Commit c0c18d7c authored by RomainFeron's avatar RomainFeron
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Finished first major doc update

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<p><a class="el" href="structMapResults.html" title="MapResults struct. ">MapResults</a> struct.
<p><a class="el" href="structMapResults.html" title="MapResults struct.">MapResults</a> struct.
<a href="structMapResults.html#details">More...</a></p>
<p><code>#include &lt;<a class="el" href="map_8h_source.html">map.h</a>&gt;</code></p>
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<div class="textblock"><p><a class="el" href="structMapResults.html" title="MapResults struct. ">MapResults</a> struct. </p>
<div class="textblock"><p><a class="el" href="structMapResults.html" title="MapResults struct.">MapResults</a> struct. </p>
<p>Store results for the "map" analysis. </p>
<p class="definition">Definition at line <a class="el" href="map_8h_source.html#l00062">62</a> of file <a class="el" href="map_8h_source.html">map.h</a>.</p>
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<p><a class="el" href="structParameters.html" title="Parameters. ">Parameters</a>.
<p><a class="el" href="structParameters.html" title="Parameters.">Parameters</a>.
<a href="structParameters.html#details">More...</a></p>
<p><code>#include &lt;<a class="el" href="parameters_8h_source.html">parameters.h</a>&gt;</code></p>
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<p>Store the value of all RADSex parameters. </p>
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<p><a class="el" href="structSignifResults.html" title="SignifResults struct. ">SignifResults</a> struct.
<p><a class="el" href="structSignifResults.html" title="SignifResults struct.">SignifResults</a> struct.
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<p><code>#include &lt;<a class="el" href="signif_8h_source.html">signif.h</a>&gt;</code></p>
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<p>Store results for the "signif" analysis. </p>
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<p>Implements the <a class="el" href="classSubset.html" title="Implements the &quot;subset&quot; analysis. ">Subset</a> class.
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<a href="subset_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span>&#160;<span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span>&#160;<span class="comment">* Copyright (C) 2020 Romain Feron</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span>&#160;<span class="comment">* This file is part of RADSex.</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span>&#160;<span class="comment">* RADSex is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span>&#160;<span class="comment">* it under the terms of the GNU General Public License as published by</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span>&#160;<span class="comment">* the Free Software Foundation, either version 3 of the License, or</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span>&#160;<span class="comment">* (at your option) any later version.</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span>&#160;<span class="comment">* RADSex is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span>&#160;<span class="comment">* but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span>&#160;<span class="comment">* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>&#160;<span class="comment">* GNU General Public License for more details.</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>&#160;<span class="comment">* You should have received a copy of the GNU General Public License</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>&#160;<span class="comment">* along with RADSex. If not, see &lt;https://www.gnu.org/licenses/&gt;.</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>&#160;<span class="comment">*/</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>&#160;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="subset_8h.html">subset.h</a>&quot;</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>&#160;</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>&#160;</div><div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="classSubset.html#a935a07811cb720682e7b9a6435dd744e"> 27</a></span>&#160;<span class="keywordtype">void</span> <a class="code" href="classSubset.html#a935a07811cb720682e7b9a6435dd744e">Subset::extra_setup</a>() {</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>&#160;</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>&#160; this-&gt;<a