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create mode 100644 docs/cpp/search/variables_b.js create mode 100644 docs/cpp/search/variables_c.html create mode 100644 docs/cpp/search/variables_c.js create mode 100644 docs/cpp/structclaragenomics_1_1PairHash-members.html create mode 100644 docs/cpp/structclaragenomics_1_1PairHash.html diff --git a/docs/cpp/aligner_8hpp_source.html b/docs/cpp/aligner_8hpp_source.html index 45cdf5434..fc9179bc9 100644 --- a/docs/cpp/aligner_8hpp_source.html +++ b/docs/cpp/aligner_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/alignment_8hpp_source.html b/docs/cpp/alignment_8hpp_source.html index 619916825..891be90e1 100644 --- a/docs/cpp/alignment_8hpp_source.html +++ b/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 -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -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> <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> {</div> <div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">public</span>:</div> -<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::string& <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>  <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>  </div> -<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::string& <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>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::string& <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>  </div> -<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <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>  </div> -<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <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>  </div> -<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <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>  </div> -<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<AlignmentState>& <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>  </div> -<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <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> };</div> -<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  </div> -<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> } <span class="comment">// namespace cudaaligner</span></div> -<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> } <span class="comment">// namespace claragenomics</span></div> +<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::string& <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>  </div> +<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <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>  </div> +<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <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>  </div> +<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <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>  </div> +<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<AlignmentState>& <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>  </div> +<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <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> };</div> +<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  </div> +<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> } <span class="comment">// namespace cudaaligner</span></div> +<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> } <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< std::string, std::string > 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< AlignmentState > & get_alignment() const =0</div><div class="ttdoc">Get the alignment between sequences.</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_aeb4a583f6fbc643c93170797ca45a876"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">claragenomics::cudaaligner::Alignment::convert_to_cigar</a></div><div class="ttdeci">virtual std::string convert_to_cigar() const =0</div><div class="ttdoc">Converts an alignment to CIGAR format. The is a reduced implementation of the CIGAR standard supporti...</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">claragenomics::cudaaligner::Alignment</a></div><div class="ttdoc">Alignment - Object encapsulating an alignment between 2 string.</div><div class="ttdef"><b>Definition:</b> alignment.hpp:34</div></div> +<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 & 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> diff --git a/docs/cpp/annotated.html b/docs/cpp/annotated.html index 8185be30c..aded9d268 100644 --- a/docs/cpp/annotated.html +++ b/docs/cpp/annotated.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -67,7 +67,7 @@ </div><!--header--> <div class="contents"> <div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory"> -<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span><span onclick="javascript:toggleLevel(4);">4</span>]</div><table class="directory"> +<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span>]</div><table class="directory"> <tr id="row_0_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_0_" class="arrow" onclick="toggleFolder('0_')">▼</span><span class="icona"><span class="icon">N</span></span><b>claragenomics</b></td><td class="desc"></td></tr> <tr id="row_0_0_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span id="arr_0_0_" class="arrow" onclick="toggleFolder('0_0_')">▼</span><span class="icona"><span class="icon">N</span></span><b>cudaaligner</b></td><td class="desc"></td></tr> <tr id="row_0_0_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html" target="_self">Aligner</a></td><td class="desc"></td></tr> @@ -75,19 +75,23 @@ <tr id="row_0_1_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span id="arr_0_1_" class="arrow" onclick="toggleFolder('0_1_')">▼</span><span class="icona"><span class="icon">N</span></span><b>cudamapper</b></td><td class="desc"></td></tr> <tr id="row_0_1_0_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html" target="_self">Anchor</a></td><td class="desc"></td></tr> <tr id="row_0_1_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html" target="_self">ArrayBlock</a></td><td class="desc"></td></tr> -<tr id="row_0_1_2_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span id="arr_0_1_2_" class="arrow" onclick="toggleFolder('0_1_2_')">▼</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" target="_self">Index</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences </td></tr> -<tr id="row_0_1_2_0_" class="even"><td class="entry"><span style="width:64px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html" target="_self">RepresentationToSketchElements</a></td><td class="desc"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html" title="RepresentationToSketchElements - representation, pointer to section of data arrays with sketch elemen...">RepresentationToSketchElements</a> - representation, pointer to section of data arrays with sketch elements with that representation and a given read_id, and a pointer to section of data arrays with sketch elements with that representation and all read_ids </td></tr> -<tr id="row_0_1_3_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html" target="_self">Overlap</a></td><td class="desc"></td></tr> -<tr id="row_0_1_4_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html" target="_self">Overlapper</a></td><td class="desc"></td></tr> -<tr id="row_0_1_5_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html" target="_self">Sequence</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html" title="Sequence - represents an individual read (name, DNA nucleotides etc)">Sequence</a> - represents an individual read (name, DNA nucleotides etc) </td></tr> -<tr id="row_0_1_6_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html" target="_self">SketchElement</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html" title="SketchElement - Contains integer representation, position, direction and read id of a kmer.">SketchElement</a> - Contains integer representation, position, direction and read id of a kmer </td></tr> +<tr id="row_0_1_2_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" target="_self">Index</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences </td></tr> +<tr id="row_0_1_3_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" target="_self">Matcher</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> - base matcher </td></tr> +<tr id="row_0_1_4_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html" target="_self">Overlap</a></td><td class="desc"></td></tr> +<tr id="row_0_1_5_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html" target="_self">Overlapper</a></td><td class="desc"></td></tr> +<tr id="row_0_1_6_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html" target="_self">Sequence</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html" title="Sequence - represents an individual read (name, DNA nucleotides etc)">Sequence</a> - represents an individual read (name, DNA nucleotides etc) </td></tr> +<tr id="row_0_1_7_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html" target="_self">SketchElement</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html" title="SketchElement - Contains integer representation, position, direction and read id of a kmer.">SketchElement</a> - Contains integer representation, position, direction and read id of a kmer </td></tr> <tr id="row_0_2_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span id="arr_0_2_" class="arrow" onclick="toggleFolder('0_2_')">▼</span><span class="icona"><span class="icon">N</span></span><b>cudapoa</b></td><td class="desc"></td></tr> <tr id="row_0_2_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html" target="_self">Batch</a></td><td class="desc"></td></tr> <tr id="row_0_2_1_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html" target="_self">Entry</a></td><td class="desc">A structure to represent a sequence entry </td></tr> <tr id="row_0_3_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span id="arr_0_3_" class="arrow" onclick="toggleFolder('0_3_')">▼</span><span class="icona"><span class="icon">N</span></span><b>io</b></td><td class="desc"></td></tr> <tr id="row_0_3_0_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html" target="_self">FastaParser</a></td><td class="desc"></td></tr> <tr id="row_0_3_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html" target="_self">FastaSequence</a></td><td class="desc">A structure to hold details of a single FASTA entry </td></tr> -<tr id="row_0_4_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1scoped__device__switch.html" target="_self">scoped_device_switch</a></td><td class="desc">A class to switch the CUDA device for the current scope using RAII </td></tr> +<tr id="row_0_4_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1DirectedGraph.html" target="_self">DirectedGraph</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1DirectedGraph.html" title="DirectedGraph Object representing a directed graph structure.">DirectedGraph</a> Object representing a directed graph structure </td></tr> +<tr id="row_0_5_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1Graph.html" target="_self">Graph</a></td><td class="desc">Object representing a generic graph structure </td></tr> +<tr id="row_0_6_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1PairHash.html" target="_self">PairHash</a></td><td class="desc"></td></tr> +<tr id="row_0_7_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1scoped__device__switch.html" target="_self">scoped_device_switch</a></td><td class="desc">A class to switch the CUDA device for the current scope using RAII </td></tr> +<tr id="row_0_8_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1UndirectedGraph.html" target="_self">UndirectedGraph</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html" title="UndirectedGraph Object representing an undirected graph structure.">UndirectedGraph</a> Object representing an undirected graph structure </td></tr> </table> </div><!-- directory --> </div><!-- contents --> diff --git a/docs/cpp/batch_8hpp_source.html b/docs/cpp/batch_8hpp_source.html index 83ed4674b..993ca639a 100644 --- a/docs/cpp/batch_8hpp_source.html +++ b/docs/cpp/batch_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -84,84 +84,90 @@ <div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  </div> <div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <claragenomics/cudapoa/cudapoa.hpp></span></div> <div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  </div> -<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <memory></span></div> -<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include <vector></span></div> -<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include <stdint.h></span></div> -<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <string></span></div> -<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <iostream></span></div> -<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <cuda_runtime_api.h></span></div> -<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  </div> -<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">namespace </span>claragenomics</div> -<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> {</div> -<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  </div> -<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">namespace </span>cudapoa</div> -<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> {</div> -<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  </div> -<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  </div> -<div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html"> 32</a></span> <span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html">Entry</a></div> -<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> {</div> -<div class="line"><a name="l00035"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4"> 35</a></span>  <span class="keyword">const</span> <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">seq</a>;</div> -<div class="line"><a name="l00037"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277"> 37</a></span>  <span class="keyword">const</span> int8_t* <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">weights</a>;</div> -<div class="line"><a name="l00039"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712"> 39</a></span>  int32_t <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712">length</a>;</div> -<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> };</div> -<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  </div> -<div class="line"><a name="l00043"></a><span class="lineno"><a class="line" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32"> 43</a></span> <span class="keyword">typedef</span> std::vector<Entry> <a class="code" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a>;</div> -<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  </div> -<div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudapoa_1_1Batch.html"> 47</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a></div> -<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> {</div> -<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">public</span>:</div> -<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">~Batch</a>() = <span class="keywordflow">default</span>;</div> -<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  </div> -<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">add_poa_group</a>(std::vector<StatusType>& per_seq_status,</div> -<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">const</span> <a class="code" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a>& poa_group) = 0;</div> -<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  </div> -<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keyword">virtual</span> int32_t <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">get_total_poas</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  </div> -<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">generate_poa</a>() = 0;</div> -<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  </div> -<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">get_consensus</a>(std::vector<std::string>& consensus,</div> -<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  std::vector<std::vector<uint16_t>>& coverage,</div> -<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  std::vector<claragenomics::cudapoa::StatusType>& output_status) = 0;</div> -<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  </div> -<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">get_msa</a>(std::vector<std::vector<std::string>>& msa,</div> -<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  std::vector<StatusType>& output_status) = 0;</div> -<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  </div> -<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keyword">virtual</span> int32_t <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">batch_id</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  </div> -<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">reset</a>() = 0;</div> -<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> };</div> -<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  </div> -<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> std::unique_ptr<Batch> <a class="code" href="group__cudapoa.html#ga81951b681c27354e2dbe7933a9f168f3">create_batch</a>(int32_t max_sequences_per_poa,</div> -<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  int32_t device_id,</div> -<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  cudaStream_t stream,</div> -<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordtype">size_t</span> max_mem,</div> -<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  int8_t output_mask,</div> -<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  int16_t gap_score,</div> -<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  int16_t mismatch_score,</div> -<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  int16_t match_score,</div> -<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">bool</span> cuda_banded_alignment);</div> -<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  </div> -<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  </div> -<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> } <span class="comment">// namespace cudapoa</span></div> -<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  </div> -<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> } <span class="comment">// namespace claragenomics</span></div> +<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <claragenomics/utils/graph.hpp></span></div> +<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  </div> +<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include <memory></span></div> +<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <vector></span></div> +<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <stdint.h></span></div> +<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <string></span></div> +<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <iostream></span></div> +<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <cuda_runtime_api.h></span></div> +<div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  </div> +<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keyword">namespace </span>claragenomics</div> +<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> {</div> +<div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  </div> +<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keyword">namespace </span>cudapoa</div> +<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> {</div> +<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  </div> +<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  </div> +<div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html"> 34</a></span> <span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html">Entry</a></div> +<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> {</div> +<div class="line"><a name="l00037"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4"> 37</a></span>  <span class="keyword">const</span> <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">seq</a>;</div> +<div class="line"><a name="l00039"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277"> 39</a></span>  <span class="keyword">const</span> int8_t* <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">weights</a>;</div> +<div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712"> 41</a></span>  int32_t <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712">length</a>;</div> +<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> };</div> +<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  </div> +<div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32"> 45</a></span> <span class="keyword">typedef</span> std::vector<Entry> <a class="code" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a>;</div> +<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  </div> +<div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudapoa_1_1Batch.html"> 49</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a></div> +<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> {</div> +<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">~Batch</a>() = <span class="keywordflow">default</span>;</div> +<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  </div> +<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">add_poa_group</a>(std::vector<StatusType>& per_seq_status,</div> +<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keyword">const</span> <a