Commit 4c5b2647 authored by RomainFeron's avatar RomainFeron
Browse files

Updated doc files

parent 1677244e
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SOURCEDIR = .
BUILDDIR = _build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
......@@ -32,19 +32,19 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = "My Project"
PROJECT_NAME = "RADSex"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER =
PROJECT_NUMBER = 1.0.0
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF =
PROJECT_BRIEF = "RAD-Sequencing analysis pipeline for sex determination"
# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
# in the documentation. The maximum height of the logo should not exceed 55
......@@ -58,7 +58,7 @@ PROJECT_LOGO =
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = doxygen
OUTPUT_DIRECTORY =
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
......@@ -473,13 +473,13 @@ EXTRACT_ALL = NO
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = NO
EXTRACT_PRIVATE = YES
# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
# methods of a class will be included in the documentation.
# The default value is: NO.
EXTRACT_PRIV_VIRTUAL = NO
EXTRACT_PRIV_VIRTUAL = YES
# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
# scope will be included in the documentation.
......@@ -491,7 +491,7 @@ EXTRACT_PACKAGE = NO
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = NO
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO,
......@@ -829,7 +829,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = ../src
INPUT = ../../src
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
......@@ -1039,7 +1039,7 @@ USE_MDFILE_AS_MAINPAGE =
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = NO
SOURCE_BROWSER = YES
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
......@@ -1058,7 +1058,7 @@ STRIP_CODE_COMMENTS = YES
# entity all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = NO
REFERENCED_BY_RELATION = YES
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
......@@ -1514,7 +1514,7 @@ DISABLE_INDEX = NO
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = NO
GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
......@@ -1708,7 +1708,7 @@ EXTRA_SEARCH_MAPPINGS =
# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
# The default value is: YES.
GENERATE_LATEX = YES
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
......
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.17"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>RADSex: /home/romain/work/code/RadSex/src/analysis.cpp File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtreedata.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">RADSex
&#160;<span id="projectnumber">1.0.0</span>
</div>
<div id="projectbrief">RAD-Sequencing analysis pipeline for sex determination</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.17 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(document).ready(function(){initNavTree('analysis_8cpp.html',''); initResizable(); });
/* @license-end */
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div class="header">
<div class="headertitle">
<div class="title">analysis.cpp File Reference</div> </div>
</div><!--header-->
<div class="contents">
<p>Implements the <a class="el" href="classAnalysis.html" title="Base class for analyses subclasses.">Analysis</a> base class.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &quot;<a class="el" href="analysis_8h_source.html">analysis.h</a>&quot;</code><br />
</div>
<p><a href="analysis_8cpp_source.html">Go to the source code of this file.</a></p>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Implements the <a class="el" href="classAnalysis.html" title="Base class for analyses subclasses.">Analysis</a> base class. </p>
<p class="definition">Definition in file <a class="el" href="analysis_8cpp_source.html">analysis.cpp</a>.</p>
</div></div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="analysis_8cpp.html">analysis.cpp</a></li>
<li class="footer">Generated by
<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.17 </li>
</ul>
</div>
</body>
</html>
This diff is collapsed.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.17"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>RADSex: /home/romain/work/code/RadSex/src/analysis.h File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtreedata.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">RADSex
&#160;<span id="projectnumber">1.0.0</span>
</div>
<div id="projectbrief">RAD-Sequencing analysis pipeline for sex determination</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.17 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(document).ready(function(){initNavTree('analysis_8h.html',''); initResizable(); });
/* @license-end */
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> </div>
<div class="headertitle">
<div class="title">analysis.h File Reference</div> </div>
</div><!--header-->
<div class="contents">
<p>Defines the <a class="el" href="classAnalysis.html" title="Base class for analyses subclasses.">Analysis</a> base class.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &quot;<a class="el" href="markers__table_8h_source.html">markers_table.h</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="parameters_8h_source.html">parameters.h</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="popmap_8h_source.html">popmap.h</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="utils_8h_source.html">utils.h</a>&quot;</code><br />
</div>
<p><a href="analysis_8h_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classAnalysis.html">Analysis</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Base class for analyses subclasses. <a href="classAnalysis.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Defines the <a class="el" href="classAnalysis.html" title="Base class for analyses subclasses.">Analysis</a> base class. </p>
<p class="definition">Definition in file <a class="el" href="analysis_8h_source.html">analysis.h</a>.</p>
</div></div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="analysis_8h.html">analysis.h</a></li>
<li class="footer">Generated by
<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.17 </li>
</ul>
</div>
</body>
</html>
This diff is collapsed.
