Skip to content

Commit

Permalink
Doxygen doc of C++code
Browse files Browse the repository at this point in the history
  • Loading branch information
GDelevoye committed Oct 29, 2023
1 parent da2b5dc commit c7fc8f0
Show file tree
Hide file tree
Showing 625 changed files with 36,076 additions and 0 deletions.
112 changes: 112 additions & 0 deletions docs/html/CIGAR_8cpp.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,112 @@
<!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" lang="en-US">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=11"/>
<meta name="generator" content="Doxygen 1.9.8"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>My Project: src/lib/CIGAR.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="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 id="projectrow">
<td id="projectalign">
<div id="projectname">My Project
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.9.8 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @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:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */
</script>
<div id="main-nav"></div>
<!-- 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">
<div id="MSearchResults">
<div class="SRPage">
<div id="SRIndex">
<div id="SRResults"></div>
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
</div>
</div>
</div>
</div>

<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_c85d3e3c5052e9ad9ce18c6863244a25.html">lib</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#namespaces">Namespaces</a> &#124;
<a href="#func-members">Functions</a> </div>
<div class="headertitle"><div class="title">CIGAR.cpp File Reference</div></div>
</div><!--header-->
<div class="contents">
<div class="textblock"><code>#include &quot;<a class="el" href="CIGAR_8hpp_source.html">CIGAR.hpp</a>&quot;</code><br />
<code>#include &lt;iostream&gt;</code><br />
<code>#include &lt;string&gt;</code><br />
<code>#include &lt;vector&gt;</code><br />
</div><div class="textblock"><div class="dynheader">
Include dependency graph for CIGAR.cpp:</div>
<div class="dyncontent">
<div class="center"><img src="CIGAR_8cpp__incl.png" border="0" usemap="#asrc_2lib_2CIGAR_8cpp" alt=""/></div>
</div>
</div><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="namespaces" name="namespaces"></a>
Namespaces</h2></td></tr>
<tr class="memitem:namespacecf" id="r_namespacecf"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecf.html">cf</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:a3481ae25b51113b78dd0c221fd6e38fd" id="r_a3481ae25b51113b78dd0c221fd6e38fd"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecf.html#a3481ae25b51113b78dd0c221fd6e38fd">cf::listdigits_to_number</a> (std::vector&lt; int &gt; listdigits)</td></tr>
<tr class="memdesc:a3481ae25b51113b78dd0c221fd6e38fd"><td class="mdescLeft">&#160;</td><td class="mdescRight">From a vector of int [1,4,5,6] (for instance), returns 1456. <br /></td></tr>
<tr class="separator:a3481ae25b51113b78dd0c221fd6e38fd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0c14fc17770cce1509ef587cd952b0a8" id="r_a0c14fc17770cce1509ef587cd952b0a8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcigarfilter__plugin_1_1CIGAR.html">cigarfilter_plugin::CIGAR</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecf.html#a0c14fc17770cce1509ef587cd952b0a8">cf::get_CIGAR</a> (const std::string &amp;inputstring)</td></tr>
<tr class="memdesc:a0c14fc17770cce1509ef587cd952b0a8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the total number of insertions, deletions, etc... In a .sam line. <br /></td></tr>
<tr class="separator:a0c14fc17770cce1509ef587cd952b0a8"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by&#160;<a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.8
</small></address>
</body>
</html>
23 changes: 23 additions & 0 deletions docs/html/CIGAR_8cpp__incl.dot
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
digraph "src/lib/CIGAR.cpp"
{
// LATEX_PDF_SIZE
bgcolor="transparent";
edge [fontname=Helvetica,fontsize=10,labelfontname=Helvetica,labelfontsize=10];
node [fontname=Helvetica,fontsize=10,shape=box,height=0.2,width=0.4];
Node1 [id="Node000001",label="src/lib/CIGAR.cpp",height=0.2,width=0.4,color="gray40", fillcolor="grey60", style="filled", fontcolor="black",tooltip=" "];
Node1 -> Node2 [id="edge1_Node000001_Node000002",color="steelblue1",style="solid",tooltip=" "];
Node2 [id="Node000002",label="CIGAR.hpp",height=0.2,width=0.4,color="grey40", fillcolor="white", style="filled",URL="$CIGAR_8hpp.html",tooltip="Implementation of the CIGAR parsing."];
Node2 -> Node3 [id="edge2_Node000002_Node000003",color="steelblue1",style="solid",tooltip=" "];
Node3 [id="Node000003",label="vector",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node2 -> Node4 [id="edge3_Node000002_Node000004",color="steelblue1",style="solid",tooltip=" "];
Node4 [id="Node000004",label="map",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node2 -> Node5 [id="edge4_Node000002_Node000005",color="steelblue1",style="solid",tooltip=" "];
Node5 [id="Node000005",label="set",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node2 -> Node6 [id="edge5_Node000002_Node000006",color="steelblue1",style="solid",tooltip=" "];
Node6 [id="Node000006",label="cigarfilter_plugin.hpp",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node1 -> Node7 [id="edge6_Node000001_Node000007",color="steelblue1",style="solid",tooltip=" "];
Node7 [id="Node000007",label="iostream",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node1 -> Node8 [id="edge7_Node000001_Node000008",color="steelblue1",style="solid",tooltip=" "];
Node8 [id="Node000008",label="string",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node1 -> Node3 [id="edge8_Node000001_Node000003",color="steelblue1",style="solid",tooltip=" "];
}
135 changes: 135 additions & 0 deletions docs/html/CIGAR_8hpp.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,135 @@
<!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" lang="en-US">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=11"/>
<meta name="generator" content="Doxygen 1.9.8"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>My Project: src/lib/CIGAR.hpp 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="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 id="projectrow">
<td id="projectalign">
<div id="projectname">My Project
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.9.8 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @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:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */
</script>
<div id="main-nav"></div>
<!-- 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">
<div id="MSearchResults">
<div class="SRPage">
<div id="SRIndex">
<div id="SRResults"></div>
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
</div>
</div>
</div>
</div>