class="code" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a>& poa_group) = 0;</div> +<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  </div> +<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">virtual</span> int32_t <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">get_total_poas</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  </div> +<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">generate_poa</a>() = 0;</div> +<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  </div> +<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">get_consensus</a>(std::vector<std::string>& consensus,</div> +<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  std::vector<std::vector<uint16_t>>& coverage,</div> +<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  std::vector<claragenomics::cudapoa::StatusType>& output_status) = 0;</div> +<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  </div> +<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">get_msa</a>(std::vector<std::vector<std::string>>& msa,</div> +<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  std::vector<StatusType>& output_status) = 0;</div> +<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  </div> +<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">get_graphs</a>(std::vector<DirectedGraph>& graphs,</div> +<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  std::vector<StatusType>& output_status) = 0;</div> +<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  </div> +<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keyword">virtual</span> int32_t <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">batch_id</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  </div> +<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">reset</a>() = 0;</div> +<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> };</div> +<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  </div> +<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> std::unique_ptr<Batch> <a class="code" href="group__cudapoa.html#ga81951b681c27354e2dbe7933a9f168f3">create_batch</a>(int32_t max_sequences_per_poa,</div> +<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  int32_t device_id,</div> +<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  cudaStream_t stream,</div> +<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordtype">size_t</span> max_mem,</div> +<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  int8_t output_mask,</div> +<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  int16_t gap_score,</div> +<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  int16_t mismatch_score,</div> +<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  int16_t match_score,</div> +<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordtype">bool</span> cuda_banded_alignment);</div> +<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  </div> +<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  </div> +<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> } <span class="comment">// namespace cudapoa</span></div> +<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  </div> +<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> } <span class="comment">// namespace claragenomics</span></div> </div><!-- fragment --></div><!-- contents --> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_ab70c94f0a2b161abd8fce03f487c2db1"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">claragenomics::cudapoa::Batch::~Batch</a></div><div class="ttdeci">virtual ~Batch()=default</div><div class="ttdoc">CudapoaBatch has a custom dtor, so declare ~Batch virtual and give it a default implementation.</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_ab807c4b01c2cddcdebb32952df13c0ec"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">claragenomics::cudapoa::Batch::batch_id</a></div><div class="ttdeci">virtual int32_t batch_id() const =0</div><div class="ttdoc">Return batch ID.</div></div> <div class="ttc" id="agroup__cudapoa_html_ga81951b681c27354e2dbe7933a9f168f3"><div class="ttname"><a href="group__cudapoa.html#ga81951b681c27354e2dbe7933a9f168f3">claragenomics::cudapoa::create_batch</a></div><div class="ttdeci">std::unique_ptr< Batch > create_batch(int32_t max_sequences_per_poa, int32_t device_id, cudaStream_t stream, size_t max_mem, int8_t output_mask, int16_t gap_score, int16_t mismatch_score, int16_t match_score, bool cuda_banded_alignment)</div><div class="ttdoc">Creates a new CUDA Batch object.</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_ab8564c38982af7716c70b06d029fb277"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">claragenomics::cudapoa::Entry::weights</a></div><div class="ttdeci">const int8_t * weights</div><div class="ttdoc">Pointer to array of weight per base in sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:37</div></div> +<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_ab8564c38982af7716c70b06d029fb277"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">claragenomics::cudapoa::Entry::weights</a></div><div class="ttdeci">const int8_t * weights</div><div class="ttdoc">Pointer to array of weight per base in sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:39</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a7387b746531d4e8ac1e5806ac2824f09"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">claragenomics::cudapoa::Batch::generate_poa</a></div><div class="ttdeci">virtual void generate_poa()=0</div><div class="ttdoc">Run partial order alignment algorithm over all POAs.</div></div> <div class="ttc" id="agroup__cudapoa_html_ga8ece5291074f6e07073b797d34ec24d0"><div class="ttname"><a href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">claragenomics::cudapoa::StatusType</a></div><div class="ttdeci">StatusType</div><div class="ttdoc">CUDA POA error type.</div><div class="ttdef"><b>Definition:</b> cudapoa.hpp:22</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_ab39956c82d5d5a2d8df1b1695e15d9d2"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">claragenomics::cudapoa::Batch::get_msa</a></div><div class="ttdeci">virtual StatusType get_msa(std::vector< std::vector< std::string >> &msa, std::vector< StatusType > &output_status)=0</div><div class="ttdoc">Get the multiple sequence alignments for each POA.</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a8f2f44e7b4d7f51d8ba68323841dcdf0"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">claragenomics::cudapoa::Batch::add_poa_group</a></div><div class="ttdeci">virtual StatusType add_poa_group(std::vector< StatusType > &per_seq_status, const Group &poa_group)=0</div><div class="ttdoc">Add a new group to the batch to run POA algorithm on. Based on the constraints of the batch,...</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_af2b27869811283b869700c181a75cfdc"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">claragenomics::cudapoa::Batch::get_total_poas</a></div><div class="ttdeci">virtual int32_t get_total_poas() const =0</div><div class="ttdoc">Get total number of partial order alignments in batch.</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_a4ada5ced9af7930c95d7a49fb5ecdac4"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">claragenomics::cudapoa::Entry::seq</a></div><div class="ttdeci">const char * seq</div><div class="ttdoc">Pointer to string representing sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:35</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></div><div class="ttdef"><b>Definition:</b> batch.hpp:47</div></div> +<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_a4ada5ced9af7930c95d7a49fb5ecdac4"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">claragenomics::cudapoa::Entry::seq</a></div><div class="ttdeci">const char * seq</div><div class="ttdoc">Pointer to string representing sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:37</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></div><div class="ttdef"><b>Definition:</b> batch.hpp:49</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_aa8de262cb7c43d7219f7064bb700e7ae"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">claragenomics::cudapoa::Batch::reset</a></div><div class="ttdeci">virtual void reset()=0</div><div class="ttdoc">Reset batch. Must do before re-using batch.</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html">claragenomics::cudapoa::Entry</a></div><div class="ttdoc">A structure to represent a sequence entry.</div><div class="ttdef"><b>Definition:</b> batch.hpp:32</div></div> +<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html">claragenomics::cudapoa::Entry</a></div><div class="ttdoc">A structure to represent a sequence entry.</div><div class="ttdef"><b>Definition:</b> batch.hpp:34</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a3224d1595caa5950c34708f4b7d64fe0"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">claragenomics::cudapoa::Batch::get_consensus</a></div><div class="ttdeci">virtual StatusType get_consensus(std::vector< std::string > &consensus, std::vector< std::vector< uint16_t >> &coverage, std::vector< claragenomics::cudapoa::StatusType > &output_status)=0</div><div class="ttdoc">Get the consensus for each POA.</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_a2211688d275c808bf9b4f85336db6712"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712">claragenomics::cudapoa::Entry::length</a></div><div class="ttdeci">int32_t length</div><div class="ttdoc">Length of sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:39</div></div> -<div class="ttc" id="agroup__cudapoa_html_ga6b301a3a6ac7edccc403ec75e7497d32"><div class="ttname"><a href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">claragenomics::cudapoa::Group</a></div><div class="ttdeci">std::vector< Entry > Group</div><div class="ttdoc">A type defining the set and order of Entry's in which a POA is processed.</div><div class="ttdef"><b>Definition:</b> batch.hpp:43</div></div> +<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_a2211688d275c808bf9b4f85336db6712"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712">claragenomics::cudapoa::Entry::length</a></div><div class="ttdeci">int32_t length</div><div class="ttdoc">Length of sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:41</div></div> +<div class="ttc" id="agroup__cudapoa_html_ga6b301a3a6ac7edccc403ec75e7497d32"><div class="ttname"><a href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">claragenomics::cudapoa::Group</a></div><div class="ttdeci">std::vector< Entry > Group</div><div class="ttdoc">A type defining the set and order of Entry's in which a POA is processed.</div><div class="ttdef"><b>Definition:</b> batch.hpp:45</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a0949cca1e89a40d759b0ca371512bb16"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">claragenomics::cudapoa::Batch::get_graphs</a></div><div class="ttdeci">virtual void get_graphs(std::vector< DirectedGraph > &graphs, std::vector< StatusType > &output_status)=0</div><div class="ttdoc">Get the graph representation for each POA.</div></div> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> Generated by  <a href="http://www.doxygen.org/index.html"> diff --git a/docs/cpp/classclaragenomics_1_1DirectedGraph-members.html b/docs/cpp/classclaragenomics_1_1DirectedGraph-members.html new file mode 100644 index 000000000..43e9f66cf --- /dev/null +++ b/docs/cpp/classclaragenomics_1_1DirectedGraph-members.html @@ -0,0 +1,102 @@ +<!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" 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 <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1DirectedGraph.html">DirectedGraph</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="headertitle"> +<div class="title">claragenomics::DirectedGraph Member List</div> </div> +</div><!--header--> +<div class="contents"> + +<p>This is the complete list of members for <a class="el" href="classclaragenomics_1_1DirectedGraph.html">claragenomics::DirectedGraph</a>, including all inherited members.</p> +<table class="directory"> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">add_edge</a>(node_id_t node_id_from, node_id_t node_id_to, edge_weight_t weight=0)</td><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html">claragenomics::DirectedGraph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a>(edge_t edge)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html">claragenomics::DirectedGraph</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html">claragenomics::DirectedGraph</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a>(std::ostringstream &dot_str, const std::string &node_separator) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">empty_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">get_adjacent_nodes</a>(node_id_t node) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">get_edges</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">get_node_ids</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">get_node_label</a>(node_id_t node) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html">claragenomics::DirectedGraph</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a>(std::ostringstream &dot_str) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">serialize_to_dot</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1DirectedGraph.html">claragenomics::DirectedGraph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">set_node_label</a>(node_id_t node, const std::string &label)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a>(edge_t edge)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> +</table></div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/classclaragenomics_1_1DirectedGraph.html b/docs/cpp/classclaragenomics_1_1DirectedGraph.html new file mode 100644 index 000000000..1c3e97641 --- /dev/null +++ b/docs/cpp/classclaragenomics_1_1DirectedGraph.html @@ -0,0 +1,281 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: claragenomics::DirectedGraph Class 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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1DirectedGraph.html">DirectedGraph</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="summary"> +<a href="#pub-types">Public Types</a> | +<a href="#pub-methods">Public Member Functions</a> | +<a href="classclaragenomics_1_1DirectedGraph-members.html">List of all members</a> </div> + <div class="headertitle"> +<div class="title">claragenomics::DirectedGraph Class Reference</div> </div> +</div><!--header--> +<div class="contents"> + +<p><a class="el" href="classclaragenomics_1_1DirectedGraph.html" title="DirectedGraph Object representing a directed graph structure.">DirectedGraph</a> Object representing a directed graph structure. + <a href="classclaragenomics_1_1DirectedGraph.html#details">More...</a></p> + +<p><code>#include <<a class="el" href="graph_8hpp_source.html">graph.hpp</a>></code></p> +<div class="dynheader"> +Inheritance diagram for claragenomics::DirectedGraph:</div> +<div class="dyncontent"> +<div class="center"><img src="classclaragenomics_1_1DirectedGraph__inherit__graph.png" border="0" usemap="#claragenomics_1_1DirectedGraph_inherit__map" alt="Inheritance graph"/></div> +<map name="claragenomics_1_1DirectedGraph_inherit__map" id="claragenomics_1_1DirectedGraph_inherit__map"> +<area shape="rect" title="DirectedGraph Object representing a directed graph structure." alt="" coords="5,80,204,107"/> +<area shape="rect" href="classclaragenomics_1_1Graph.html" title="Object representing a generic graph structure." alt="" coords="30,5,179,32"/> +</map> +<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div> +<div class="dynheader"> +Collaboration diagram for claragenomics::DirectedGraph:</div> +<div class="dyncontent"> +<div class="center"><img src="classclaragenomics_1_1DirectedGraph__coll__graph.png" border="0" usemap="#claragenomics_1_1DirectedGraph_coll__map" alt="Collaboration graph"/></div> +<map name="claragenomics_1_1DirectedGraph_coll__map" id="claragenomics_1_1DirectedGraph_coll__map"> +<area shape="rect" title="DirectedGraph Object representing a directed graph structure." alt="" coords="5,80,204,107"/> +<area shape="rect" href="classclaragenomics_1_1Graph.html" title="Object representing a generic graph structure." alt="" coords="30,5,179,32"/> +</map> +<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div> +<table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a> +Public Types</h2></td></tr> +<tr class="memitem:a0f9734799fc19b94b0621c956ce5508d"><td class="memItemLeft" align="right" valign="top"><a id="a0f9734799fc19b94b0621c956ce5508d"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> = int32_t</td></tr> +<tr class="memdesc:a0f9734799fc19b94b0621c956ce5508d"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for node ID. <br /></td></tr> +<tr class="separator:a0f9734799fc19b94b0621c956ce5508d"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ad5388bf7676b6e35a6e62c034e2993b5"><td class="memItemLeft" align="right" valign="top"><a id="ad5388bf7676b6e35a6e62c034e2993b5"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> = int32_t</td></tr> +<tr class="memdesc:ad5388bf7676b6e35a6e62c034e2993b5"><td class="mdescLeft"> </td><td class="mdescRight">Tpyedef for edge weight. <br /></td></tr> +<tr class="separator:ad5388bf7676b6e35a6e62c034e2993b5"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a3892123fce03f805e54ce0076e6b68dc"><td class="memItemLeft" align="right" valign="top"><a id="a3892123fce03f805e54ce0076e6b68dc"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> = std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> ></td></tr> +<tr class="memdesc:a3892123fce03f805e54ce0076e6b68dc"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for edge. <br /></td></tr> +<tr class="separator:a3892123fce03f805e54ce0076e6b68dc"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="inherit_header pub_types_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:a0f9734799fc19b94b0621c956ce5508d inherit pub_types_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a0f9734799fc19b94b0621c956ce5508d"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> = int32_t</td></tr> +<tr class="memdesc:a0f9734799fc19b94b0621c956ce5508d inherit pub_types_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for node ID. <br /></td></tr> +<tr class="separator:a0f9734799fc19b94b0621c956ce5508d inherit pub_types_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ad5388bf7676b6e35a6e62c034e2993b5 inherit pub_types_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="ad5388bf7676b6e35a6e62c034e2993b5"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> = int32_t</td></tr> +<tr class="memdesc:ad5388bf7676b6e35a6e62c034e2993b5 inherit pub_types_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Tpyedef for edge weight. <br /></td></tr> +<tr class="separator:ad5388bf7676b6e35a6e62c034e2993b5 inherit pub_types_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a3892123fce03f805e54ce0076e6b68dc inherit pub_types_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a3892123fce03f805e54ce0076e6b68dc"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> = std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> ></td></tr> +<tr class="memdesc:a3892123fce03f805e54ce0076e6b68dc inherit pub_types_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for edge. <br /></td></tr> +<tr class="separator:a3892123fce03f805e54ce0076e6b68dc inherit pub_types_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> +Public Member Functions</h2></td></tr> +<tr class="memitem:a85c21aed5db9c7d81cb6003841410371"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">add_edge</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_from, <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_to, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> weight=0)</td></tr> +<tr class="memdesc:a85c21aed5db9c7d81cb6003841410371"><td class="mdescLeft"> </td><td class="mdescRight">Add directed edges to graph. <a href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">More...</a><br /></td></tr> +<tr class="separator:a85c21aed5db9c7d81cb6003841410371"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a7844605760f22a2a60e27c23178497b3"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">serialize_to_dot</a> () const</td></tr> +<tr class="memdesc:a7844605760f22a2a60e27c23178497b3"><td class="mdescLeft"> </td><td class="mdescRight">Serialize graph structure to dot format. <a href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">More...</a><br /></td></tr> +<tr class="separator:a7844605760f22a2a60e27c23178497b3"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="inherit_header pub_methods_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:ab52b2707de415931f1990ee338b29eeb inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">get_adjacent_nodes</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node) const</td></tr> +<tr class="memdesc:ab52b2707de415931f1990ee338b29eeb inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Get a list of adjacent nodes to a given node. <a href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">More...</a><br /></td></tr> +<tr class="separator:ab52b2707de415931f1990ee338b29eeb inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a1b51bca4b58c9922b375c983415ec0c8 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">get_node_ids</a> () const</td></tr> +<tr class="memdesc:a1b51bca4b58c9922b375c983415ec0c8 inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">List all node IDs in the graph. <a href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">More...