Merge pull request #245 from clara-genomics/update-cpp-docs

[docs] update checked in doxygen docs

docs/cpp/aligner_8hpp_source.html

@@ -22,7 +22,7 @@
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   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">ClaraGenomicsAnalysis
-   &#160;<span id="projectnumber">0.3.0</span>
+   &#160;<span id="projectnumber">0.4.0</span>
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docs/cpp/alignment_8hpp_source.html

@@ -22,7 +22,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">ClaraGenomicsAnalysis
-   &#160;<span id="projectnumber">0.3.0</span>
+   &#160;<span id="projectnumber">0.4.0</span>
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@@ -99,23 +99,25 @@
 <div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">   34</a></span>&#160;<span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">Alignment</a></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;<span class="keyword">public</span>:</div>
-<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::string&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">get_query_sequence</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">~Alignment</a>() = <span class="keywordflow">default</span>;</div>
 <div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160; </div>
-<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::string&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4a61cdee74c32930f49cb878fc17db57">get_target_sequence</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::string&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">get_query_sequence</a>() <span class="keyword">const</span> = 0;</div>
 <div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160; </div>
-<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;    <span class="keyword">virtual</span> std::string <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">convert_to_cigar</a>() <span class="keyword">const</span> = 0;</div>
-<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160; </div>
-<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab22457c02ac00ec205dcd5a75b253881">get_alignment_type</a>() <span class="keyword">const</span> = 0;</div>
-<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160; </div>
-<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">get_status</a>() <span class="keyword">const</span> = 0;</div>
-<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160; </div>
-<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;AlignmentState&gt;&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">get_alignment</a>() <span class="keyword">const</span> = 0;</div>
-<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160; </div>
-<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">FormattedAlignment</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">format_alignment</a>() <span class="keyword">const</span> = 0;</div>
-<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;};</div>
-<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160; </div>
-<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;} <span class="comment">// namespace cudaaligner</span></div>
-<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
+<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::string&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4a61cdee74c32930f49cb878fc17db57">get_target_sequence</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160; </div>
+<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">virtual</span> std::string <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">convert_to_cigar</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160; </div>
+<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab22457c02ac00ec205dcd5a75b253881">get_alignment_type</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160; </div>
+<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">get_status</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160; </div>
+<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;AlignmentState&gt;&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">get_alignment</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160; </div>
+<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">FormattedAlignment</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">format_alignment</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;};</div>
+<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160; </div>
+<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;} <span class="comment">// namespace cudaaligner</span></div>
+<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
 </div><!-- fragment --></div><!-- contents -->
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a7665f284b7929998357c89461e444f78"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">claragenomics::cudaaligner::Alignment::get_status</a></div><div class="ttdeci">virtual StatusType get_status() const =0</div><div class="ttdoc">Return status of alignment.</div></div>
 <div class="ttc" id="agroup__cudaaligner_html_ga228dcdd4bf0cf40c64786cce6b045c40"><div class="ttname"><a href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">claragenomics::cudaaligner::FormattedAlignment</a></div><div class="ttdeci">std::pair&lt; std::string, std::string &gt; FormattedAlignment</div><div class="ttdef"><b>Definition:</b> alignment.hpp:31</div></div>
@@ -124,6 +126,7 @@
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a5139f26517193e077000dcddfbc15f70"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">claragenomics::cudaaligner::Alignment::get_alignment</a></div><div class="ttdeci">virtual const std::vector&lt; AlignmentState &gt; &amp; get_alignment() const =0</div><div class="ttdoc">Get the alignment between sequences.</div></div>
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+<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a6479df67f21d643782abfed873218ea8"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">claragenomics::cudaaligner::Alignment::~Alignment</a></div><div class="ttdeci">virtual ~Alignment()=default</div><div class="ttdoc">Virtual destructor.</div></div>
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_ab29dceafccd3cb0a2e87023c5d48a780"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">claragenomics::cudaaligner::Alignment::get_query_sequence</a></div><div class="ttdeci">virtual const std::string &amp; get_query_sequence() const =0</div><div class="ttdoc">Returns query sequence.</div></div>
 <div class="ttc" id="agroup__cudaaligner_html_gafcccbe51c86f9772ccf837fc433f518b"><div class="ttname"><a href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">claragenomics::cudaaligner::AlignmentType</a></div><div class="ttdeci">AlignmentType</div><div class="ttdoc">AlignmentType - Enum for storing type of alignment.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:36</div></div>
 <div class="ttc" id="agroup__cudaaligner_html_ga7d6424e11f69650b1d4eabef0cf4f602"><div class="ttname"><a href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">claragenomics::cudaaligner::StatusType</a></div><div class="ttdeci">StatusType</div><div class="ttdoc">CUDA Aligner error type.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:25</div></div>