<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_c85d3e3c5052e9ad9ce18c6863244a25.html">lib</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#namespaces">Namespaces</a> &#124;
<a href="#func-members">Functions</a> &#124;
<a href="#var-members">Variables</a> </div>
<div class="headertitle"><div class="title">CIGAR.hpp File Reference</div></div>
</div><!--header-->
<div class="contents">

<p>Implementation of the CIGAR parsing.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &lt;vector&gt;</code><br />
<code>#include &lt;map&gt;</code><br />
<code>#include &lt;set&gt;</code><br />
<code>#include &quot;cigarfilter_plugin.hpp&quot;</code><br />
</div><div class="textblock"><div class="dynheader">
Include dependency graph for CIGAR.hpp:</div>
<div class="dyncontent">
<div class="center"><img src="CIGAR_8hpp__incl.png" border="0" usemap="#asrc_2lib_2CIGAR_8hpp" alt=""/></div>
</div>
</div><div class="textblock"><div class="dynheader">
This graph shows which files directly or indirectly include this file:</div>
<div class="dyncontent">
<div class="center"><img src="CIGAR_8hpp__dep__incl.png" border="0" usemap="#asrc_2lib_2CIGAR_8hppdep" alt=""/></div>
</div>
</div>
<p><a href="CIGAR_8hpp_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 id="namespaces" name="namespaces"></a>
Namespaces</h2></td></tr>
<tr class="memitem:namespacecf" id="r_namespacecf"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecf.html">cf</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:a3481ae25b51113b78dd0c221fd6e38fd" id="r_a3481ae25b51113b78dd0c221fd6e38fd"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecf.html#a3481ae25b51113b78dd0c221fd6e38fd">cf::listdigits_to_number</a> (std::vector&lt; int &gt; listdigits)</td></tr>
<tr class="memdesc:a3481ae25b51113b78dd0c221fd6e38fd"><td class="mdescLeft">&#160;</td><td class="mdescRight">From a vector of int [1,4,5,6] (for instance), returns 1456. <br /></td></tr>
<tr class="separator:a3481ae25b51113b78dd0c221fd6e38fd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0c14fc17770cce1509ef587cd952b0a8" id="r_a0c14fc17770cce1509ef587cd952b0a8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcigarfilter__plugin_1_1CIGAR.html">cigarfilter_plugin::CIGAR</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecf.html#a0c14fc17770cce1509ef587cd952b0a8">cf::get_CIGAR</a> (const std::string &amp;inputstring)</td></tr>
<tr class="memdesc:a0c14fc17770cce1509ef587cd952b0a8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the total number of insertions, deletions, etc... In a .sam line. <br /></td></tr>
<tr class="separator:a0c14fc17770cce1509ef587cd952b0a8"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="var-members" name="var-members"></a>
Variables</h2></td></tr>
<tr class="memitem:ae20676cc51b82e5cfad0b3dd136c03d7" id="r_ae20676cc51b82e5cfad0b3dd136c03d7"><td class="memItemLeft" align="right" valign="top">static size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecf.html#ae20676cc51b82e5cfad0b3dd136c03d7">cf::pow10</a> [10]</td></tr>
<tr class="memdesc:ae20676cc51b82e5cfad0b3dd136c03d7"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compilation-time optimization so that we don't compute pows of floats (or double) at runtime. <br /></td></tr>
<tr class="separator:ae20676cc51b82e5cfad0b3dd136c03d7"><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>Implementation of the CIGAR parsing. </p>
<dl class="section warning"><dt>Warning</dt><dd>Contains some hard-coded compile-time optimizations and relies on a correct CIGAR </dd></dl>
<dl class="section author"><dt>Author</dt><dd>DELEVOYE Guillaume </dd></dl>