</a><br /></td></tr> +<tr class="separator:a1b51bca4b58c9922b375c983415ec0c8 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ac96335c01273c0dd74d2628e7bf38794 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">const std::vector< std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">get_edges</a> () const</td></tr> +<tr class="memdesc:ac96335c01273c0dd74d2628e7bf38794 inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Get a list of all edges in the graph. <a href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">More...</a><br /></td></tr> +<tr class="separator:ac96335c01273c0dd74d2628e7bf38794 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a9861d50dbee863befed15eb8daacff3d inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">set_node_label</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node, const std::string &label)</td></tr> +<tr class="memdesc:a9861d50dbee863befed15eb8daacff3d inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Add string labels to a node ID. <a href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">More...</a><br /></td></tr> +<tr class="separator:a9861d50dbee863befed15eb8daacff3d inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a47bd2f14a355fbbd801846b0af305389 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">get_node_label</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node) const</td></tr> +<tr class="memdesc:a47bd2f14a355fbbd801846b0af305389 inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Get the label associated with a node. <a href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">More...</a><br /></td></tr> +<tr class="separator:a47bd2f14a355fbbd801846b0af305389 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> +Additional Inherited Members</h2></td></tr> +<tr class="inherit_header pro_methods_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:a1df5a4be1fc2f71130436e9f718e85ac inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</td></tr> +<tr class="memdesc:a1df5a4be1fc2f71130436e9f718e85ac inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Check if a directed edge exists in the grph. <a href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">More...</a><br /></td></tr> +<tr class="separator:a1df5a4be1fc2f71130436e9f718e85ac inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a0043ec8f35f7491c06915c887d31ea77 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</td></tr> +<tr class="memdesc:a0043ec8f35f7491c06915c887d31ea77 inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Update the adjacent nodes based on edge information. <a href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">More...</a><br /></td></tr> +<tr class="separator:a0043ec8f35f7491c06915c887d31ea77 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a95ef438f6035c2240bf277645ad27cb9 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a> (std::ostringstream &dot_str) const</td></tr> +<tr class="memdesc:a95ef438f6035c2240bf277645ad27cb9 inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Serialize node labels to dot format. <a href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">More...</a><br /></td></tr> +<tr class="separator:a95ef438f6035c2240bf277645ad27cb9 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a88dda0ee0cffa26a188a041593d2fcd5 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a> (std::ostringstream &dot_str, const std::string &node_separator) const</td></tr> +<tr class="memdesc:a88dda0ee0cffa26a188a041593d2fcd5 inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Serialize edges to dot format. <a href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">More...</a><br /></td></tr> +<tr class="separator:a88dda0ee0cffa26a188a041593d2fcd5 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="inherit_header pro_attribs_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:a8b53264154b5caed266385a007e33404 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a8b53264154b5caed266385a007e33404"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a></td></tr> +<tr class="memdesc:a8b53264154b5caed266385a007e33404 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">List of adjacent nodes per node ID. <br /></td></tr> +<tr class="separator:a8b53264154b5caed266385a007e33404 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a4089c636086324cae1f2a2bde56c8b33 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a4089c636086324cae1f2a2bde56c8b33"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a>, <a class="el" href="structclaragenomics_1_1PairHash.html">PairHash</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a></td></tr> +<tr class="memdesc:a4089c636086324cae1f2a2bde56c8b33 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">All edges in the graph. <br /></td></tr> +<tr class="separator:a4089c636086324cae1f2a2bde56c8b33 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a5da2769d7e5bebd1d74c4899e3aad2c5 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a5da2769d7e5bebd1d74c4899e3aad2c5"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a></td></tr> +<tr class="memdesc:a5da2769d7e5bebd1d74c4899e3aad2c5 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Label per node. <br /></td></tr> +<tr class="separator:a5da2769d7e5bebd1d74c4899e3aad2c5 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ada271fc17a3a6e86f5dcc78c4caa729c inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="ada271fc17a3a6e86f5dcc78c4caa729c"></a> +const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">empty_</a></td></tr> +<tr class="memdesc:ada271fc17a3a6e86f5dcc78c4caa729c inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">An empty list representing no connectivity. <br /></td></tr> +<tr class="separator:ada271fc17a3a6e86f5dcc78c4caa729c inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +</table> +<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> +<div class="textblock"><p><a class="el" href="classclaragenomics_1_1DirectedGraph.html" title="DirectedGraph Object representing a directed graph structure.">DirectedGraph</a> Object representing a directed graph structure. </p> +</div><h2 class="groupheader">Member Function Documentation</h2> +<a id="a85c21aed5db9c7d81cb6003841410371"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a85c21aed5db9c7d81cb6003841410371">◆ </a></span>add_edge()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">void claragenomics::DirectedGraph::add_edge </td> + <td>(</td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> </td> + <td class="paramname"><em>node_id_from</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> </td> + <td class="paramname"><em>node_id_to</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> </td> + <td class="paramname"><em>weight</em> = <code>0</code> </td> + </tr> + <tr> + <td></td> + <td>)</td> + <td></td><td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Add directed edges to graph. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">node_id_from</td><td>Source node ID </td></tr> + <tr><td class="paramname">node_id_to</td><td>Sink node ID </td></tr> + <tr><td class="paramname">weight</td><td>Edge weight </td></tr> + </table> + </dd> +</dl> + +</div> +</div> +<a id="a7844605760f22a2a60e27c23178497b3"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a7844605760f22a2a60e27c23178497b3">◆ </a></span>serialize_to_dot()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">std::string claragenomics::DirectedGraph::serialize_to_dot </td> + <td>(</td> + <td class="paramname"></td><td>)</td> + <td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Serialize graph structure to dot format. </p> +<dl class="section return"><dt>Returns</dt><dd>A string encoding the graph in dot format </dd></dl> + +</div> +</div> +<hr/>The documentation for this class was generated from the following file:<ul> +<li>common/utils/include/claragenomics/utils/<a class="el" href="graph_8hpp_source.html">graph.hpp</a></li> +</ul> +</div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a 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+<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">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1Graph.html">Graph</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="headertitle"> +<div class="title">claragenomics::Graph Member List</div> </div> +</div><!--header--> +<div class="contents"> + +<p>This is the complete list of members for <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a>, including all inherited members.</p> +<table class="directory"> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a>(edge_t edge)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a>(std::ostringstream &dot_str, const std::string &node_separator) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">empty_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">get_adjacent_nodes</a>(node_id_t node) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">get_edges</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">get_node_ids</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">get_node_label</a>(node_id_t node) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a>(std::ostringstream &dot_str) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">set_node_label</a>(node_id_t node, const std::string &label)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a>(edge_t edge)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> +</table></div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/classclaragenomics_1_1Graph.html b/docs/cpp/classclaragenomics_1_1Graph.html new file mode 100644 index 000000000..7f2ad7619 --- /dev/null +++ b/docs/cpp/classclaragenomics_1_1Graph.html @@ -0,0 +1,495 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: claragenomics::Graph Class 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 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+<script type="text/javascript" src="menu.js"></script> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1Graph.html">Graph</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="summary"> +<a href="#pub-types">Public Types</a> | +<a href="#pub-methods">Public Member Functions</a> | +<a href="#pro-methods">Protected Member Functions</a> | +<a href="#pro-attribs">Protected Attributes</a> | +<a href="classclaragenomics_1_1Graph-members.html">List of all members</a> </div> + <div class="headertitle"> +<div class="title">claragenomics::Graph Class Reference</div> </div> +</div><!--header--> +<div class="contents"> + +<p>Object representing a generic graph structure. + <a href="classclaragenomics_1_1Graph.html#details">More...</a></p> + +<p><code>#include <<a class="el" href="graph_8hpp_source.html">graph.hpp</a>></code></p> +<div class="dynheader"> +Inheritance diagram for claragenomics::Graph:</div> +<div class="dyncontent"> +<div class="center"><img src="classclaragenomics_1_1Graph__inherit__graph.png" border="0" usemap="#claragenomics_1_1Graph_inherit__map" alt="Inheritance graph"/></div> +<map name="claragenomics_1_1Graph_inherit__map" id="claragenomics_1_1Graph_inherit__map"> +<area shape="rect" title="Object representing a generic graph structure." alt="" coords="135,5,285,32"/> +<area shape="rect" href="classclaragenomics_1_1DirectedGraph.html" title="DirectedGraph Object representing a directed graph structure." alt="" coords="5,87,204,114"/> +<area shape="rect" href="classclaragenomics_1_1UndirectedGraph.html" title="UndirectedGraph Object representing an undirected graph structure." alt="" coords="228,80,405,121"/> +</map> +<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div> +<table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a> +Public Types</h2></td></tr> +<tr class="memitem:a0f9734799fc19b94b0621c956ce5508d"><td class="memItemLeft" align="right" valign="top"><a id="a0f9734799fc19b94b0621c956ce5508d"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> = int32_t</td></tr> +<tr class="memdesc:a0f9734799fc19b94b0621c956ce5508d"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for node ID. <br /></td></tr> +<tr class="separator:a0f9734799fc19b94b0621c956ce5508d"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ad5388bf7676b6e35a6e62c034e2993b5"><td class="memItemLeft" align="right" valign="top"><a id="ad5388bf7676b6e35a6e62c034e2993b5"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> = int32_t</td></tr> +<tr class="memdesc:ad5388bf7676b6e35a6e62c034e2993b5"><td class="mdescLeft"> </td><td class="mdescRight">Tpyedef for edge weight. <br /></td></tr> +<tr class="separator:ad5388bf7676b6e35a6e62c034e2993b5"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a3892123fce03f805e54ce0076e6b68dc"><td class="memItemLeft" align="right" valign="top"><a id="a3892123fce03f805e54ce0076e6b68dc"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> = std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> ></td></tr> +<tr class="memdesc:a3892123fce03f805e54ce0076e6b68dc"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for edge. <br /></td></tr> +<tr class="separator:a3892123fce03f805e54ce0076e6b68dc"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> +Public Member Functions</h2></td></tr> +<tr class="memitem:ab52b2707de415931f1990ee338b29eeb"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">get_adjacent_nodes</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node) const</td></tr> +<tr class="memdesc:ab52b2707de415931f1990ee338b29eeb"><td class="mdescLeft"> </td><td class="mdescRight">Get a list of adjacent nodes to a given node. <a href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">More...</a><br /></td></tr> +<tr class="separator:ab52b2707de415931f1990ee338b29eeb"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a1b51bca4b58c9922b375c983415ec0c8"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">get_node_ids</a> () const</td></tr> +<tr class="memdesc:a1b51bca4b58c9922b375c983415ec0c8"><td class="mdescLeft"> </td><td class="mdescRight">List all node IDs in the graph. <a href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">More...</a><br /></td></tr> +<tr class="separator:a1b51bca4b58c9922b375c983415ec0c8"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ac96335c01273c0dd74d2628e7bf38794"><td class="memItemLeft" align="right" valign="top">const std::vector< std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">get_edges</a> () const</td></tr> +<tr class="memdesc:ac96335c01273c0dd74d2628e7bf38794"><td class="mdescLeft"> </td><td class="mdescRight">Get a list of all edges in the graph. <a href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">More...</a><br /></td></tr> +<tr class="separator:ac96335c01273c0dd74d2628e7bf38794"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a9861d50dbee863befed15eb8daacff3d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">set_node_label</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node, const std::string &label)</td></tr> +<tr class="memdesc:a9861d50dbee863befed15eb8daacff3d"><td class="mdescLeft"> </td><td class="mdescRight">Add string labels to a node ID. <a href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">More...</a><br /></td></tr> +<tr class="separator:a9861d50dbee863befed15eb8daacff3d"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a47bd2f14a355fbbd801846b0af305389"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">get_node_label</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node) const</td></tr> +<tr class="memdesc:a47bd2f14a355fbbd801846b0af305389"><td class="mdescLeft"> </td><td class="mdescRight">Get the label associated with a node. <a href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">More...</a><br /></td></tr> +<tr class="separator:a47bd2f14a355fbbd801846b0af305389"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a> +Protected Member Functions</h2></td></tr> +<tr class="memitem:a1df5a4be1fc2f71130436e9f718e85ac"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</td></tr> +<tr class="memdesc:a1df5a4be1fc2f71130436e9f718e85ac"><td class="mdescLeft"> </td><td class="mdescRight">Check if a directed edge exists in the grph. <a href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">More...</a><br /></td></tr> +<tr class="separator:a1df5a4be1fc2f71130436e9f718e85ac"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a0043ec8f35f7491c06915c887d31ea77"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</td></tr> +<tr class="memdesc:a0043ec8f35f7491c06915c887d31ea77"><td class="mdescLeft"> </td><td class="mdescRight">Update the adjacent nodes based on edge information. <a href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">More...</a><br /></td></tr> +<tr class="separator:a0043ec8f35f7491c06915c887d31ea77"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a95ef438f6035c2240bf277645ad27cb9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a> (std::ostringstream &dot_str) const</td></tr> +<tr class="memdesc:a95ef438f6035c2240bf277645ad27cb9"><td class="mdescLeft"> </td><td class="mdescRight">Serialize node labels to dot format. <a href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">More...</a><br /></td></tr> +<tr class="separator:a95ef438f6035c2240bf277645ad27cb9"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a88dda0ee0cffa26a188a041593d2fcd5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a> (std::ostringstream &dot_str, const std::string &node_separator) const</td></tr> +<tr class="memdesc:a88dda0ee0cffa26a188a041593d2fcd5"><td class="mdescLeft"> </td><td class="mdescRight">Serialize edges to dot format. <a href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">More...</a><br /></td></tr> +<tr class="separator:a88dda0ee0cffa26a188a041593d2fcd5"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a> +Protected Attributes</h2></td></tr> +<tr class="memitem:a8b53264154b5caed266385a007e33404"><td class="memItemLeft" align="right" valign="top"><a id="a8b53264154b5caed266385a007e33404"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a></td></tr> +<tr class="memdesc:a8b53264154b5caed266385a007e33404"><td class="mdescLeft"> </td><td class="mdescRight">List of adjacent nodes per node ID. <br /></td></tr> +<tr class="separator:a8b53264154b5caed266385a007e33404"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a4089c636086324cae1f2a2bde56c8b33"><td class="memItemLeft" align="right" valign="top"><a id="a4089c636086324cae1f2a2bde56c8b33"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a>, <a class="el" href="structclaragenomics_1_1PairHash.html">PairHash</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a></td></tr> +<tr class="memdesc:a4089c636086324cae1f2a2bde56c8b33"><td class="mdescLeft"> </td><td class="mdescRight">All edges in the graph. <br /></td></tr> +<tr class="separator:a4089c636086324cae1f2a2bde56c8b33"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a5da2769d7e5bebd1d74c4899e3aad2c5"><td class="memItemLeft" align="right" valign="top"><a id="a5da2769d7e5bebd1d74c4899e3aad2c5"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a></td></tr> +<tr class="memdesc:a5da2769d7e5bebd1d74c4899e3aad2c5"><td class="mdescLeft"> </td><td class="mdescRight">Label per node. <br /></td></tr> +<tr class="separator:a5da2769d7e5bebd1d74c4899e3aad2c5"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ada271fc17a3a6e86f5dcc78c4caa729c"><td class="memItemLeft" align="right" valign="top"><a id="ada271fc17a3a6e86f5dcc78c4caa729c"></a> +const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">empty_</a></td></tr> +<tr class="memdesc:ada271fc17a3a6e86f5dcc78c4caa729c"><td class="mdescLeft"> </td><td class="mdescRight">An empty list representing no connectivity. <br /></td></tr> +<tr class="separator:ada271fc17a3a6e86f5dcc78c4caa729c"><td class="memSeparator" colspan="2"> </td></tr> +</table> +<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> +<div class="textblock"><p>Object representing a generic graph structure. </p> +</div><h2 class="groupheader">Member Function Documentation</h2> +<a id="a1df5a4be1fc2f71130436e9f718e85ac"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a1df5a4be1fc2f71130436e9f718e85ac">◆ </a></span>directed_edge_exists()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">bool claragenomics::Graph::directed_edge_exists </td> + <td>(</td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> </td> + <td class="paramname"><em>edge</em></td><td>)</td> + <td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Check if a directed edge exists in the grph. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">edge</td><td>A directed edge </td></tr> + </table> + </dd> +</dl> +<dl class="section return"><dt>Returns</dt><dd>Boolean result of check </dd></dl> + +</div> +</div> +<a id="a88dda0ee0cffa26a188a041593d2fcd5"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a88dda0ee0cffa26a188a041593d2fcd5">◆ </a></span>edges_to_dot()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">void claragenomics::Graph::edges_to_dot </td> + <td>(</td> + <td class="paramtype">std::ostringstream & </td> + <td class="paramname"><em>dot_str</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype">const std::string & </td> + <td class="paramname"><em>node_separator</em> </td> + </tr> + <tr> + <td></td> + <td>)</td> + <td></td><td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Serialize edges to dot format. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">dot_str</td><td>Output string stream to serialize labels to </td></tr> + <tr><td class="paramname">node_separator</td><td>DOT delimiter for edge description </td></tr> + </table> + </dd> +</dl> + +</div> +</div> +<a id="ab52b2707de415931f1990ee338b29eeb"></a> +<h2 class="memtitle"><span class="permalink"><a href="#ab52b2707de415931f1990ee338b29eeb">◆ </a></span>get_adjacent_nodes()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">const std::vector<<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>>& claragenomics::Graph::get_adjacent_nodes </td> + <td>(</td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> </td> + <td class="paramname"><em>node</em></td><td>)</td> + <td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Get a list of adjacent nodes to a given node. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">node</td><td>Node for which adjacent nodes are requested </td></tr> + </table> + </dd> +</dl> +<dl class="section return"><dt>Returns</dt><dd>Vector of adjacent node IDs </dd></dl> + +</div> +</div> +<a id="ac96335c01273c0dd74d2628e7bf38794"></a> +<h2 class="memtitle"><span class="permalink"><a href="#ac96335c01273c0dd74d2628e7bf38794">◆ </a></span>get_edges()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">const std::vector<std::pair<<a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a>> > claragenomics::Graph::get_edges </td> + <td>(</td> + <td class="paramname"></td><td>)</td> + <td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Get a list of all edges in the graph. </p> +<dl class="section return"><dt>Returns</dt><dd>A vector of edges </dd></dl> + +</div> +</div> +<a id="a1b51bca4b58c9922b375c983415ec0c8"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a1b51bca4b58c9922b375c983415ec0c8">◆ </a></span>get_node_ids()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">const std::vector<<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>> claragenomics::Graph::get_node_ids </td> + <td>(</td> + <td class="paramname"></td><td>)</td> + <td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>List all node IDs in the graph. </p> +<dl class="section return"><dt>Returns</dt><dd>A vector of node IDs </dd></dl> + +</div> +</div> +<a id="a47bd2f14a355fbbd801846b0af305389"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a47bd2f14a355fbbd801846b0af305389">◆ </a></span>get_node_label()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">std::string claragenomics::Graph::get_node_label </td> + <td>(</td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> </td> + <td class="paramname"><em>node</em></td><td>)</td> + <td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Get the label associated with a node. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">node</td><td>node ID for label query </td></tr> + </table> + </dd> +</dl> +<dl class="section return"><dt>Returns</dt><dd>String label for associated node. Returns empty string if </dd></dl> + +</div> +</div> +<a id="a95ef438f6035c2240bf277645ad27cb9"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a95ef438f6035c2240bf277645ad27cb9">◆ </a></span>node_labels_to_dot()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">void claragenomics::Graph::node_labels_to_dot </td> + <td>(</td> + <td class="paramtype">std::ostringstream & </td> + <td class="paramname"><em>dot_str</em></td><td>)</td> + <td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Serialize node labels to dot format. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">dot_str</td><td>Output string stream to serialize labels to </td></tr> + </table> + </dd> +</dl> + +</div> +</div> +<a id="a9861d50dbee863befed15eb8daacff3d"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a9861d50dbee863befed15eb8daacff3d">◆ </a></span>set_node_label()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">void claragenomics::Graph::set_node_label </td> + <td>(</td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> </td> + <td class="paramname"><em>node</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype">const std::string & </td> + <td class="paramname"><em>label</em> </td> + </tr> + <tr> + <td></td> + <td>)</td> + <td></td><td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Add string labels to a node ID. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">node</td><td>ID of node </td></tr> + <tr><td class="paramname">label</td><td>Label to attach to that node ID </td></tr> + </table> + </dd> +</dl> + +</div> +</div> +<a id="a0043ec8f35f7491c06915c887d31ea77"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a0043ec8f35f7491c06915c887d31ea77">◆ </a></span>update_adject_nodes()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">void claragenomics::Graph::update_adject_nodes </td> + <td>(</td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> </td> + <td class="paramname"><em>edge</em></td><td>)</td> + <td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Update the adjacent nodes based on edge information. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">edge</td><td>A directed edge </td></tr> + </table> + </dd> +</dl> + +</div> +</div> +<hr/>The documentation for this class was generated from the following file:<ul> +<li>common/utils/include/claragenomics/utils/<a class="el" href="graph_8hpp_source.html">graph.hpp</a></li> +</ul> +</div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/classclaragenomics_1_1Graph__inherit__graph.map b/docs/cpp/classclaragenomics_1_1Graph__inherit__graph.map new file 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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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: Member 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="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">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">UndirectedGraph</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="headertitle"> +<div class="title">claragenomics::UndirectedGraph Member List</div> </div> +</div><!--header--> +<div class="contents"> + +<p>This is the complete list of members for <a class="el" href="classclaragenomics_1_1UndirectedGraph.html">claragenomics::UndirectedGraph</a>, including all inherited members.</p> +<table class="directory"> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">add_edge</a>(node_id_t node_id_from, node_id_t node_id_to, edge_weight_t weight=0)</td><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">claragenomics::UndirectedGraph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a>(edge_t edge)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">claragenomics::UndirectedGraph</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">claragenomics::UndirectedGraph</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a>(std::ostringstream &dot_str, const std::string &node_separator) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">empty_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">get_adjacent_nodes</a>(node_id_t node) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">get_edges</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">get_node_ids</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">get_node_label</a>(node_id_t node) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> typedef</td><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">claragenomics::UndirectedGraph</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a></td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a>(std::ostringstream &dot_str) const</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">serialize_to_dot</a>() const</td><td class="entry"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">claragenomics::UndirectedGraph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">set_node_label</a>(node_id_t node, const std::string &label)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a>(edge_t edge)</td><td class="entry"><a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr> +</table></div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/classclaragenomics_1_1UndirectedGraph.html b/docs/cpp/classclaragenomics_1_1UndirectedGraph.html new file mode 100644 index 000000000..c7432833d --- /dev/null +++ b/docs/cpp/classclaragenomics_1_1UndirectedGraph.html @@ -0,0 +1,281 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: claragenomics::UndirectedGraph Class 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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">UndirectedGraph</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="summary"> +<a href="#pub-types">Public Types</a> | +<a href="#pub-methods">Public Member Functions</a> | +<a href="classclaragenomics_1_1UndirectedGraph-members.html">List of all members</a> </div> + <div class="headertitle"> +<div class="title">claragenomics::UndirectedGraph Class Reference</div> </div> +</div><!--header--> +<div class="contents"> + +<p><a class="el" href="classclaragenomics_1_1UndirectedGraph.html" title="UndirectedGraph Object representing an undirected graph structure.">UndirectedGraph</a> Object representing an undirected graph structure. + <a href="classclaragenomics_1_1UndirectedGraph.html#details">More...</a></p> + +<p><code>#include <<a class="el" href="graph_8hpp_source.html">graph.hpp</a>></code></p> +<div class="dynheader"> +Inheritance diagram for claragenomics::UndirectedGraph:</div> +<div class="dyncontent"> +<div class="center"><img src="classclaragenomics_1_1UndirectedGraph__inherit__graph.png" border="0" usemap="#claragenomics_1_1UndirectedGraph_inherit__map" alt="Inheritance graph"/></div> +<map name="claragenomics_1_1UndirectedGraph_inherit__map" id="claragenomics_1_1UndirectedGraph_inherit__map"> +<area shape="rect" title="UndirectedGraph Object representing an undirected graph structure." alt="" coords="5,80,183,121"/> +<area shape="rect" href="classclaragenomics_1_1Graph.html" title="Object representing a generic graph structure." alt="" coords="19,5,169,32"/> +</map> +<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div> +<div class="dynheader"> +Collaboration diagram for claragenomics::UndirectedGraph:</div> +<div class="dyncontent"> +<div class="center"><img src="classclaragenomics_1_1UndirectedGraph__coll__graph.png" border="0" usemap="#claragenomics_1_1UndirectedGraph_coll__map" alt="Collaboration graph"/></div> +<map name="claragenomics_1_1UndirectedGraph_coll__map" id="claragenomics_1_1UndirectedGraph_coll__map"> +<area shape="rect" title="UndirectedGraph Object representing an undirected graph structure." alt="" coords="5,80,183,121"/> +<area shape="rect" href="classclaragenomics_1_1Graph.html" title="Object representing a generic graph structure." alt="" coords="19,5,169,32"/> +</map> +<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div> +<table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a> +Public Types</h2></td></tr> +<tr class="memitem:a0f9734799fc19b94b0621c956ce5508d"><td class="memItemLeft" align="right" valign="top"><a id="a0f9734799fc19b94b0621c956ce5508d"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> = int32_t</td></tr> +<tr class="memdesc:a0f9734799fc19b94b0621c956ce5508d"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for node ID. <br /></td></tr> +<tr class="separator:a0f9734799fc19b94b0621c956ce5508d"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ad5388bf7676b6e35a6e62c034e2993b5"><td class="memItemLeft" align="right" valign="top"><a id="ad5388bf7676b6e35a6e62c034e2993b5"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> = int32_t</td></tr> +<tr class="memdesc:ad5388bf7676b6e35a6e62c034e2993b5"><td class="mdescLeft"> </td><td class="mdescRight">Tpyedef for edge weight. <br /></td></tr> +<tr class="separator:ad5388bf7676b6e35a6e62c034e2993b5"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a3892123fce03f805e54ce0076e6b68dc"><td class="memItemLeft" align="right" valign="top"><a id="a3892123fce03f805e54ce0076e6b68dc"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> = std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> ></td></tr> +<tr class="memdesc:a3892123fce03f805e54ce0076e6b68dc"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for edge. <br /></td></tr> +<tr class="separator:a3892123fce03f805e54ce0076e6b68dc"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="inherit_header pub_types_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:a0f9734799fc19b94b0621c956ce5508d inherit pub_types_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a0f9734799fc19b94b0621c956ce5508d"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> = int32_t</td></tr> +<tr class="memdesc:a0f9734799fc19b94b0621c956ce5508d inherit pub_types_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for node ID. <br /></td></tr> +<tr class="separator:a0f9734799fc19b94b0621c956ce5508d inherit pub_types_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ad5388bf7676b6e35a6e62c034e2993b5 inherit pub_types_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="ad5388bf7676b6e35a6e62c034e2993b5"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> = int32_t</td></tr> +<tr class="memdesc:ad5388bf7676b6e35a6e62c034e2993b5 inherit pub_types_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Tpyedef for edge weight. <br /></td></tr> +<tr class="separator:ad5388bf7676b6e35a6e62c034e2993b5 inherit pub_types_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a3892123fce03f805e54ce0076e6b68dc inherit pub_types_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a3892123fce03f805e54ce0076e6b68dc"></a> +using </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> = std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> ></td></tr> +<tr class="memdesc:a3892123fce03f805e54ce0076e6b68dc inherit pub_types_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Typedef for edge. <br /></td></tr> +<tr class="separator:a3892123fce03f805e54ce0076e6b68dc inherit pub_types_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> +Public Member Functions</h2></td></tr> +<tr class="memitem:a47c5ee6b9616ab24222526f4dcd1fb04"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">add_edge</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_from, <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_to, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> weight=0)</td></tr> +<tr class="memdesc:a47c5ee6b9616ab24222526f4dcd1fb04"><td class="mdescLeft"> </td><td class="mdescRight">Add undirected edges to graph. <a href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">More...</a><br /></td></tr> +<tr class="separator:a47c5ee6b9616ab24222526f4dcd1fb04"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a64b119c6ca6049b081ddde7db3c87e3f"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">serialize_to_dot</a> () const</td></tr> +<tr class="memdesc:a64b119c6ca6049b081ddde7db3c87e3f"><td class="mdescLeft"> </td><td class="mdescRight">Serialize graph structure to dot format. <a href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">More...</a><br /></td></tr> +<tr class="separator:a64b119c6ca6049b081ddde7db3c87e3f"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="inherit_header pub_methods_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:ab52b2707de415931f1990ee338b29eeb inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">get_adjacent_nodes</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node) const</td></tr> +<tr class="memdesc:ab52b2707de415931f1990ee338b29eeb inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Get a list of adjacent nodes to a given node. <a href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">More...</a><br /></td></tr> +<tr class="separator:ab52b2707de415931f1990ee338b29eeb inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a1b51bca4b58c9922b375c983415ec0c8 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">get_node_ids</a> () const</td></tr> +<tr class="memdesc:a1b51bca4b58c9922b375c983415ec0c8 inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">List all node IDs in the graph. <a href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">More...</a><br /></td></tr> +<tr class="separator:a1b51bca4b58c9922b375c983415ec0c8 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ac96335c01273c0dd74d2628e7bf38794 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">const std::vector< std::pair< <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">get_edges</a> () const</td></tr> +<tr class="memdesc:ac96335c01273c0dd74d2628e7bf38794 inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Get a list of all edges in the graph. <a href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">More...</a><br /></td></tr> +<tr class="separator:ac96335c01273c0dd74d2628e7bf38794 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a9861d50dbee863befed15eb8daacff3d inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">set_node_label</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node, const std::string &label)</td></tr> +<tr class="memdesc:a9861d50dbee863befed15eb8daacff3d inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Add string labels to a node ID. <a href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">More...</a><br /></td></tr> +<tr class="separator:a9861d50dbee863befed15eb8daacff3d inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a47bd2f14a355fbbd801846b0af305389 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">get_node_label</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node) const</td></tr> +<tr class="memdesc:a47bd2f14a355fbbd801846b0af305389 inherit pub_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Get the label associated with a node. <a href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">More...</a><br /></td></tr> +<tr class="separator:a47bd2f14a355fbbd801846b0af305389 inherit pub_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> +Additional Inherited Members</h2></td></tr> +<tr class="inherit_header pro_methods_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:a1df5a4be1fc2f71130436e9f718e85ac inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</td></tr> +<tr class="memdesc:a1df5a4be1fc2f71130436e9f718e85ac inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Check if a directed edge exists in the grph. <a href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">More...</a><br /></td></tr> +<tr class="separator:a1df5a4be1fc2f71130436e9f718e85ac inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a0043ec8f35f7491c06915c887d31ea77 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a> (<a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</td></tr> +<tr class="memdesc:a0043ec8f35f7491c06915c887d31ea77 inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Update the adjacent nodes based on edge information. <a href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">More...</a><br /></td></tr> +<tr class="separator:a0043ec8f35f7491c06915c887d31ea77 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a95ef438f6035c2240bf277645ad27cb9 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a> (std::ostringstream &dot_str) const</td></tr> +<tr class="memdesc:a95ef438f6035c2240bf277645ad27cb9 inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Serialize node labels to dot format. <a href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">More...</a><br /></td></tr> +<tr class="separator:a95ef438f6035c2240bf277645ad27cb9 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a88dda0ee0cffa26a188a041593d2fcd5 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a> (std::ostringstream &dot_str, const std::string &node_separator) const</td></tr> +<tr class="memdesc:a88dda0ee0cffa26a188a041593d2fcd5 inherit pro_methods_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Serialize edges to dot format. <a href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">More...