299%  {}
300%  {\HCode{</li>\Hnewline}}
301
302%\ConfigureToc{subsection}
303%  {\HCode{<ul class="nav sidenav-tbi subnav">}}
304%  {}
305%  {}
306%  {\HCode{</ul>}}
307
308%\ConfigureToc{section}
309%      {\tocNesting{1}\HCode{<li class="has-subnav">}}{ }{}{}
310
311
312%\ConfigureToc{subsection}
313%      {\tocNesting{2}\HCode{<li>}}{ }{}{\HCode{</li>}}
314%\ConfigureToc{subsubsection}
315%      {\tocNesting{3}\HCode{<li>}}{ }{}{ }
316%\Configure{tableofcontents}
317%      {} {\tocNesting{0}} {} {} {}
318
319%\Configure{TocLink}{\Link{#2}{#3}#4\EndLink}
320
321\newcount\c
322  \def\tocNesting#1{%
323     \expandafter\ifx \csname level#1\endcsname\relax
324         \ifnum #1=2 \HCode{<ul class="nav sidenav-tbi subnav hide">} \else \ifnum #1>0 \HCode{<ul id="sidebarNavList" class="nav sidenav-tbi">} \fi \fi
325         \expandafter\def \csname level#1\endcsname{\HCode{</ul>}}
326     \fi
327     \c=#1 \advance\c by 1
328     \loop
329       \csname level\the\c\endcsname
330       \expandafter\let \csname level\the\c\endcsname\relax
331       \advance\c by 1
332     \ifnum \c<10   \repeat
333  }
334
335\def\hlink#1#2{\Tg<a href="#1">#2\Tg</a>\xspace}
336
337\EndPreamble
338