<dl class="section version"><dt>Version</dt><dd>0.1 </dd></dl>
<dl class="section date"><dt>Date</dt><dd>Nov 2022 </dd></dl>
</div></div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by&#160;<a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.8
</small></address>
</body>
</html>
18 changes: 18 additions & 0 deletions docs/html/CIGAR_8hpp__dep__incl.dot
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
digraph "src/lib/CIGAR.hpp"
{
// LATEX_PDF_SIZE
bgcolor="transparent";
edge [fontname=Helvetica,fontsize=10,labelfontname=Helvetica,labelfontsize=10];
node [fontname=Helvetica,fontsize=10,shape=box,height=0.2,width=0.4];
Node1 [id="Node000001",label="src/lib/CIGAR.hpp",height=0.2,width=0.4,color="gray40", fillcolor="grey60", style="filled", fontcolor="black",tooltip="Implementation of the CIGAR parsing."];
Node1 -> Node2 [id="edge1_Node000001_Node000002",dir="back",color="steelblue1",style="solid",tooltip=" "];
Node2 [id="Node000002",label="src/lib/CIGAR.cpp",height=0.2,width=0.4,color="grey40", fillcolor="white", style="filled",URL="$CIGAR_8cpp.html",tooltip=" "];
Node1 -> Node3 [id="edge2_Node000001_Node000003",dir="back",color="steelblue1",style="solid",tooltip=" "];
Node3 [id="Node000003",label="src/lib/cigarfilter.hpp",height=0.2,width=0.4,color="grey40", fillcolor="white", style="filled",URL="$cigarfilter_8hpp.html",tooltip=" "];
Node3 -> Node4 [id="edge3_Node000003_Node000004",dir="back",color="steelblue1",style="solid",tooltip=" "];
Node4 [id="Node000004",label="src/executable/main.cpp",height=0.2,width=0.4,color="grey40", fillcolor="white", style="filled",URL="$main_8cpp.html",tooltip=" "];
Node1 -> Node5 [id="edge4_Node000001_Node000005",dir="back",color="steelblue1",style="solid",tooltip=" "];
Node5 [id="Node000005",label="src/tests/CIGAR.t.cpp",height=0.2,width=0.4,color="grey40", fillcolor="white", style="filled",URL="$CIGAR_8t_8cpp.html",tooltip=" "];
Node1 -> Node6 [id="edge5_Node000001_Node000006",dir="back",color="steelblue1",style="solid",tooltip=" "];
Node6 [id="Node000006",label="src/tests/examples.t.cpp",height=0.2,width=0.4,color="grey40", fillcolor="white", style="filled",URL="$examples_8t_8cpp.html",tooltip=" "];
}
16 changes: 16 additions & 0 deletions docs/html/CIGAR_8hpp__incl.dot
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
digraph "src/lib/CIGAR.hpp"
{
// LATEX_PDF_SIZE
bgcolor="transparent";
edge [fontname=Helvetica,fontsize=10,labelfontname=Helvetica,labelfontsize=10];
node [fontname=Helvetica,fontsize=10,shape=box,height=0.2,width=0.4];
Node1 [id="Node000001",label="src/lib/CIGAR.hpp",height=0.2,width=0.4,color="gray40", fillcolor="grey60", style="filled", fontcolor="black",tooltip="Implementation of the CIGAR parsing."];
Node1 -> Node2 [id="edge1_Node000001_Node000002",color="steelblue1",style="solid",tooltip=" "];
Node2 [id="Node000002",label="vector",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node1 -> Node3 [id="edge2_Node000001_Node000003",color="steelblue1",style="solid",tooltip=" "];
Node3 [id="Node000003",label="map",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node1 -> Node4 [id="edge3_Node000001_Node000004",color="steelblue1",style="solid",tooltip=" "];
Node4 [id="Node000004",label="set",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
Node1 -> Node5 [id="edge4_Node000001_Node000005",color="steelblue1",style="solid",tooltip=" "];
Node5 [id="Node000005",label="cigarfilter_plugin.hpp",height=0.2,width=0.4,color="grey60", fillcolor="#E0E0E0", style="filled",tooltip=" "];
}
Loading

0 comments on commit c7fc8f0

Please sign in to comment.