</a><br /></td></tr> +<tr class="separator:a88dda0ee0cffa26a188a041593d2fcd5 inherit pro_methods_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="inherit_header pro_attribs_classclaragenomics_1_1Graph"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classclaragenomics_1_1Graph')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></td></tr> +<tr class="memitem:a8b53264154b5caed266385a007e33404 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a8b53264154b5caed266385a007e33404"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a></td></tr> +<tr class="memdesc:a8b53264154b5caed266385a007e33404 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">List of adjacent nodes per node ID. <br /></td></tr> +<tr class="separator:a8b53264154b5caed266385a007e33404 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a4089c636086324cae1f2a2bde56c8b33 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a4089c636086324cae1f2a2bde56c8b33"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>, <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a>, <a class="el" href="structclaragenomics_1_1PairHash.html">PairHash</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a></td></tr> +<tr class="memdesc:a4089c636086324cae1f2a2bde56c8b33 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">All edges in the graph. <br /></td></tr> +<tr class="separator:a4089c636086324cae1f2a2bde56c8b33 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a5da2769d7e5bebd1d74c4899e3aad2c5 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="a5da2769d7e5bebd1d74c4899e3aad2c5"></a> +std::unordered_map< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a>, std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a></td></tr> +<tr class="memdesc:a5da2769d7e5bebd1d74c4899e3aad2c5 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">Label per node. <br /></td></tr> +<tr class="separator:a5da2769d7e5bebd1d74c4899e3aad2c5 inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ada271fc17a3a6e86f5dcc78c4caa729c inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memItemLeft" align="right" valign="top"><a id="ada271fc17a3a6e86f5dcc78c4caa729c"></a> +const std::vector< <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">empty_</a></td></tr> +<tr class="memdesc:ada271fc17a3a6e86f5dcc78c4caa729c inherit pro_attribs_classclaragenomics_1_1Graph"><td class="mdescLeft"> </td><td class="mdescRight">An empty list representing no connectivity. <br /></td></tr> +<tr class="separator:ada271fc17a3a6e86f5dcc78c4caa729c inherit pro_attribs_classclaragenomics_1_1Graph"><td class="memSeparator" colspan="2"> </td></tr> +</table> +<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> +<div class="textblock"><p><a class="el" href="classclaragenomics_1_1UndirectedGraph.html" title="UndirectedGraph Object representing an undirected graph structure.">UndirectedGraph</a> Object representing an undirected graph structure. </p> +</div><h2 class="groupheader">Member Function Documentation</h2> +<a id="a47c5ee6b9616ab24222526f4dcd1fb04"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a47c5ee6b9616ab24222526f4dcd1fb04">◆ </a></span>add_edge()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">void claragenomics::UndirectedGraph::add_edge </td> + <td>(</td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> </td> + <td class="paramname"><em>node_id_from</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> </td> + <td class="paramname"><em>node_id_to</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype"><a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> </td> + <td class="paramname"><em>weight</em> = <code>0</code> </td> + </tr> + <tr> + <td></td> + <td>)</td> + <td></td><td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Add undirected edges to graph. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">node_id_from</td><td>Source node ID </td></tr> + <tr><td class="paramname">node_id_to</td><td>Sink node ID </td></tr> + <tr><td class="paramname">weight</td><td>Edge weight </td></tr> + </table> + </dd> +</dl> + +</div> +</div> +<a id="a64b119c6ca6049b081ddde7db3c87e3f"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a64b119c6ca6049b081ddde7db3c87e3f">◆ </a></span>serialize_to_dot()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">std::string claragenomics::UndirectedGraph::serialize_to_dot </td> + <td>(</td> + <td class="paramname"></td><td>)</td> + <td> const</td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">inline</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Serialize graph structure to dot format. </p> +<dl class="section return"><dt>Returns</dt><dd>A string encoding the graph in dot format </dd></dl> + +</div> +</div> +<hr/>The documentation for this class was generated from the following file:<ul> +<li>common/utils/include/claragenomics/utils/<a class="el" 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adcb158df..084523f35 100644 --- a/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Aligner-members.html +++ b/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Aligner-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Aligner.html b/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Aligner.html index 9776b2059..7e015e945 100644 --- a/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Aligner.html +++ b/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Aligner.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment-members.html b/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment-members.html index 415df54d1..9c6b2c9ec 100644 --- a/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment-members.html +++ b/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -80,6 +80,7 @@ <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">get_query_sequence</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">claragenomics::cudaaligner::Alignment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">get_status</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">claragenomics::cudaaligner::Alignment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4a61cdee74c32930f49cb878fc17db57">get_target_sequence</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">claragenomics::cudaaligner::Alignment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">~Alignment</a>()=default</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">claragenomics::cudaaligner::Alignment</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> </table></div><!-- contents --> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> diff --git a/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment.html b/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment.html index 19ada95e8..f10e53258 100644 --- a/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment.html +++ b/docs/cpp/classclaragenomics_1_1cudaaligner_1_1Alignment.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -81,6 +81,10 @@ <table class="memberdecls"> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> Public Member Functions</h2></td></tr> +<tr class="memitem:a6479df67f21d643782abfed873218ea8"><td class="memItemLeft" align="right" valign="top"><a id="a6479df67f21d643782abfed873218ea8"></a> +virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">~Alignment</a> ()=default</td></tr> +<tr class="memdesc:a6479df67f21d643782abfed873218ea8"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr> +<tr class="separator:a6479df67f21d643782abfed873218ea8"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:ab29dceafccd3cb0a2e87023c5d48a780"><td class="memItemLeft" align="right" valign="top"><a id="ab29dceafccd3cb0a2e87023c5d48a780"></a> virtual const std::string & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">get_query_sequence</a> () const =0</td></tr> <tr class="memdesc:ab29dceafccd3cb0a2e87023c5d48a780"><td class="mdescLeft"> </td><td class="mdescRight">Returns query sequence. <br /></td></tr> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index-members.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index-members.html index 750db639c..250699f7b 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index-members.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -73,19 +73,17 @@ <p>This is the complete list of members for <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a>, including all inherited members.</p> <table class="directory"> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afc23f3e71c65dc9ed5a9e49cf26ba645">create_index</a>(const std::vector< io::FastaParser * > &parsers, const std::uint64_t kmer_size, const std::uint64_t window_size, const std::vector< std::pair< std::uint64_t, std::uint64_t >> &ranges)</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">static</span></td></tr> - <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#acb29a3ba1a493f706a3ec25bc290b30a">create_index</a>()</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">static</span></td></tr> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a407a2466e8740a0f78a3ce876b87352b">directions_of_reads</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">create_index</a>(const io::FastaParser &parser, const read_id_t first_read_id, const read_id_t past_the_last_read_id, const std::uint64_t kmer_size, const std::uint64_t window_size, const bool hash_representations=true)</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">static</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">directions_of_reads</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">first_occurrence_of_representations</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">maximum_kmer_size</a>()</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a69fd1882260a7c55a45fe5e2a092b152">maximum_representation</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac5036778efd3c83f5bf048174a8ab824">minimum_representation</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">number_of_reads</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5c75f11d1683e4f863f14a4088a36306">positions_in_reads</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a4e5b3cf1c41146635ce9d51bbdfe2277">reached_end_of_input</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af8ad540ff0a2a244a35ae846ec745c24">read_id_and_representation_to_sketch_elements</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af03421436f827e88316c74b0b3af200e">read_id_to_read_length</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aec3176ac2d5e425b25dec14f411cbfe0">read_id_to_read_name</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aac33d8d2aa72bb227326a35f5b452de5">read_ids</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">positions_in_reads</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">read_id_to_read_length</a>(const read_id_t read_id) const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">read_id_to_read_name</a>(const read_id_t read_id) const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">read_ids</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">representations</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">unique_representations</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">~Index</a>()=default</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> </table></div><!-- contents --> <!-- start footer part --> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index.html index 5bb11076e..29c69d972 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Index.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -67,7 +67,6 @@ </div><!-- top --> <div class="header"> <div class="summary"> -<a href="#nested-classes">Classes</a> | <a href="#pub-methods">Public Member Functions</a> | <a href="#pub-static-methods">Static Public Member Functions</a> | <a href="classclaragenomics_1_1cudamapper_1_1Index-members.html">List of all members</a> </div> @@ -81,66 +80,54 @@ <p><code>#include <<a class="el" href="index_8hpp_source.html">index.hpp</a>></code></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">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html">RepresentationToSketchElements</a></td></tr> -<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html" title="RepresentationToSketchElements - representation, pointer to section of data arrays with sketch elemen...">RepresentationToSketchElements</a> - representation, pointer to section of data arrays with sketch elements with that representation and a given read_id, and a pointer to section of data arrays with sketch elements with that representation and all read_ids. <a href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#details">More...</a><br /></td></tr> -<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> -</table><table class="memberdecls"> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> Public Member Functions</h2></td></tr> <tr class="memitem:afcaccc9f9526d9c66280eca17ff3a4ac"><td class="memItemLeft" align="right" valign="top"><a id="afcaccc9f9526d9c66280eca17ff3a4ac"></a> virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">~Index</a> ()=default</td></tr> -<tr class="memdesc:afcaccc9f9526d9c66280eca17ff3a4ac"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor for <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a>. <br /></td></tr> +<tr class="memdesc:afcaccc9f9526d9c66280eca17ff3a4ac"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr> <tr class="separator:afcaccc9f9526d9c66280eca17ff3a4ac"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:a5c75f11d1683e4f863f14a4088a36306"><td class="memItemLeft" align="right" valign="top">virtual const std::vector< position_in_read_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5c75f11d1683e4f863f14a4088a36306">positions_in_reads</a> () const =0</td></tr> -<tr class="memdesc:a5c75f11d1683e4f863f14a4088a36306"><td class="mdescLeft"> </td><td class="mdescRight">returns an array of starting positions of sketch elements in their reads <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5c75f11d1683e4f863f14a4088a36306">More...</a><br /></td></tr> -<tr class="separator:a5c75f11d1683e4f863f14a4088a36306"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:aac33d8d2aa72bb227326a35f5b452de5"><td class="memItemLeft" align="right" valign="top">virtual const std::vector< read_id_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aac33d8d2aa72bb227326a35f5b452de5">read_ids</a> () const =0</td></tr> -<tr class="memdesc:aac33d8d2aa72bb227326a35f5b452de5"><td class="mdescLeft"> </td><td class="mdescRight">returns an array of reads ids for sketch elements <a href="classclaragenomics_1_1cudamapper_1_1Index.html#aac33d8d2aa72bb227326a35f5b452de5">More...</a><br /></td></tr> -<tr class="separator:aac33d8d2aa72bb227326a35f5b452de5"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:a407a2466e8740a0f78a3ce876b87352b"><td class="memItemLeft" align="right" valign="top">virtual const std::vector< <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">SketchElement::DirectionOfRepresentation</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a407a2466e8740a0f78a3ce876b87352b">directions_of_reads</a> () const =0</td></tr> -<tr class="memdesc:a407a2466e8740a0f78a3ce876b87352b"><td class="mdescLeft"> </td><td class="mdescRight">returns an array of directions in which sketch elements were read <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a407a2466e8740a0f78a3ce876b87352b">More...</a><br /></td></tr> -<tr class="separator:a407a2466e8740a0f78a3ce876b87352b"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a876d5e82f9fc36f481854f7d84e5fc80"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector< representation_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">representations</a> () const =0</td></tr> +<tr class="memdesc:a876d5e82f9fc36f481854f7d84e5fc80"><td class="mdescLeft"> </td><td class="mdescRight">returns an array of representations of sketch elements <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">More...</a><br /></td></tr> +<tr class="separator:a876d5e82f9fc36f481854f7d84e5fc80"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a5cfe03b47850170ec64d61d2dbef0401"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector< read_id_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">read_ids</a> () const =0</td></tr> +<tr class="memdesc:a5cfe03b47850170ec64d61d2dbef0401"><td class="mdescLeft"> </td><td class="mdescRight">returns an array of reads ids for sketch elements <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">More...</a><br /></td></tr> +<tr class="separator:a5cfe03b47850170ec64d61d2dbef0401"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a66e5d024befc410221610f454eff7183"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector< position_in_read_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">positions_in_reads</a> () const =0</td></tr> +<tr class="memdesc:a66e5d024befc410221610f454eff7183"><td class="mdescLeft"> </td><td class="mdescRight">returns an array of starting positions of sketch elements in their reads <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">More...</a><br /></td></tr> +<tr class="separator:a66e5d024befc410221610f454eff7183"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a5824f352fd89f69c9acc14430a3aa6cd"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector< <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">SketchElement::DirectionOfRepresentation</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">directions_of_reads</a> () const =0</td></tr> +<tr class="memdesc:a5824f352fd89f69c9acc14430a3aa6cd"><td class="mdescLeft"> </td><td class="mdescRight">returns an array of directions in which sketch elements were read <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">More...</a><br /></td></tr> +<tr class="separator:a5824f352fd89f69c9acc14430a3aa6cd"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ac59d309eeb226592a96622fec2b307fd"><td class="memItemLeft" align="right" valign="top">virtual const std::string & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">read_id_to_read_name</a> (const read_id_t read_id) const =0</td></tr> +<tr class="memdesc:ac59d309eeb226592a96622fec2b307fd"><td class="mdescLeft"> </td><td class="mdescRight">returns read name of read with the given read_id <a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">More...</a><br /></td></tr> +<tr class="separator:ac59d309eeb226592a96622fec2b307fd"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:af44999c8852d5915d585c55a1a95c74a"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector< representation_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">unique_representations</a> () const =0</td></tr> +<tr class="memdesc:af44999c8852d5915d585c55a1a95c74a"><td class="mdescLeft"> </td><td class="mdescRight">returns an array where each representation is recorder only once, sorted by representation <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">More...</a><br /></td></tr> +<tr class="separator:af44999c8852d5915d585c55a1a95c74a"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:af4f69a9003fedb9ca11665d5faa43bff"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector< std::uint32_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">first_occurrence_of_representations</a> () const =0</td></tr> +<tr class="memdesc:af4f69a9003fedb9ca11665d5faa43bff"><td class="mdescLeft"> </td><td class="mdescRight">returns first occurrence of corresponding representation from <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a" title="returns an array where each representation is recorder only once, sorted by representation">unique_representations()</a> in data arrays <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">More...</a><br /></td></tr> +<tr class="separator:af4f69a9003fedb9ca11665d5faa43bff"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a59186cdd6dbfd21baeb07e80bd4354d4"><td class="memItemLeft" align="right" valign="top">virtual const std::uint32_t & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">read_id_to_read_length</a> (const read_id_t read_id) const =0</td></tr> +<tr class="memdesc:a59186cdd6dbfd21baeb07e80bd4354d4"><td class="mdescLeft"> </td><td class="mdescRight">returns read length for the read with the gived read_id <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">More...</a><br /></td></tr> +<tr class="separator:a59186cdd6dbfd21baeb07e80bd4354d4"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:ac9e936ae3809c82894a22a5ddb6bb937"><td class="memItemLeft" align="right" valign="top">virtual std::uint64_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">number_of_reads</a> () const =0</td></tr> <tr class="memdesc:ac9e936ae3809c82894a22a5ddb6bb937"><td class="mdescLeft"> </td><td class="mdescRight">returns number of reads in input data <a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">More...</a><br /></td></tr> <tr class="separator:ac9e936ae3809c82894a22a5ddb6bb937"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:aec3176ac2d5e425b25dec14f411cbfe0"><td class="memItemLeft" align="right" valign="top">virtual const std::vector< std::string > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aec3176ac2d5e425b25dec14f411cbfe0">read_id_to_read_name</a> () const =0</td></tr> -<tr class="memdesc:aec3176ac2d5e425b25dec14f411cbfe0"><td class="mdescLeft"> </td><td class="mdescRight">returns mapping of internal read id that goes from 0 to number_of_reads-1 to actual read name from the input <a href="classclaragenomics_1_1cudamapper_1_1Index.html#aec3176ac2d5e425b25dec14f411cbfe0">More...</a><br /></td></tr> -<tr class="separator:aec3176ac2d5e425b25dec14f411cbfe0"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:af03421436f827e88316c74b0b3af200e"><td class="memItemLeft" align="right" valign="top">virtual const std::vector< std::uint32_t > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af03421436f827e88316c74b0b3af200e">read_id_to_read_length</a> () const =0</td></tr> -<tr class="memdesc:af03421436f827e88316c74b0b3af200e"><td class="mdescLeft"> </td><td class="mdescRight">returns mapping of internal read id that goes from 0 to read lengths for that read <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af03421436f827e88316c74b0b3af200e">More...</a><br /></td></tr> -<tr class="separator:af03421436f827e88316c74b0b3af200e"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:ac5036778efd3c83f5bf048174a8ab824"><td class="memItemLeft" align="right" valign="top">virtual std::uint64_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac5036778efd3c83f5bf048174a8ab824">minimum_representation</a> () const =0</td></tr> -<tr class="memdesc:ac5036778efd3c83f5bf048174a8ab824"><td class="mdescLeft"> </td><td class="mdescRight">minimum possible representation <a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac5036778efd3c83f5bf048174a8ab824">More...</a><br /></td></tr> -<tr class="separator:ac5036778efd3c83f5bf048174a8ab824"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:a69fd1882260a7c55a45fe5e2a092b152"><td class="memItemLeft" align="right" valign="top">virtual std::uint64_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a69fd1882260a7c55a45fe5e2a092b152">maximum_representation</a> () const =0</td></tr> -<tr class="memdesc:a69fd1882260a7c55a45fe5e2a092b152"><td class="mdescLeft"> </td><td class="mdescRight">maximum possible representation <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a69fd1882260a7c55a45fe5e2a092b152">More...