......@@ -5,10 +5,14 @@
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.17"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>My Project: Class List</title>
<title>RADSex: Class List</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtreedata.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
......@@ -21,8 +25,10 @@
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">My Project
<div id="projectname">RADSex
&#160;<span id="projectnumber">1.0.0</span>
</div>
<div id="projectbrief">RAD-Sequencing analysis pipeline for sex determination</div>
</td>
</tr>
</tbody>
......@@ -46,6 +52,22 @@ $(function() {
/* @license-end */</script>
<div id="main-nav"></div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(document).ready(function(){initNavTree('annotated.html',''); initResizable(); });
/* @license-end */
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
......@@ -67,23 +89,36 @@ $(function() {
<div class="contents">
<div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory">
<table class="directory">
<tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structAlignedMarker.html" target="_self">AlignedMarker</a></td><td class="desc"></td></tr>
<tr id="row_1_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classCustomFormatter.html" target="_self">CustomFormatter</a></td><td class="desc">Custom CLI11 Formatter </td></tr>
<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structDepthResults.html" target="_self">DepthResults</a></td><td class="desc">DepthsResults struct </td></tr>
<tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structDistribResults.html" target="_self">DistribResults</a></td><td class="desc"><a class="el" href="structDistribResults.html" title="DistribResults struct.">DistribResults</a> struct </td></tr>
<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structInputFile.html" target="_self">InputFile</a></td><td class="desc"></td></tr>
<tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structMarker.html" target="_self">Marker</a></td><td class="desc"></td></tr>
<tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structMarkersQueue.html" target="_self">MarkersQueue</a></td><td class="desc"></td></tr>
<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structParameters.html" target="_self">Parameters</a></td><td class="desc"></td></tr>
<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structPopmap.html" target="_self">Popmap</a></td><td class="desc"></td></tr>
<tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structAlignedMarker.html" target="_self">AlignedMarker</a></td><td class="desc"><a class="el" href="structAlignedMarker.html" title="AlignedMarker struct.">AlignedMarker</a> struct </td></tr>
<tr id="row_1_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classAnalysis.html" target="_self">Analysis</a></td><td class="desc">Base class for analyses subclasses </td></tr>
<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classCustomFormatter.html" target="_self">CustomFormatter</a></td><td class="desc">Custom CLI11 Formatter </td></tr>
<tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classDepth.html" target="_self">Depth</a></td><td class="desc">Implements the "depth" analysis </td></tr>
<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structDepthResults.html" target="_self">DepthResults</a></td><td class="desc"><a class="el" href="structDepthResults.html" title="DepthResults struct.">DepthResults</a> struct </td></tr>
<tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classDistrib.html" target="_self">Distrib</a></td><td class="desc">Implements the "distrib" analysis </td></tr>
<tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structDistribResults.html" target="_self">DistribResults</a></td><td class="desc"><a class="el" href="structDistribResults.html" title="DistribResults struct.">DistribResults</a> struct </td></tr>
<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classFreq.html" target="_self">Freq</a></td><td class="desc">Implements the "freq" analysis </td></tr>
<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classHeader.html" target="_self">Header</a></td><td class="desc"><a class="el" href="classHeader.html" title="Header class.">Header</a> class </td></tr>
<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structInputFile.html" target="_self">InputFile</a></td><td class="desc"><a class="el" href="structInputFile.html" title="InputFile struct.">InputFile</a> struct </td></tr>
<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMap.html" target="_self">Map</a></td><td class="desc">Implements the "map" analysis </td></tr>
<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structMapResults.html" target="_self">MapResults</a></td><td class="desc"><a class="el" href="structMapResults.html" title="MapResults struct.">MapResults</a> struct </td></tr>
<tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMarker.html" target="_self">Marker</a></td><td class="desc"><a class="el" href="classMarker.html" title="Marker class.">Marker</a> class </td></tr>
<tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMarkersTable.html" target="_self">MarkersTable</a></td><td class="desc"><a class="el" href="classMarkersTable.html" title="MarkersTable class.">MarkersTable</a> class </td></tr>
<tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structParameters.html" target="_self">Parameters</a></td><td class="desc"><a class="el" href="structParameters.html" title="Parameters.">Parameters</a> </td></tr>
<tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classPopmap.html" target="_self">Popmap</a></td><td class="desc"><a class="el" href="classPopmap.html" title="Popmap class.">Popmap</a> class </td></tr>
<tr id="row_16_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classSignif.html" target="_self">Signif</a></td><td class="desc">Implements the "signif" analysis </td></tr>
<tr id="row_17_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structSignifResults.html" target="_self">SignifResults</a></td><td class="desc"><a class="el" href="structSignifResults.html" title="SignifResults struct.">SignifResults</a> struct </td></tr>
<tr id="row_18_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classSubset.html" target="_self">Subset</a></td><td class="desc">Implements the "subset" analysis </td></tr>
</table>
</div><!-- directory -->
</div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.17
</small></address>
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="footer">Generated by
<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.17 </li>
</ul>
</div>
</body>
</html>
var annotated_dup =
[
[ "AlignedMarker", "structAlignedMarker.html", "structAlignedMarker" ],
[ "Analysis", "classAnalysis.html", "classAnalysis" ],
[ "CustomFormatter", "classCustomFormatter.html", "classCustomFormatter" ],
[ "Depth", "classDepth.html", "classDepth" ],
[ "DepthResults", "structDepthResults.html", "structDepthResults" ],
[ "Distrib", "classDistrib.html", "classDistrib" ],
[ "DistribResults", "structDistribResults.html", "structDistribResults" ],
[ "Freq", "classFreq.html", "classFreq" ],
[ "Header", "classHeader.html", "classHeader" ],
[ "InputFile", "structInputFile.html", "structInputFile" ],
[ "Map", "classMap.html", "classMap" ],
[ "MapResults", "structMapResults.html", "structMapResults" ],
[ "Marker", "classMarker.html", "classMarker" ],
[ "MarkersTable", "classMarkersTable.html", "classMarkersTable" ],
[ "Parameters", "structParameters.html", "structParameters" ],
[ "Popmap", "classPopmap.html", "classPopmap" ],
[ "Signif", "classSignif.html", "classSignif" ],
[ "SignifResults", "structSignifResults.html", "structSignifResults" ],
[ "Subset", "classSubset.html", "classSubset" ]
];
\ No newline at end of file
......@@ -5,10 +5,14 @@
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.17"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>My Project: /home/romain/work/code/RadSex/src/arg_parser.h File Reference</title>
<title>RADSex: /home/romain/work/code/RadSex/src/arg_parser.h File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtreedata.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
......@@ -21,8 +25,10 @@
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">My Project
<div id="projectname">RADSex
&#160;<span id="projectnumber">1.0.0</span>
</div>
<div id="projectbrief">RAD-Sequencing analysis pipeline for sex determination</div>
</td>
</tr>
</tbody>
......@@ -45,6 +51,23 @@ $(function() {
});
/* @license-end */</script>
<div id="main-nav"></div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(document).ready(function(){initNavTree('arg__parser_8h.html',''); initResizable(); });
/* @license-end */
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
......@@ -59,11 +82,6 @@ $(function() {
</iframe>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> &#124;
......@@ -72,6 +90,9 @@ $(function() {
<div class="title">arg_parser.h File Reference</div> </div>
</div><!--header-->
<div class="contents">
<p>Implements CLI11 overriding classes for CLI parsing.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &lt;iostream&gt;</code><br />
<code>#include &lt;stdio.h&gt;</code><br />
<code>#include &quot;CLI11/CLI11.hpp&quot;</code><br />
......@@ -92,7 +113,11 @@ Functions</h2></td></tr>
<tr class="memdesc:ada75fff12f517de0fbfeb1324100e16b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Print CLI parsing failure message. <a href="arg__parser_8h.html#ada75fff12f517de0fbfeb1324100e16b">More...</a><br /></td></tr>
<tr class="separator:ada75fff12f517de0fbfeb1324100e16b"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<h2 class="groupheader">Function Documentation</h2>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Implements CLI11 overriding classes for CLI parsing. </p>
<p class="definition">Definition in file <a class="el" href="arg__parser_8h_source.html">arg_parser.h</a>.</p>
</div><h2 class="groupheader">Function Documentation</h2>
<a id="ada75fff12f517de0fbfeb1324100e16b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ada75fff12f517de0fbfeb1324100e16b">&#9670;&nbsp;</a></span>failure_message()</h2>
......@@ -138,14 +163,22 @@ Functions</h2></td></tr>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A string containing the error message </dd></dl>
<p class="definition">Definition at line <a class="el" href="arg__parser_8h_source.html#l00044">44</a> of file <a class="el" href="arg__parser_8h_source.html">arg_parser.h</a>.</p>
<p class="reference">Referenced by <a class="el" href="main_8cpp_source.html#l00044">parse_args()</a>.</p>
</div>
</div>
</div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.17
</small></address>