class="code" href="classSubset.html#a58e930ceeaba63f8ab8bdf870aa3e6cf">output_file</a> = <a class="code" href="utils_8h.html#ab33b713fe0754a5f7729a22cedc0fa9b">open_output</a>(<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a9cb286258590de65042051e194654fdc">output_file_path</a>);</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>&#160; <span class="keywordflow">if</span> (not <a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">output_fasta</a>) this-&gt;<a class="code" href="classSubset.html#a58e930ceeaba63f8ab8bdf870aa3e6cf">output_file</a> &lt;&lt; <a class="code" href="utils_8h.html#ac5169aeb75bd397c83c20b965cfdbfc6">print_list</a>(this-&gt;<a class="code" href="classAnalysis.html#a3b9bc8b0dcc0ecea11d3a12969397ba7">markers_table</a>.<a class="code" href="classMarkersTable.html#a355de34437483f69d063ebae100a8089">header</a>.<a class="code" href="classHeader.html#a3e5bb0f13d849e5635a0731f13ae58fd">header</a>, <span class="stringliteral">&quot;\t&quot;</span>) &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>&#160;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>&#160;}</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>&#160;</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>&#160;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>&#160;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>&#160;</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>&#160;</div><div class="line"><a name="l00038"></a><span class="lineno"><a class="line" href="classSubset.html#a546e6785585f2c3b25f8f1d53ac80cdf"> 38</a></span>&#160;<span class="keywordtype">void</span> <a class="code" href="classSubset.html#a546e6785585f2c3b25f8f1d53ac80cdf">Subset::process_marker</a>(<a class="code" href="classMarker.html">Marker</a>&amp; marker) {</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>&#160;</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>&#160; <span class="keywordflow">if</span> (marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">group1</a>] &gt;= this-&gt;parameters.subset_min_group1 and marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">group1</a>] &lt;= this-&gt;parameters.subset_max_group1 and</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>&#160; marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">group2</a>] &gt;= this-&gt;parameters.subset_min_group2 and marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">group2</a>] &lt;= this-&gt;parameters.subset_max_group2 and</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>&#160; marker.<a class="code" href="classMarker.html#a3dbbb17e3bd5a194b879d983714b04b2">n_individuals</a> &gt;= this-&gt;parameters.subset_min_individuals and marker.<a class="code" href="classMarker.html#a3dbbb17e3bd5a194b879d983714b04b2">n_individuals</a> &lt;= this-&gt;parameters.subset_max_individuals) {</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>&#160;</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>&#160; marker.<a class="code" href="classMarker.html#ae4685d12aeaed673dc151a561af85db6">p</a> = <a class="code" href="stats_8cpp.html#a748519ef79463c2bc861ef5f2f950cd0">get_p_association</a>(marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">group1</a>], marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">group2</a>], this-&gt;popmap.get_count(<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">group1</a>), this-&gt;<a class="code" href="classAnalysis.html#a964cb61cb6b983aefe7fb2f272d1a330">popmap</a>.<a class="code" href="classPopmap.html#a84116d0a16650cde1b7d4bca949b81c6">get_count</a>(<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">group2</a>));</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>&#160;</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>&#160; this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">output_fasta</a> ? marker.<a class="code" href="classMarker.html#ac00868d8b7876c3bd7e71857d7823608">output_as_fasta</a>(this-&gt;<a class="code" href="classSubset.html#a58e930ceeaba63f8ab8bdf870aa3e6cf">output_file</a>, this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#ab362fca31d273c139ca30abdf9d2966e">min_depth</a>) : marker.<a class="code" href="classMarker.html#a7a77022130f28fcbe6243a3dcd29ecb8">output_as_table</a>(this-&gt;<a class="code" href="classSubset.html#a58e930ceeaba63f8ab8bdf870aa3e6cf">output_file</a>);</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>&#160;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>&#160; }</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>&#160;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>&#160;}</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>&#160;</div><div class="ttc" id="classMarker_html_a7a77022130f28fcbe6243a3dcd29ecb8"><div class="ttname"><a href="classMarker.html#a7a77022130f28fcbe6243a3dcd29ecb8">Marker::output_as_table</a></div><div class="ttdeci">void output_as_table(std::ofstream &amp;output_file) const</div><div class="ttdoc">Output a marker in table format. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8cpp_source.html#l00056">marker.cpp:56</a></div></div>