</a><br /></td></tr> -<tr class="separator:a69fd1882260a7c55a45fe5e2a092b152"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:af8ad540ff0a2a244a35ae846ec745c24"><td class="memItemLeft" align="right" valign="top">virtual const std::vector< std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html">RepresentationToSketchElements</a> > > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af8ad540ff0a2a244a35ae846ec745c24">read_id_and_representation_to_sketch_elements</a> () const =0</td></tr> -<tr class="memdesc:af8ad540ff0a2a244a35ae846ec745c24"><td class="mdescLeft"> </td><td class="mdescRight">For each read_id (outer vector) returns a vector in which each element contains a representation from that read, pointer to section of data arrays with sketch elements with that representation and that read_id, and pointer to section of data arrays with skecth elements with that representation and all read_ids. There elements are sorted by representation in increasing order. <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af8ad540ff0a2a244a35ae846ec745c24">More...</a><br /></td></tr> -<tr class="separator:af8ad540ff0a2a244a35ae846ec745c24"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:a4e5b3cf1c41146635ce9d51bbdfe2277"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a4e5b3cf1c41146635ce9d51bbdfe2277">reached_end_of_input</a> () const =0</td></tr> -<tr class="memdesc:a4e5b3cf1c41146635ce9d51bbdfe2277"><td class="mdescLeft"> </td><td class="mdescRight">Returns whether there are any more reads to process in the reads file (e.g FASTA file) <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a4e5b3cf1c41146635ce9d51bbdfe2277">More...</a><br /></td></tr> -<tr class="separator:a4e5b3cf1c41146635ce9d51bbdfe2277"><td class="memSeparator" colspan="2"> </td></tr> </table><table class="memberdecls"> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a> Static Public Member Functions</h2></td></tr> -<tr class="memitem:afc23f3e71c65dc9ed5a9e49cf26ba645"><td class="memItemLeft" align="right" valign="top">static std::unique_ptr< <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afc23f3e71c65dc9ed5a9e49cf26ba645">create_index</a> (const std::vector< <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">io::FastaParser</a> * > &parsers, const std::uint64_t kmer_size, const std::uint64_t window_size, const std::vector< std::pair< std::uint64_t, std::uint64_t >> &ranges)</td></tr> -<tr class="memdesc:afc23f3e71c65dc9ed5a9e49cf26ba645"><td class="mdescLeft"> </td><td class="mdescRight">generates a mapping of (k,w)-kmer-representation to all of its occurrences for one or more sequences <a href="classclaragenomics_1_1cudamapper_1_1Index.html#afc23f3e71c65dc9ed5a9e49cf26ba645">More...</a><br /></td></tr> -<tr class="separator:afc23f3e71c65dc9ed5a9e49cf26ba645"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:acb29a3ba1a493f706a3ec25bc290b30a"><td class="memItemLeft" align="right" valign="top">static std::unique_ptr< <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#acb29a3ba1a493f706a3ec25bc290b30a">create_index</a> ()</td></tr> -<tr class="memdesc:acb29a3ba1a493f706a3ec25bc290b30a"><td class="mdescLeft"> </td><td class="mdescRight">creates an empty <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> <a href="classclaragenomics_1_1cudamapper_1_1Index.html#acb29a3ba1a493f706a3ec25bc290b30a">More...</a><br /></td></tr> -<tr class="separator:acb29a3ba1a493f706a3ec25bc290b30a"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:af9247d4b637615bf5912acc57b27b919"><td class="memItemLeft" align="right" valign="top">static uint64_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">maximum_kmer_size</a> ()</td></tr> -<tr class="memdesc:af9247d4b637615bf5912acc57b27b919"><td class="mdescLeft"> </td><td class="mdescRight">Return the maximum kmer length allowable. This is just the size of the representation in bits divided by two (since 2 bits are required to represent a DNA nucleotide). <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">More...</a><br /></td></tr> +<tr class="memdesc:af9247d4b637615bf5912acc57b27b919"><td class="mdescLeft"> </td><td class="mdescRight">Return the maximum kmer length allowable. <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">More...</a><br /></td></tr> <tr class="separator:af9247d4b637615bf5912acc57b27b919"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a47c3cb89daa4076243dd5977acfb7ccf"><td class="memItemLeft" align="right" valign="top">static std::unique_ptr< <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">create_index</a> (const <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">io::FastaParser</a> &parser, const read_id_t first_read_id, const read_id_t past_the_last_read_id, const std::uint64_t kmer_size, const std::uint64_t window_size, const bool hash_representations=true)</td></tr> +<tr class="memdesc:a47c3cb89daa4076243dd5977acfb7ccf"><td class="mdescLeft"> </td><td class="mdescRight">generates a mapping of (k,w)-kmer-representation to all of its occurrences for one or more sequences <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">More...</a><br /></td></tr> +<tr class="separator:a47c3cb89daa4076243dd5977acfb7ccf"><td class="memSeparator" colspan="2"> </td></tr> </table> <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> <div class="textblock"><p><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences. </p> </div><h2 class="groupheader">Member Function Documentation</h2> -<a id="acb29a3ba1a493f706a3ec25bc290b30a"></a> -<h2 class="memtitle"><span class="permalink"><a href="#acb29a3ba1a493f706a3ec25bc290b30a">◆ </a></span>create_index() <span class="overload">[1/2]</span></h2> +<a id="a47c3cb89daa4076243dd5977acfb7ccf"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a47c3cb89daa4076243dd5977acfb7ccf">◆ </a></span>create_index()</h2> <div class="memitem"> <div class="memproto"> @@ -151,36 +138,20 @@ <h2 class="memtitle"><span class="permalink"><a href="#acb29a3ba1a493f706a3ec25b <tr> <td class="memname">static std::unique_ptr<<a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>> claragenomics::cudamapper::Index::create_index </td> <td>(</td> - <td class="paramname"></td><td>)</td> + <td class="paramtype">const <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">io::FastaParser</a> & </td> + <td class="paramname"><em>parser</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> <td></td> + <td class="paramtype">const read_id_t </td> + <td class="paramname"><em>first_read_id</em>, </td> </tr> - </table> - </td> - <td class="mlabels-right"> -<span class="mlabels"><span class="mlabel">static</span></span> </td> - </tr> -</table> -</div><div class="memdoc"> - -<p>creates an empty <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> </p> -<dl class="section return"><dt>Returns</dt><dd>empty instacne of <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> </dd></dl> - -</div> -</div> -<a id="afc23f3e71c65dc9ed5a9e49cf26ba645"></a> -<h2 class="memtitle"><span class="permalink"><a href="#afc23f3e71c65dc9ed5a9e49cf26ba645">◆ </a></span>create_index() <span class="overload">[2/2]</span></h2> - -<div class="memitem"> -<div class="memproto"> -<table class="mlabels"> - <tr> - <td class="mlabels-left"> - <table class="memname"> <tr> - <td class="memname">static std::unique_ptr<<a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>> claragenomics::cudamapper::Index::create_index </td> - <td>(</td> - <td class="paramtype">const std::vector< <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">io::FastaParser</a> * > & </td> - <td class="paramname"><em>parsers</em>, </td> + <td class="paramkey"></td> + <td></td> + <td class="paramtype">const read_id_t </td> + <td class="paramname"><em>past_the_last_read_id</em>, </td> </tr> <tr> <td class="paramkey"></td> @@ -197,8 +168,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#afc23f3e71c65dc9ed5a9e49c <tr> <td class="paramkey"></td> <td></td> - <td class="paramtype">const std::vector< std::pair< std::uint64_t, std::uint64_t >> & </td> - <td class="paramname"><em>ranges</em> </td> + <td class="paramtype">const bool </td> + <td class="paramname"><em>hash_representations</em> = <code>true</code> </td> </tr> <tr> <td></td> @@ -216,10 +187,12 @@ <h2 class="memtitle"><span class="permalink"><a href="#afc23f3e71c65dc9ed5a9e49c <p>generates a mapping of (k,w)-kmer-representation to all of its occurrences for one or more sequences </p> <dl class="params"><dt>Parameters</dt><dd> <table class="params"> - <tr><td class="paramname">parsers</td><td>Vector of parsers for each element in ranges. Size of this vector must match size of ranges. </td></tr> + <tr><td class="paramname">parser</td><td>parser for the whole input file (part that goes into this index is determined by first_read_id and past_the_last_read_id) </td></tr> + <tr><td class="paramname">first_read_id</td><td>read_id of the first read to the included in this index </td></tr> + <tr><td class="paramname">past_the_last_read_id</td><td>read_id+1 of the last read to be included in this index </td></tr> <tr><td class="paramname">kmer_size</td><td>k - the kmer length </td></tr> - <tr><td class="paramname">window_size</td><td>w - the length of the sliding window used to find sketch elements </td></tr> - <tr><td class="paramname">ranges</td><td>- the ranges of reads in the query file to use for mapping, index by their position (e.g in the FASTA file) </td></tr> + <tr><td class="paramname">window_size</td><td>w - the length of the sliding window used to find sketch elements (i.e. the number of adjacent kmers in a window, adjacent = shifted by one basepair) </td></tr> + <tr><td class="paramname">hash_representations</td><td>- if true, hash kmer representations </td></tr> </table> </dd> </dl> @@ -227,8 +200,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#afc23f3e71c65dc9ed5a9e49c </div> </div> -<a id="a407a2466e8740a0f78a3ce876b87352b"></a> -<h2 class="memtitle"><span class="permalink"><a href="#a407a2466e8740a0f78a3ce876b87352b">◆ </a></span>directions_of_reads()</h2> +<a id="a5824f352fd89f69c9acc14430a3aa6cd"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a5824f352fd89f69c9acc14430a3aa6cd">◆ </a></span>directions_of_reads()</h2> <div class="memitem"> <div class="memproto"> @@ -237,7 +210,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a407a2466e8740a0f78a3ce87 <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual const std::vector<<a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">SketchElement::DirectionOfRepresentation</a>>& claragenomics::cudamapper::Index::directions_of_reads </td> + <td class="memname">virtual const thrust::device_vector<<a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">SketchElement::DirectionOfRepresentation</a>>& claragenomics::cudamapper::Index::directions_of_reads </td> <td>(</td> <td class="paramname"></td><td>)</td> <td> const</td> @@ -255,36 +228,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#a407a2466e8740a0f78a3ce87 </div> </div> -<a id="af9247d4b637615bf5912acc57b27b919"></a> -<h2 class="memtitle"><span class="permalink"><a href="#af9247d4b637615bf5912acc57b27b919">◆ </a></span>maximum_kmer_size()</h2> - -<div class="memitem"> -<div class="memproto"> -<table class="mlabels"> - <tr> - <td class="mlabels-left"> - <table class="memname"> - <tr> - <td class="memname">static uint64_t claragenomics::cudamapper::Index::maximum_kmer_size </td> - <td>(</td> - <td class="paramname"></td><td>)</td> - <td></td> - </tr> - </table> - </td> - <td class="mlabels-right"> -<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td> - </tr> -</table> -</div><div class="memdoc"> - -<p>Return the maximum kmer length allowable. This is just the size of the representation in bits divided by two (since 2 bits are required to represent a DNA nucleotide). </p> -<dl class="section return"><dt>Returns</dt><dd>Return the maximum kmer length allowable </dd></dl> - -</div> -</div> -<a id="a69fd1882260a7c55a45fe5e2a092b152"></a> -<h2 class="memtitle"><span class="permalink"><a href="#a69fd1882260a7c55a45fe5e2a092b152">◆ </a></span>maximum_representation()</h2> +<a id="af4f69a9003fedb9ca11665d5faa43bff"></a> +<h2 class="memtitle"><span class="permalink"><a href="#af4f69a9003fedb9ca11665d5faa43bff">◆ </a></span>first_occurrence_of_representations()</h2> <div class="memitem"> <div class="memproto"> @@ -293,7 +238,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a69fd1882260a7c55a45fe5e2 <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual std::uint64_t claragenomics::cudamapper::Index::maximum_representation </td> + <td class="memname">virtual const thrust::device_vector<std::uint32_t>& claragenomics::cudamapper::Index::first_occurrence_of_representations </td> <td>(</td> <td class="paramname"></td><td>)</td> <td> const</td> @@ -306,13 +251,13 @@ <h2 class="memtitle"><span class="permalink"><a href="#a69fd1882260a7c55a45fe5e2 </table> </div><div class="memdoc"> -<p>maximum possible representation </p> -<dl class="section return"><dt>Returns</dt><dd>the largest possible representation </dd></dl> +<p>returns first occurrence of corresponding representation from <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a" title="returns an array where each representation is recorder only once, sorted by representation">unique_representations()</a> in data arrays </p> +<dl class="section return"><dt>Returns</dt><dd>first occurrence of corresponding representation from <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a" title="returns an array where each representation is recorder only once, sorted by representation">unique_representations()</a> in data arrays </dd></dl> </div> </div> -<a id="ac5036778efd3c83f5bf048174a8ab824"></a> -<h2 class="memtitle"><span class="permalink"><a href="#ac5036778efd3c83f5bf048174a8ab824">◆ </a></span>minimum_representation()</h2> +<a id="af9247d4b637615bf5912acc57b27b919"></a> +<h2 class="memtitle"><span class="permalink"><a href="#af9247d4b637615bf5912acc57b27b919">◆ </a></span>maximum_kmer_size()</h2> <div class="memitem"> <div class="memproto"> @@ -321,21 +266,21 @@ <h2 class="memtitle"><span class="permalink"><a href="#ac5036778efd3c83f5bf04817 <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual std::uint64_t claragenomics::cudamapper::Index::minimum_representation </td> + <td class="memname">static uint64_t claragenomics::cudamapper::Index::maximum_kmer_size </td> <td>(</td> <td class="paramname"></td><td>)</td> - <td> const</td> + <td></td> </tr> </table> </td> <td class="mlabels-right"> -<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td> +<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td> </tr> </table> </div><div class="memdoc"> -<p>minimum possible representation </p> -<dl class="section return"><dt>Returns</dt><dd>the smallest possible representation </dd></dl> +<p>Return the maximum kmer length allowable. </p> +<dl class="section return"><dt>Returns</dt><dd>Return the maximum kmer length allowable </dd></dl> </div> </div> @@ -367,8 +312,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#ac9e936ae3809c82894a22a5d </div> </div> -<a id="a5c75f11d1683e4f863f14a4088a36306"></a> -<h2 class="memtitle"><span class="permalink"><a href="#a5c75f11d1683e4f863f14a4088a36306">◆ </a></span>positions_in_reads()</h2> +<a id="a66e5d024befc410221610f454eff7183"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a66e5d024befc410221610f454eff7183">◆ </a></span>positions_in_reads()</h2> <div class="memitem"> <div class="memproto"> @@ -377,7 +322,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a5c75f11d1683e4f863f14a40 <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual const std::vector<position_in_read_t>& claragenomics::cudamapper::Index::positions_in_reads </td> + <td class="memname">virtual const thrust::device_vector<position_in_read_t>& claragenomics::cudamapper::Index::positions_in_reads </td> <td>(</td> <td class="paramname"></td><td>)</td> <td> const</td> @@ -395,8 +340,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#a5c75f11d1683e4f863f14a40 </div> </div> -<a id="a4e5b3cf1c41146635ce9d51bbdfe2277"></a> -<h2 class="memtitle"><span class="permalink"><a href="#a4e5b3cf1c41146635ce9d51bbdfe2277">◆ </a></span>reached_end_of_input()</h2> +<a id="a59186cdd6dbfd21baeb07e80bd4354d4"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a59186cdd6dbfd21baeb07e80bd4354d4">◆ </a></span>read_id_to_read_length()</h2> <div class="memitem"> <div class="memproto"> @@ -405,9 +350,10 @@ <h2 class="memtitle"><span class="permalink"><a href="#a4e5b3cf1c41146635ce9d51b <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual bool claragenomics::cudamapper::Index::reached_end_of_input </td> + <td class="memname">virtual const std::uint32_t& claragenomics::cudamapper::Index::read_id_to_read_length </td> <td>(</td> - <td class="paramname"></td><td>)</td> + <td class="paramtype">const read_id_t </td> + <td class="paramname"><em>read_id</em></td><td>)</td> <td> const</td> </tr> </table> @@ -418,13 +364,19 @@ <h2 class="memtitle"><span class="permalink"><a href="#a4e5b3cf1c41146635ce9d51b </table> </div><div class="memdoc"> -<p>Returns whether there are any more reads to process in the reads file (e.g FASTA file) </p> -<dl class="section return"><dt>Returns</dt><dd>Returns whether there are any more reads to process in the reads file (e.g FASTA file) </dd></dl> +<p>returns read length for the read with the gived read_id </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">read_id</td><td></td></tr> + </table> + </dd> +</dl> +<dl class="section return"><dt>Returns</dt><dd>read length for the read with the gived read_id </dd></dl> </div> </div> -<a id="af8ad540ff0a2a244a35ae846ec745c24"></a> -<h2 class="memtitle"><span class="permalink"><a href="#af8ad540ff0a2a244a35ae846ec745c24">◆ </a></span>read_id_and_representation_to_sketch_elements()</h2> +<a id="ac59d309eeb226592a96622fec2b307fd"></a> +<h2 class="memtitle"><span class="permalink"><a href="#ac59d309eeb226592a96622fec2b307fd">◆ </a></span>read_id_to_read_name()</h2> <div class="memitem"> <div class="memproto"> @@ -433,9 +385,10 @@ <h2 class="memtitle"><span class="permalink"><a href="#af8ad540ff0a2a244a35ae846 <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual const std::vector<std::vector<<a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html">RepresentationToSketchElements</a>> >& claragenomics::cudamapper::Index::read_id_and_representation_to_sketch_elements </td> + <td class="memname">virtual const std::string& claragenomics::cudamapper::Index::read_id_to_read_name </td> <td>(</td> - <td class="paramname"></td><td>)</td> + <td class="paramtype">const read_id_t </td> + <td class="paramname"><em>read_id</em></td><td>)</td> <td> const</td> </tr> </table> @@ -446,13 +399,19 @@ <h2 class="memtitle"><span class="permalink"><a href="#af8ad540ff0a2a244a35ae846 </table> </div><div class="memdoc"> -<p>For each read_id (outer vector) returns a vector in which each element contains a representation from that read, pointer to section of data arrays with sketch elements with that representation and that read_id, and pointer to section of data arrays with skecth elements with that representation and all read_ids. There elements are sorted by representation in increasing order. </p> -<dl class="section return"><dt>Returns</dt><dd>the mapping </dd></dl> +<p>returns read name of read with the given read_id </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">read_id</td><td></td></tr> + </table> + </dd> +</dl> +<dl class="section return"><dt>Returns</dt><dd>read name of read with the given read_id </dd></dl> </div> </div> -<a id="af03421436f827e88316c74b0b3af200e"></a> -<h2 class="memtitle"><span class="permalink"><a href="#af03421436f827e88316c74b0b3af200e">◆ </a></span>read_id_to_read_length()</h2> +<a id="a5cfe03b47850170ec64d61d2dbef0401"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a5cfe03b47850170ec64d61d2dbef0401">◆ </a></span>read_ids()</h2> <div class="memitem"> <div class="memproto"> @@ -461,7 +420,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#af03421436f827e88316c74b0 <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual const std::vector<std::uint32_t>& claragenomics::cudamapper::Index::read_id_to_read_length </td> + <td class="memname">virtual const thrust::device_vector<read_id_t>& claragenomics::cudamapper::Index::read_ids </td> <td>(</td> <td class="paramname"></td><td>)</td> <td> const</td> @@ -474,13 +433,13 @@ <h2 class="memtitle"><span class="permalink"><a href="#af03421436f827e88316c74b0 </table> </div><div class="memdoc"> -<p>returns mapping of internal read id that goes from 0 to read lengths for that read </p> -<dl class="section return"><dt>Returns</dt><dd>mapping of internal read id that goes from 0 to read lengths for that read </dd></dl> +<p>returns an array of reads ids for sketch elements </p> +<dl class="section return"><dt>Returns</dt><dd>an array of reads ids for sketch elements </dd></dl> </div> </div> -<a id="aec3176ac2d5e425b25dec14f411cbfe0"></a> -<h2 class="memtitle"><span class="permalink"><a href="#aec3176ac2d5e425b25dec14f411cbfe0">◆ </a></span>read_id_to_read_name()</h2> +<a id="a876d5e82f9fc36f481854f7d84e5fc80"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a876d5e82f9fc36f481854f7d84e5fc80">◆ </a></span>representations()</h2> <div class="memitem"> <div class="memproto"> @@ -489,7 +448,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#aec3176ac2d5e425b25dec14f <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual const std::vector<std::string>& claragenomics::cudamapper::Index::read_id_to_read_name </td> + <td class="memname">virtual const thrust::device_vector<representation_t>& claragenomics::cudamapper::Index::representations </td> <td>(</td> <td class="paramname"></td><td>)</td> <td> const</td> @@ -502,13 +461,13 @@ <h2 class="memtitle"><span class="permalink"><a href="#aec3176ac2d5e425b25dec14f </table> </div><div class="memdoc"> -<p>returns mapping of internal read id that goes from 0 to number_of_reads-1 to actual read name from the input </p> -<dl class="section return"><dt>Returns</dt><dd>mapping of internal read id that goes from 0 to number_of_reads-1 to actual read name from the input </dd></dl> +<p>returns an array of representations of sketch elements </p> +<dl class="section return"><dt>Returns</dt><dd>an array of representations of sketch elements </dd></dl> </div> </div> -<a id="aac33d8d2aa72bb227326a35f5b452de5"></a> -<h2 class="memtitle"><span class="permalink"><a href="#aac33d8d2aa72bb227326a35f5b452de5">◆ </a></span>read_ids()</h2> +<a id="af44999c8852d5915d585c55a1a95c74a"></a> +<h2 class="memtitle"><span class="permalink"><a href="#af44999c8852d5915d585c55a1a95c74a">◆ </a></span>unique_representations()</h2> <div class="memitem"> <div class="memproto"> @@ -517,7 +476,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#aac33d8d2aa72bb227326a35f <td class="mlabels-left"> <table class="memname"> <tr> - <td class="memname">virtual const std::vector<read_id_t>& claragenomics::cudamapper::Index::read_ids </td> + <td class="memname">virtual const thrust::device_vector<representation_t>& claragenomics::cudamapper::Index::unique_representations </td> <td>(</td> <td class="paramname"></td><td>)</td> <td> const</td> @@ -530,8 +489,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#aac33d8d2aa72bb227326a35f </table> </div><div class="memdoc"> -<p>returns an array of reads ids for sketch elements </p> -<dl class="section return"><dt>Returns</dt><dd>an array of reads ids for sketch elements </dd></dl> +<p>returns an array where each representation is recorder only once, sorted by representation </p> +<dl class="section return"><dt>Returns</dt><dd>an array where each representation is recorder only once, sorted by representation </dd></dl> </div> </div> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Matcher-members.