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Fix documentation building #823

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merged 2 commits into from Jul 21, 2016
Merged

Fix documentation building #823

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37a4d1e
only align to '_' if there is one in the function
satta Jul 21, 2016
1157ab1
update documentation
satta Jul 21, 2016
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5 changes: 4 additions & 1 deletion gtdata/modules/gtdoclib/docvisitorlatex.lua
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Expand Up @@ -131,7 +131,10 @@ function DocVisitorLaTeX:visit_method(desc)
else
name = trim(desc.name)
end
local aligncol = string.find(name, '_') - 1
local aligncol = string.len(name) + 1
if string.find(name, '_') then
aligncol = string.find(name, '_') - 1
end
if desc.args then
args = align(trim(desc.args),aligncol)
else
Expand Down
77 changes: 43 additions & 34 deletions www/genometools.org/htdocs/docs.html
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Expand Up @@ -143,81 +143,81 @@ <h2>Sole functions</h2>
Reload <code>gt</code> module.
</p>
<hr>
<a name="export"></a>
<a name="features_contain_marked"></a>

<code> export()</code>
<code> features_contain_marked(features)</code>
<p>
Export the content of <code>gt</code> table to the global environment.
Returns true if the given array of <code>features</code> contains a marked feature, false otherwise.
</p>
<hr>
<a name="display"></a>
<a name="features_show"></a>

<code> display(filename)</code>
<code> features_show(features)</code>
<p>
Call external 'display' program for file <code>filename</code>.
Print the given array of <code>features</code> to stdout.
</p>
<hr>
<a name="show_table"></a>
<a name="features_get_marked"></a>

<code> show_table(tbl)</code>
<code> features_get_marked(features)</code>
<p>
Show all keys and values of table <code>tbl</code>.
Return all marked <code>features</code> (an array) as an array or nil if <code>features</code> contains no marked features.
</p>
<hr>
<a name="show"></a>
<a name="features_show_marked"></a>

<code> show(all)</code>
<code> features_show_marked(features)</code>
<p>
Show content of the <code>gt</code> table.
Print all marked <code>features</code> (an array) to stdout.
</p>
<hr>
<a name="re"></a>
<a name="features_mRNAs2genes"></a>

<code> re()</code>
<code> features_mRNAs2genes(in_features)</code>
<p>
Reload the <code>gt</code> module and export its content to the global environment.
Return an array of genome features which contains a separate gene feature for each mRNA in <code>in_features</code>.
</p>
<hr>
<a name="features_contain_marked"></a>
<a name="features_extract_sequences"></a>

<code> features_contain_marked(features)</code>
<code> features_extract_sequences(features, type, join, region_mapping)</code>
<p>
Returns true if the given array of <code>features</code> contains a marked feature, false otherwise.
Return an array with the sequences of the given features.
</p>
<hr>
<a name="features_show"></a>
<a name="export"></a>

<code> features_show(features)</code>
<code> export()</code>
<p>
Print the given array of <code>features</code> to stdout.
Export the content of <code>gt</code> table to the global environment.
</p>
<hr>
<a name="features_get_marked"></a>
<a name="display"></a>

<code> features_get_marked(features)</code>
<code> display(filename)</code>
<p>
Return all marked <code>features</code> (an array) as an array or nil if <code>features</code> contains no marked features.
Call external 'display' program for file <code>filename</code>.
</p>
<hr>
<a name="features_show_marked"></a>
<a name="show_table"></a>

<code> features_show_marked(features)</code>
<code> show_table(tbl)</code>
<p>
Print all marked <code>features</code> (an array) to stdout.
Show all keys and values of table <code>tbl</code>.
</p>
<hr>
<a name="features_mRNAs2genes"></a>
<a name="show"></a>

<code> features_mRNAs2genes(in_features)</code>
<code> show(all)</code>
<p>
Return an array of genome features which contains a separate gene feature for each mRNA in <code>in_features</code>.
Show content of the <code>gt</code> table.
</p>
<hr>
<a name="features_extract_sequences"></a>
<a name="re"></a>