<div class="ttc" id="structParameters_html_aebb77195a9b4edb3f37df32bec3d9eba"><div class="ttname"><a href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">Parameters::group2</a></div><div class="ttdeci">std::string group2</div><div class="ttdoc">Name of the secondfirst group for analysis comparing two groups. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00050">parameters.h:50</a></div></div>
<div class="ttc" id="classMarker_html"><div class="ttname"><a href="classMarker.html">Marker</a></div><div class="ttdoc">Marker class. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00037">marker.h:37</a></div></div>
<div class="ttc" id="classAnalysis_html_a964cb61cb6b983aefe7fb2f272d1a330"><div class="ttname"><a href="classAnalysis.html#a964cb61cb6b983aefe7fb2f272d1a330">Analysis::popmap</a></div><div class="ttdeci">Popmap popmap</div><div class="ttdoc">Popmap instance storing group for each individual. </div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00059">analysis.h:59</a></div></div>
<div class="ttc" id="classMarker_html_a3dbbb17e3bd5a194b879d983714b04b2"><div class="ttname"><a href="classMarker.html#a3dbbb17e3bd5a194b879d983714b04b2">Marker::n_individuals</a></div><div class="ttdeci">uint n_individuals</div><div class="ttdoc">Total number of individuals in which the marker is present. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00045">marker.h:45</a></div></div>
<div class="ttc" id="classAnalysis_html_a3b9bc8b0dcc0ecea11d3a12969397ba7"><div class="ttname"><a href="classAnalysis.html#a3b9bc8b0dcc0ecea11d3a12969397ba7">Analysis::markers_table</a></div><div class="ttdeci">MarkersTable markers_table</div><div class="ttdoc">Markers table instance implementing the markers table parser and markers queue. </div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00060">analysis.h:60</a></div></div>
<div class="ttc" id="classSubset_html_a546e6785585f2c3b25f8f1d53ac80cdf"><div class="ttname"><a href="classSubset.html#a546e6785585f2c3b25f8f1d53ac80cdf">Subset::process_marker</a></div><div class="ttdeci">void process_marker(Marker &amp;marker)</div><div class="ttdoc">Process a single marker. </div><div class="ttdef"><b>Definition:</b> <a href="subset_8cpp_source.html#l00038">subset.cpp:38</a></div></div>
<div class="ttc" id="classPopmap_html_a84116d0a16650cde1b7d4bca949b81c6"><div class="ttname"><a href="classPopmap.html#a84116d0a16650cde1b7d4bca949b81c6">Popmap::get_count</a></div><div class="ttdeci">uint get_count(const std::string &amp;group) const</div><div class="ttdoc">Get individual count for a group. </div><div class="ttdef"><b>Definition:</b> <a href="popmap_8cpp_source.html#l00117">popmap.cpp:117</a></div></div>
<div class="ttc" id="utils_8h_html_ab33b713fe0754a5f7729a22cedc0fa9b"><div class="ttname"><a href="utils_8h.html#ab33b713fe0754a5f7729a22cedc0fa9b">open_output</a></div><div class="ttdeci">std::ofstream open_output(const std::string &amp;output_file_path)</div><div class="ttdoc">Open an output file and check that the file is open properly. </div><div class="ttdef"><b>Definition:</b> <a href="utils_8h_source.html#l00175">utils.h:175</a></div></div>
<div class="ttc" id="structParameters_html_a5da0bb1f08576f6646881a1e4f8b7c25"><div class="ttname"><a href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">Parameters::output_fasta</a></div><div class="ttdeci">bool output_fasta</div><div class="ttdoc">If true, markers are outputted in FASTA format. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00046">parameters.h:46</a></div></div>
<div class="ttc" id="classMarker_html_ac00868d8b7876c3bd7e71857d7823608"><div class="ttname"><a href="classMarker.html#ac00868d8b7876c3bd7e71857d7823608">Marker::output_as_fasta</a></div><div class="ttdeci">void output_as_fasta(std::ofstream &amp;output_file, const uint min_depth) const</div><div class="ttdoc">Output a marker in FASTA format. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8cpp_source.html#l00068">marker.cpp:68</a></div></div>