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Matcher-members.html new file mode 100644 index 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class="title">claragenomics::cudamapper::Matcher Member List</div> </div> +</div><!--header--> +<div class="contents"> + +<p>This is the complete list of members for <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">claragenomics::cudamapper::Matcher</a>, including all inherited members.</p> +<table class="directory"> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">anchors</a>()=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">claragenomics::cudamapper::Matcher</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">create_matcher</a>(const Index &query_index, const Index &target_index)</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">claragenomics::cudamapper::Matcher</a></td><td class="entry"><span class="mlabel">static</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac2f70fb6b1876d0fa81fd8c0189191ab">~Matcher</a>()=default</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">claragenomics::cudamapper::Matcher</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> +</table></div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Matcher.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Matcher.html new file mode 100644 index 000000000..9d082f2da --- /dev/null +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Matcher.html @@ -0,0 +1,187 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: claragenomics::cudamapper::Matcher Class 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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><b>cudamapper</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">Matcher</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="summary"> +<a href="#pub-methods">Public Member Functions</a> | +<a href="#pub-static-methods">Static Public Member Functions</a> | +<a href="classclaragenomics_1_1cudamapper_1_1Matcher-members.html">List of all members</a> </div> + <div class="headertitle"> +<div class="title">claragenomics::cudamapper::Matcher Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span><div class="ingroups"><a class="el" href="group__cudamapper.html">CUDA mapper package</a></div></div> </div> +</div><!--header--> +<div class="contents"> + +<p><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> - base matcher. + <a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#details">More...</a></p> + +<p><code>#include <<a class="el" href="matcher_8hpp_source.html">matcher.hpp</a>></code></p> +<table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> +Public Member Functions</h2></td></tr> +<tr class="memitem:ac2f70fb6b1876d0fa81fd8c0189191ab"><td class="memItemLeft" align="right" valign="top"><a id="ac2f70fb6b1876d0fa81fd8c0189191ab"></a> +virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac2f70fb6b1876d0fa81fd8c0189191ab">~Matcher</a> ()=default</td></tr> +<tr class="memdesc:ac2f70fb6b1876d0fa81fd8c0189191ab"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr> +<tr class="separator:ac2f70fb6b1876d0fa81fd8c0189191ab"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ac3de5ba06b0c7ef0329caf71ae98f2d2"><td class="memItemLeft" align="right" valign="top">virtual thrust::device_vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">anchors</a> ()=0</td></tr> +<tr class="memdesc:ac3de5ba06b0c7ef0329caf71ae98f2d2"><td class="mdescLeft"> </td><td class="mdescRight">returns anchors <a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">More...</a><br /></td></tr> +<tr class="separator:ac3de5ba06b0c7ef0329caf71ae98f2d2"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a> +Static Public Member Functions</h2></td></tr> +<tr class="memitem:ae65a1507ddf1bf2aa046fc0eacfea752"><td class="memItemLeft" align="right" valign="top">static std::unique_ptr< <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">Matcher</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">create_matcher</a> (const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &query_index, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &target_index)</td></tr> +<tr class="memdesc:ae65a1507ddf1bf2aa046fc0eacfea752"><td class="mdescLeft"> </td><td class="mdescRight">Creates a <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> object. <a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">More...</a><br /></td></tr> +<tr class="separator:ae65a1507ddf1bf2aa046fc0eacfea752"><td class="memSeparator" colspan="2"> </td></tr> +</table> +<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> +<div class="textblock"><p><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> - base matcher. </p> +</div><h2 class="groupheader">Member Function Documentation</h2> +<a id="ac3de5ba06b0c7ef0329caf71ae98f2d2"></a> +<h2 class="memtitle"><span class="permalink"><a href="#ac3de5ba06b0c7ef0329caf71ae98f2d2">◆ </a></span>anchors()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">virtual thrust::device_vector<<a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a>>& claragenomics::cudamapper::Matcher::anchors </td> + <td>(</td> + <td class="paramname"></td><td>)</td> + <td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>returns anchors </p> +<dl class="section return"><dt>Returns</dt><dd>anchors </dd></dl> + +</div> +</div> +<a id="ae65a1507ddf1bf2aa046fc0eacfea752"></a> +<h2 class="memtitle"><span class="permalink"><a href="#ae65a1507ddf1bf2aa046fc0eacfea752">◆ </a></span>create_matcher()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">static std::unique_ptr<<a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">Matcher</a>> claragenomics::cudamapper::Matcher::create_matcher </td> + <td>(</td> + <td class="paramtype">const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> & </td> + <td class="paramname"><em>query_index</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype">const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> & </td> + <td class="paramname"><em>target_index</em> </td> + </tr> + <tr> + <td></td> + <td>)</td> + <td></td><td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">static</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Creates a <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> object. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">query_index</td><td></td></tr> + <tr><td class="paramname">target_index</td><td></td></tr> + </table> + </dd> +</dl> +<dl class="section return"><dt>Returns</dt><dd>matcher </dd></dl> + +</div> +</div> +<hr/>The documentation for this class was generated from the following file:<ul> +<li>cudamapper/include/claragenomics/cudamapper/<a class="el" href="matcher_8hpp_source.html">matcher.hpp</a></li> +</ul> +</div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper-members.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper-members.html index 361454711..df3d62f78 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper-members.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -74,7 +74,7 @@ <p>This is the complete list of members for <a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a>, including all inherited members.</p> <table class="directory"> <tr class="even"><td class="entry"><a class="el" href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">filter_overlaps</a>(std::vector< Overlap > &filtered_overlaps, const std::vector< Overlap > &overlaps, size_t min_residues=5, size_t min_overlap_len=0)</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></td><td class="entry"><span class="mlabel">static</span></td></tr> - <tr><td class="entry"><a class="el" href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">get_overlaps</a>(std::vector< Overlap > &overlaps, std::vector< Anchor > &anchors, const Index &index)=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">get_overlaps</a>(std::vector< Overlap > &overlaps, thrust::device_vector< Anchor > &anchors, const Index &index_query, const Index &index_target)=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">print_paf</a>(const std::vector< Overlap > &overlaps)</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></td><td class="entry"><span class="mlabel">static</span></td></tr> <tr><td class="entry"><a class="el" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">~Overlapper</a>()=default</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> </table></div><!-- contents --> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper.html index b2889915a..611664ac8 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Overlapper.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -83,9 +83,9 @@ virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">~Overlapper</a> ()=default</td></tr> <tr class="memdesc:ga569c8855bdf9806d3747b26fc7e98975"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor for <a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a>. <br /></td></tr> <tr class="separator:ga569c8855bdf9806d3747b26fc7e98975"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:ga5498f3d8b5eff6481c67fdf0a049c300"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">get_overlaps</a> (std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> > &overlaps, std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> > &anchors, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &index)=0</td></tr> -<tr class="memdesc:ga5498f3d8b5eff6481c67fdf0a049c300"><td class="mdescLeft"> </td><td class="mdescRight">returns overlaps for a set of reads <a href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">More...</a><br /></td></tr> -<tr class="separator:ga5498f3d8b5eff6481c67fdf0a049c300"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">get_overlaps</a> (std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> > &overlaps, thrust::device_vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> > &anchors, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &index_query, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &index_target)=0</td></tr> +<tr class="memdesc:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="mdescLeft"> </td><td class="mdescRight">returns overlaps for a set of reads <a href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">More...</a><br /></td></tr> +<tr class="separator:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="memSeparator" colspan="2"> </td></tr> </table><table class="memberdecls"> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a> Static Public Member Functions</h2></td></tr> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence-members.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence-members.html index 60a802ef0..991665443 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence-members.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence.html index facead973..980e29eb6 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1Sequence.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement-members.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement-members.html index 22ea95fef..7e81dd0b7 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement-members.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement.html b/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement.html index b831ba40d..4f321f3a9 100644 --- a/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement.html +++ b/docs/cpp/classclaragenomics_1_1cudamapper_1_1SketchElement.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch-members.html b/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch-members.html index c315c6f47..1ffb79841 100644 --- a/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch-members.html +++ b/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -77,10 +77,11 @@ <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">batch_id</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">generate_poa</a>()=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">get_consensus</a>(std::vector< std::string > &consensus, std::vector< std::vector< uint16_t >> &coverage, std::vector< claragenomics::cudapoa::StatusType > &output_status)=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">get_msa</a>(std::vector< std::vector< std::string >> &msa, std::vector< StatusType > &output_status)=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">get_total_poas</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">reset</a>()=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> - <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">~Batch</a>()=default</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">get_graphs</a>(std::vector< DirectedGraph > &graphs, std::vector< StatusType > &output_status)=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">get_msa</a>(std::vector< std::vector< std::string >> &msa, std::vector< StatusType > &output_status)=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">get_total_poas</a>() const =0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">reset</a>()=0</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> + <tr class="even"><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">~Batch</a>()=default</td><td class="entry"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> </table></div><!-- contents --> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> diff --git a/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch.html b/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch.html index b0e0595f9..fc9e8c852 100644 --- a/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch.html +++ b/docs/cpp/classclaragenomics_1_1cudapoa_1_1Batch.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -98,6 +98,9 @@ <tr class="memitem:ab39956c82d5d5a2d8df1b1695e15d9d2"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">get_msa</a> (std::vector< std::vector< std::string >> &msa, std::vector< <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> > &output_status)=0</td></tr> <tr class="memdesc:ab39956c82d5d5a2d8df1b1695e15d9d2"><td class="mdescLeft"> </td><td class="mdescRight">Get the multiple sequence alignments for each POA. <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">More...</a><br /></td></tr> <tr class="separator:ab39956c82d5d5a2d8df1b1695e15d9d2"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a0949cca1e89a40d759b0ca371512bb16"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">get_graphs</a> (std::vector< <a class="el" href="classclaragenomics_1_1DirectedGraph.html">DirectedGraph</a> > &graphs, std::vector< <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> > &output_status)=0</td></tr> +<tr class="memdesc:a0949cca1e89a40d759b0ca371512bb16"><td class="mdescLeft"> </td><td class="mdescRight">Get the graph representation for each POA. <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">More...</a><br /></td></tr> +<tr class="separator:a0949cca1e89a40d759b0ca371512bb16"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:ab807c4b01c2cddcdebb32952df13c0ec"><td class="memItemLeft" align="right" valign="top">virtual int32_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">batch_id</a> () const =0</td></tr> <tr class="memdesc:ab807c4b01c2cddcdebb32952df13c0ec"><td class="mdescLeft"> </td><td class="mdescRight">Return batch ID. <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">More...</a><br /></td></tr> <tr class="separator:ab807c4b01c2cddcdebb32952df13c0ec"><td class="memSeparator" colspan="2"> </td></tr> @@ -228,6 +231,52 @@ <h2 class="memtitle"><span class="permalink"><a href="#a3224d1595caa5950c34708f4 <table class="params"> <tr><td class="paramname">consensus</td><td>Reference to vector where consensus strings will be returned </td></tr> <tr><td class="paramname">coverage</td><td>Reference to vector where coverage of each base in each consensus string is returned </td></tr> + <tr><td class="paramname">output_status</td><td>Reference to vector where the errors during kernel execution is captured</td></tr> + </table> + </dd> +</dl> +<dl class="section return"><dt>Returns</dt><dd>Status indicating whether consensus generation is available for this batch. </dd></dl> + +</div> +</div> +<a id="a0949cca1e89a40d759b0ca371512bb16"></a> +<h2 class="memtitle"><span class="permalink"><a href="#a0949cca1e89a40d759b0ca371512bb16">◆ </a></span>get_graphs()</h2> + +<div class="memitem"> +<div class="memproto"> +<table class="mlabels"> + <tr> + <td class="mlabels-left"> + <table class="memname"> + <tr> + <td class="memname">virtual void claragenomics::cudapoa::Batch::get_graphs </td> + <td>(</td> + <td class="paramtype">std::vector< <a class="el" href="classclaragenomics_1_1DirectedGraph.html">DirectedGraph</a> > & </td> + <td class="paramname"><em>graphs</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype">std::vector< <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> > & </td> + <td class="paramname"><em>output_status</em> </td> + </tr> + <tr> + <td></td> + <td>)</td> + <td></td><td></td> + </tr> + </table> + </td> + <td class="mlabels-right"> +<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td> + </tr> +</table> +</div><div class="memdoc"> + +<p>Get the graph representation for each POA. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">graphs</td><td>Reference to a vector where directed graph of each poa is returned. </td></tr> <tr><td class="paramname">output_status</td><td>Reference to vector where the errors during kernel execution is captured </td></tr> </table> </dd> @@ -273,10 +322,11 @@ <h2 class="memtitle"><span class="permalink"><a href="#ab39956c82d5d5a2d8df1b169 <dl class="params"><dt>Parameters</dt><dd> <table class="params"> <tr><td class="paramname">msa</td><td>Reference to vector where msa strings of each poa is returned </td></tr> - <tr><td class="paramname">output_status</td><td>Reference to vector where the errors during kernel execution is captured </td></tr> + <tr><td class="paramname">output_status</td><td>Reference to vector where the errors during kernel execution is captured</td></tr> </table> </dd> </dl> +<dl class="section return"><dt>Returns</dt><dd>Status indicating whether MSA generation is available for this batch. </dd></dl> </div> </div> diff --git a/docs/cpp/classclaragenomics_1_1io_1_1FastaParser-members.html b/docs/cpp/classclaragenomics_1_1io_1_1FastaParser-members.html index eca4b0dbd..2a2559097 100644 --- a/docs/cpp/classclaragenomics_1_1io_1_1FastaParser-members.html +++ b/docs/cpp/classclaragenomics_1_1io_1_1FastaParser-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1io_1_1FastaParser.html b/docs/cpp/classclaragenomics_1_1io_1_1FastaParser.html index 814f390de..bb994c688 100644 --- a/docs/cpp/classclaragenomics_1_1io_1_1FastaParser.html +++ b/docs/cpp/classclaragenomics_1_1io_1_1FastaParser.