<code> features_extract_sequences(features, type, join, region_mapping)</code>
<code> re()</code>
<p>
Return an array with the sequences of the given features.
Reload the <code>gt</code> module and export its content to the global environment.
</p>
<hr>
<a name="Alphabet"></a>
Expand Down Expand Up @@ -1000,6 +1000,13 @@ <h2>Class RegionMapping</h2>
Returns a new region mapping which maps everything onto sequence file <code>seqfile</code>.
</p>
<hr>
<a name="region_mapping:get_sequence"></a>

<code> region_mapping:get_sequence(seqid, start, end)</code>
<p>
Use <code>region_mapping</code> to extract the sequence from <code>start</code> to <code>end</code> of the given sequence ID <code>seqid</code>.
</p>
<hr>
<a name="RegionNode"></a>
<h2>Class RegionNode</h2>
<a name="region_node_new"></a>
Expand Down Expand Up @@ -1339,6 +1346,8 @@ <h2>Index</h2>

<a href="#re"><code>re</code></a><br>

<a href="#region_mapping:get_sequence"><code>region_mapping:get_sequence</code></a><br>

<a href="#region_mapping_new_seqfile"><code>region_mapping_new_seqfile</code></a><br>

<a href="#region_node_new"><code>region_node_new</code></a><br>
Expand Down Expand Up @@ -1378,7 +1387,7 @@ <h2>Index</h2>
<div id="footer">
Copyright &copy; 2008-2016
The <i>GenomeTools</i> authors.
Last update: 2016-04-12
Last update: 2016-07-21
</div>
</div>
<!-- Piwik -->
Expand Down
20 changes: 10 additions & 10 deletions www/genometools.org/htdocs/libgenometools.html
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Expand Up @@ -371,6 +371,15 @@ <h2>Sole functions</h2>
<code>dest_type</code>. The duplicated features does not inherit the children.
</p>
<hr>
<a name="GtTrackSelectorFunc"></a>

<code>void GtTrackSelectorFunc(GtBlock*, GtStr*, void*)</code>
<p>
A <code>GtTrackSelectorFunc</code> is a callback function which sets a <code>GtStr</code> to a
string to be used as a track identifier for assignment of a <code>GtBlock</code>
to a given track.
</p>
<hr>
<a name="GtTrackOrderingFunc"></a>

<code>int GtTrackOrderingFunc(const char *s1, const char *s2, void *data)</code>
Expand All @@ -382,15 +391,6 @@ <h2>Sole functions</h2>
ordering of <code>s1</code> and <code>s2</code>.
</p>
<hr>
<a name="GtTrackSelectorFunc"></a>

<code>void GtTrackSelectorFunc(GtBlock*, GtStr*, void*)</code>
<p>
A <code>GtTrackSelectorFunc</code> is a callback function which sets a <code>GtStr</code> to a
string to be used as a track identifier for assignment of a <code>GtBlock</code>
to a given track.
</p>
<hr>
<a name="GtAddIntronsStream"></a>
<h2>Class GtAddIntronsStream</h2>

Expand Down Expand Up @@ -12076,7 +12076,7 @@ <h2>Index</h2>
<div id="footer">
Copyright &copy; 2008-2016
The <i>GenomeTools</i> authors.
Last update: 2016-04-12
Last update: 2016-07-21
</div>
</div>
<!-- Piwik -->
Expand Down
8 changes: 8 additions & 0 deletions www/genometools.org/htdocs/tools/gt_seed_extend.html
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Expand Up @@ -177,6 +177,14 @@ <h2 id="_description">DESCRIPTION</h2>
</p>
</dd>
<dt class="hdlist1">
<strong>-kmerfile</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
Use pre-calculated k-mers from file (if exist) (default: yes)
</p>
</dd>
<dt class="hdlist1">
<strong>-v</strong> [<em>yes|no</em>]
</dt>
<dd>
Expand Down