<div class="ttc" id="utils_8h_html_ac5169aeb75bd397c83c20b965cfdbfc6"><div class="ttname"><a href="utils_8h.html#ac5169aeb75bd397c83c20b965cfdbfc6">print_list</a></div><div class="ttdeci">std::string print_list(const T &amp;list, const std::string &amp;sep=&quot;, &quot;)</div><div class="ttdoc">Print a container as a &quot;sep&quot;-separated string. </div><div class="ttdef"><b>Definition:</b> <a href="utils_8h_source.html#l00281">utils.h:281</a></div></div>
<div class="ttc" id="subset_8h_html"><div class="ttname"><a href="subset_8h.html">subset.h</a></div><div class="ttdoc">Defines the Subset class implementing the &quot;subset&quot; analysis. </div></div>
<div class="ttc" id="structParameters_html_a3ce2dc3d06c4b8f4398fb119931ce88a"><div class="ttname"><a href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">Parameters::group1</a></div><div class="ttdeci">std::string group1</div><div class="ttdoc">Name of the first group for analysis comparing two groups. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00049">parameters.h:49</a></div></div>
<div class="ttc" id="classAnalysis_html_a8abd4de209925cb46571d4db97977d32"><div class="ttname"><a href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">Analysis::parameters</a></div><div class="ttdeci">Parameters parameters</div><div class="ttdoc">Store RADSex parameters. </div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00054">analysis.h:54</a></div></div>
<div class="ttc" id="classMarker_html_a6c79b442c33bf8de73d2f2c081347e2a"><div class="ttname"><a href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">Marker::group_counts</a></div><div class="ttdeci">std::unordered_map&lt; std::string, uint &gt; group_counts</div><div class="ttdoc">Map storing group counts for the marker {group -&gt; number of individuals in which the marker is presen...</div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00044">marker.h:44</a></div></div>
<div class="ttc" id="classMarker_html_ae4685d12aeaed673dc151a561af85db6"><div class="ttname"><a href="classMarker.html#ae4685d12aeaed673dc151a561af85db6">Marker::p</a></div><div class="ttdeci">float p</div><div class="ttdoc">P-value of association with group. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00046">marker.h:46</a></div></div>
<div class="ttc" id="classSubset_html_a58e930ceeaba63f8ab8bdf870aa3e6cf"><div class="ttname"><a href="classSubset.html#a58e930ceeaba63f8ab8bdf870aa3e6cf">Subset::output_file</a></div><div class="ttdeci">std::ofstream output_file</div><div class="ttdoc">Output file stream. </div><div class="ttdef"><b>Definition:</b> <a href="subset_8h_source.html#l00090">subset.h:90</a></div></div>
<div class="ttc" id="structParameters_html_ab362fca31d273c139ca30abdf9d2966e"><div class="ttname"><a href="structParameters.html#ab362fca31d273c139ca30abdf9d2966e">Parameters::min_depth</a></div><div class="ttdeci">uint min_depth</div><div class="ttdoc">Minimum depth to consider a marker present in an individual. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00054">parameters.h:54</a></div></div>
<div class="ttc" id="stats_8cpp_html_a748519ef79463c2bc861ef5f2f950cd0"><div class="ttname"><a href="stats_8cpp.html#a748519ef79463c2bc861ef5f2f950cd0">get_p_association</a></div><div class="ttdeci">double get_p_association(uint n_group1, uint n_group2, uint total_group1, uint total_group2)</div><div class="ttdoc">Compute the p-value of association with group with a Chi-squared test. </div><div class="ttdef"><b>Definition:</b> <a href="stats_8cpp_source.html#l00065">stats.cpp:65</a></div></div>
<div class="ttc" id="classSubset_html_a935a07811cb720682e7b9a6435dd744e"><div class="ttname"><a href="classSubset.html#a935a07811cb720682e7b9a6435dd744e">Subset::extra_setup</a></div><div class="ttdeci">void extra_setup()</div><div class="ttdoc">Extra setup steps. </div><div class="ttdef"><b>Definition:</b> <a href="subset_8cpp_source.html#l00027">subset.cpp:27</a></div></div>
<div class="ttc" id="structParameters_html_a9cb286258590de65042051e194654fdc"><div class="ttname"><a href="structParameters.html#a9cb286258590de65042051e194654fdc">Parameters::output_file_path</a></div><div class="ttdeci">std::string output_file_path</div><div class="ttdoc">Path to the output file for any analysis. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00042">parameters.h:42</a></div></div>
<div class="ttc" id="classHeader_html_a3e5bb0f13d849e5635a0731f13ae58fd"><div class="ttname"><a href="classHeader.html#a3e5bb0f13d849e5635a0731f13ae58fd">Header::header</a></div><div class="ttdeci">std::vector&lt; std::string &gt; header</div><div class="ttdoc">Vector storing all the fields in the markers table&amp;#39;s header. </div><div class="ttdef"><b>Definition:</b> <a href="markers__table_8h_source.html#l00049">markers_table.h:49</a></div></div>