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1scoped__device__switch-members.html b/docs/cpp/classclaragenomics_1_1scoped__device__switch-members.html index b0de9d603..dbe44b53e 100644 --- a/docs/cpp/classclaragenomics_1_1scoped__device__switch-members.html +++ b/docs/cpp/classclaragenomics_1_1scoped__device__switch-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classclaragenomics_1_1scoped__device__switch.html b/docs/cpp/classclaragenomics_1_1scoped__device__switch.html index 49adc7a48..786d63ac5 100644 --- a/docs/cpp/classclaragenomics_1_1scoped__device__switch.html +++ b/docs/cpp/classclaragenomics_1_1scoped__device__switch.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/classes.html b/docs/cpp/classes.html index 497bc127f..e600ef8ec 100644 --- a/docs/cpp/classes.html +++ b/docs/cpp/classes.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -66,51 +66,64 @@ <div class="title">Class Index</div> </div> </div><!--header--> <div class="contents"> -<div class="qindex"><a class="qindex" href="#letter_a">a</a> | <a class="qindex" href="#letter_b">b</a> | <a class="qindex" href="#letter_e">e</a> | <a class="qindex" href="#letter_f">f</a> | <a class="qindex" href="#letter_i">i</a> | <a class="qindex" href="#letter_o">o</a> | <a class="qindex" href="#letter_r">r</a> | <a class="qindex" href="#letter_s">s</a></div> +<div class="qindex"><a class="qindex" href="#letter_a">a</a> | <a class="qindex" href="#letter_b">b</a> | <a class="qindex" href="#letter_d">d</a> | <a class="qindex" 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cellpadding="0"><tr><td><div class="ah">  i  </div></td></tr></table> +<td valign="top"><a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html">FastaSequence</a> (claragenomics::io)   </td> +<td rowspan="2" valign="bottom"><a name="letter_o"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  o  </div></td></tr></table> </td> -<td rowspan="2" valign="bottom"><a name="letter_r"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  r  </div></td></tr></table> +<td valign="top"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html">Sequence</a> (claragenomics::cudamapper)   </td> +</tr> +<tr><td rowspan="2" valign="bottom"><a name="letter_g"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  g  </div></td></tr></table> </td> <td valign="top"><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html">SketchElement</a> (claragenomics::cudamapper)   </td> </tr> 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(claragenomics)   </td> +<td valign="top"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a> (claragenomics::cudamapper)   </td> +</tr> +<tr><td valign="top"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> (claragenomics::cudamapper)   </td> +<td rowspan="2" valign="bottom"><a name="letter_i"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  i  </div></td></tr></table> +</td> +<td rowspan="2" valign="bottom"><a name="letter_p"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  p  </div></td></tr></table> +</td> +<td valign="top"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html">UndirectedGraph</a> (claragenomics)   </td> +</tr> +<tr><td valign="top"><a class="el" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html">ArrayBlock</a> (claragenomics::cudamapper)   </td> <td valign="top"><a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html">Entry</a> (claragenomics::cudapoa)   </td> -<td valign="top"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> (claragenomics::cudamapper)   </td> -<td valign="top"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html">Index::RepresentationToSketchElements</a> (claragenomics::cudamapper)   </td> <td></td></tr> -<tr><td valign="top"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">Alignment</a> (claragenomics::cudaaligner)   </td> +<tr><td rowspan="2" valign="bottom"><a name="letter_b"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  b  </div></td></tr></table> +</td> <td rowspan="2" valign="bottom"><a name="letter_f"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  f  </div></td></tr></table> </td> -<td rowspan="2" valign="bottom"><a name="letter_o"></a><table border="0" 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+<tr><td valign="top"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a> (claragenomics::cudapoa)   </td> <td valign="top"><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">FastaParser</a> (claragenomics::io)   </td> -<td valign="top"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> (claragenomics::cudamapper)   </td> -<td valign="top"><a class="el" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a> (claragenomics)   </td> <td></td></tr> -<tr><td rowspan="2" valign="bottom"><a name="letter_b"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  b  </div></td></tr></table> -</td> -<td valign="top"><a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html">FastaSequence</a> (claragenomics::io)   </td> -<td valign="top"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a> (claragenomics::cudamapper)   </td> -<td 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href="#letter_o">o</a> | <a class="qindex" href="#letter_r">r</a> | <a class="qindex" href="#letter_s">s</a></div> +<div class="qindex"><a class="qindex" href="#letter_a">a</a> | <a class="qindex" href="#letter_b">b</a> | <a class="qindex" href="#letter_d">d</a> | <a class="qindex" href="#letter_e">e</a> | <a class="qindex" href="#letter_f">f</a> | <a class="qindex" href="#letter_g">g</a> | <a class="qindex" href="#letter_i">i</a> | <a class="qindex" href="#letter_m">m</a> | <a class="qindex" href="#letter_o">o</a> | <a class="qindex" href="#letter_p">p</a> | <a class="qindex" href="#letter_s">s</a> | <a class="qindex" href="#letter_u">u</a></div> </div><!-- contents --> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> diff --git a/docs/cpp/cudaaligner_8hpp_source.html b/docs/cpp/cudaaligner_8hpp_source.html index 14e716e98..4f1571e65 100644 --- a/docs/cpp/cudaaligner_8hpp_source.html +++ b/docs/cpp/cudaaligner_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/cudamapper_8hpp_source.html b/docs/cpp/cudamapper_8hpp_source.html index b68c73eae..a8016611a 100644 --- a/docs/cpp/cudamapper_8hpp_source.html +++ b/docs/cpp/cudamapper_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/cudapoa_8hpp_source.html b/docs/cpp/cudapoa_8hpp_source.html index ba1371f74..0807baedd 100644 --- a/docs/cpp/cudapoa_8hpp_source.html +++ b/docs/cpp/cudapoa_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/cudautils_8hpp.html b/docs/cpp/cudautils_8hpp.html index ba7d7f0e8..577d5b511 100644 --- a/docs/cpp/cudautils_8hpp.html +++ b/docs/cpp/cudautils_8hpp.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -68,6 +68,7 @@ <div class="header"> <div class="summary"> <a href="#nested-classes">Classes</a> | +<a href="#define-members">Macros</a> | <a href="#func-members">Functions</a> </div> <div class="headertitle"> <div class="title">cudautils.hpp File Reference</div> </div> @@ -77,6 +78,19 @@ <code>#include <<a class="el" href="logging_8hpp_source.html">claragenomics/logging/logging.hpp</a>></code><br /> <code>#include <cuda_runtime_api.h></code><br /> <code>#include <cassert></code><br /> +</div><div class="textblock"><div class="dynheader"> +Include dependency graph for cudautils.hpp:</div> +<div class="dyncontent"> +<div class="center"><img src="cudautils_8hpp__incl.png" border="0" usemap="#common_2utils_2include_2claragenomics_2utils_2cudautils_8hpp" alt=""/></div> +<map name="common_2utils_2include_2claragenomics_2utils_2cudautils_8hpp" id="common_2utils_2include_2claragenomics_2utils_2cudautils_8hpp"> +<area shape="rect" title=" " alt="" coords="196,5,341,61"/> +<area shape="rect" href="cudaversions_8hpp_source.html" title=" " alt="" coords="5,199,140,240"/> +<area shape="rect" href="logging_8hpp.html" title=" " alt="" coords="111,109,261,151"/> +<area shape="rect" title=" " alt="" coords="285,117,420,143"/> +<area shape="rect" title=" " alt="" coords="444,117,509,143"/> +<area shape="rect" title=" " alt="" coords="164,206,277,233"/> +</map> +</div> </div> <p><a href="cudautils_8hpp_source.html">Go to the source code of this file.</a></p> <table class="memberdecls"> @@ -88,6 +102,9 @@ </table><table class="memberdecls"> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="define-members"></a> Macros</h2></td></tr> +<tr class="memitem:gaded61355db08f1d76bc24edc008d4224"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudautils.html#gaded61355db08f1d76bc24edc008d4224">CGA_NVTX_RANGE</a>(varname, label)</td></tr> +<tr class="memdesc:gaded61355db08f1d76bc24edc008d4224"><td class="mdescLeft"> </td><td class="mdescRight">Dummy implementation for CGA_NVTX_RANGE macro. <a href="group__cudautils.html#gaded61355db08f1d76bc24edc008d4224">More...</a><br /></td></tr> +<tr class="separator:gaded61355db08f1d76bc24edc008d4224"><td class="memSeparator" colspan="2"> </td></tr> <tr><td colspan="2"><div class="groupHeader"></div></td></tr> <tr class="memitem:ga161535c48fe399e086ac6277b527fb41"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">CGA_CU_CHECK_ERR</a>(ans)</td></tr> <tr class="memdesc:ga161535c48fe399e086ac6277b527fb41"><td class="mdescLeft"> </td><td class="mdescRight">Log on CUDA error in enclosed expression. <a href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">More...</a><br /></td></tr> diff --git a/docs/cpp/cudautils_8hpp__incl.map b/docs/cpp/cudautils_8hpp__incl.map new file mode 100644 index 000000000..f7d93a93f --- /dev/null +++ b/docs/cpp/cudautils_8hpp__incl.map @@ -0,0 +1,8 @@ +<map id="common/utils/include/claragenomics/utils/cudautils.hpp" name="common/utils/include/claragenomics/utils/cudautils.hpp"> +<area shape="rect" id="node1" title=" " alt="" coords="196,5,341,61"/> +<area shape="rect" id="node2" href="$cudaversions_8hpp_source.html" title=" " alt="" 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id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -88,89 +88,112 @@ <div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <cuda_runtime_api.h></span></div> <div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <cassert></span></div> <div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  </div> -<div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  </div> -<div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41"> 27</a></span> <span class="preprocessor">#define CGA_CU_CHECK_ERR(ans) \</span></div> -<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor"> { \</span></div> -<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor"> claragenomics::cudautils::gpu_assert((ans), __FILE__, __LINE__); \</span></div> -<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor"> }</span></div> -<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  </div> -<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  </div> -<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">namespace </span>claragenomics</div> -<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> {</div> -<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  </div> -<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">namespace </span>cudautils</div> -<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> {</div> -<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  </div> -<div class="line"><a name="l00046"></a><span class="lineno"><a class="line" href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f"> 46</a></span> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f">gpu_assert</a>(cudaError_t code, <span class="keyword">const</span> <span class="keywordtype">char</span>* file, <span class="keywordtype">int</span> line)</div> -<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div> -<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#ifdef CGA_DEVICE_SYNCHRONIZE</span></div> -<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="comment">// This device synchronize forces the most recent CUDA call to fully</span></div> -<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="comment">// complete, increasing the chance of catching the CUDA error near the</span></div> -<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="comment">// offending function. Only run if existing code is success to avoid</span></div> -<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="comment">// potentially overwriting previous error code.</span></div> -<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordflow">if</span> (code == cudaSuccess)</div> -<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  {</div> -<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  code = cudaDeviceSynchronize();</div> -<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  }</div> -<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#endif</span></div> -<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  </div> -<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">if</span> (code != cudaSuccess)</div> -<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  {</div> -<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  std::string err = <span class="stringliteral">"GPU Error:: "</span> +</div> -<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  std::string(cudaGetErrorString(code)) +</div> -<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="stringliteral">" "</span> + std::string(file) +</div> -<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="stringliteral">" "</span> + std::to_string(line);</div> -<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <a class="code" href="group__logging.html#gacd5f9588e4976ef45d2ddece37b78003">CGA_LOG_ERROR</a>(<span class="stringliteral">"{}\n"</span>, err);</div> -<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="comment">// In Debug mode, this assert will cause a debugger trap</span></div> -<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="comment">// which is beneficial when debugging errors.</span></div> -<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  assert(<span class="keyword">false</span>);</div> -<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  std::abort();</div> -<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  }</div> -<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> }</div> -<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  </div> -<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="keyword">template</span> <<span class="keyword">typename</span> IntType, <span class="keywordtype">int</span>32_t boundary></div> -<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> __host__ __device__ __forceinline__</div> -<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  IntType</div> -<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="cudautils_8hpp.html#a9ace0fde2c5420f52b40ca77276943ca"> 82</a></span>  <a class="code" href="cudautils_8hpp.html#a9ace0fde2c5420f52b40ca77276943ca">align</a>(<span class="keyword">const</span> IntType& value)</div> -<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> {</div> -<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  static_assert((boundary & (boundary - 1)) == 0, <span class="stringliteral">"Boundary for align must be power of 2"</span>);</div> -<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordflow">return</span> (value + boundary) & ~(boundary - 1);</div> -<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> }</div> -<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  </div> -<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> } <span class="comment">// namespace cudautils</span></div> -<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  </div> -<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1scoped__device__switch.html"> 95</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a></div> -<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> {</div> -<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="keyword">public</span>:</div> -<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650"> 101</a></span>  <span class="keyword">explicit</span> <a class="code" href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650">scoped_device_switch</a>(int32_t device_id)</div> -<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  {</div> -<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <a class="code" href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">CGA_CU_CHECK_ERR</a>(cudaGetDevice(&device_id_before_));</div> -<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <a class="code" href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">CGA_CU_CHECK_ERR</a>(cudaSetDevice(device_id));</div> -<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  }</div> -<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  </div> -<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1scoped__device__switch.html#ad17a140b9fc9badff82487e685013125"> 108</a></span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html#ad17a140b9fc9badff82487e685013125">~scoped_device_switch</a>()</div> -<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  {</div> -<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  cudaSetDevice(device_id_before_);</div> -<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  }</div> -<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  </div> -<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a>() = <span class="keyword">delete</span>;</div> -<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a>(<a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a> <span class="keyword">const</span>&) = <span class="keyword">delete</span>;</div> -<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a>& operator=(<a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a> <span class="keyword">const</span>&) = <span class="keyword">delete</span>;</div> -<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  </div> -<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="keyword">private</span>:</div> -<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  int32_t device_id_before_;</div> -<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> };</div> -<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  </div> -<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> } <span class="comment">// namespace claragenomics</span></div> +<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#ifdef CGA_PROFILING</span></div> +<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <nvToolsExt.h></span></div> +<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#endif // CGA_PROFILING</span></div> +<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  </div> +<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  </div> +<div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41"> 31</a></span> <span class="preprocessor">#define CGA_CU_CHECK_ERR(ans) \</span></div> +<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor"> { \</span></div> +<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor"> claragenomics::cudautils::gpu_assert((ans), __FILE__, __LINE__); \</span></div> +<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor"> }</span></div> +<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  </div> +<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  </div> +<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">namespace </span>claragenomics</div> +<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> {</div> +<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  </div> +<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">namespace </span>cudautils</div> +<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> {</div> +<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  </div> +<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f"> 50</a></span> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f">gpu_assert</a>(cudaError_t code, <span class="keyword">const</span> <span class="keywordtype">char</span>* file, <span class="keywordtype">int</span> line)</div> +<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> {</div> +<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#ifdef CGA_DEVICE_SYNCHRONIZE</span></div> +<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="comment">// This device synchronize forces the most recent CUDA call to fully</span></div> +<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="comment">// complete, increasing the chance of catching the CUDA error near the</span></div> +<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="comment">// offending function. Only run if existing code is success to avoid</span></div> +<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="comment">// potentially overwriting previous error code.</span></div> +<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordflow">if</span> (code == cudaSuccess)</div> +<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  {</div> +<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  code = cudaDeviceSynchronize();</div> +<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  }</div> +<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="preprocessor">#endif</span></div> +<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  </div> +<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordflow">if</span> (code != cudaSuccess)</div> +<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  {</div> +<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  std::string err = <span class="stringliteral">"GPU Error:: "</span> +</div> +<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  std::string(cudaGetErrorString(code)) +</div> +<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="stringliteral">" "</span> + std::string(file) +</div> +<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="stringliteral">" "</span> + std::to_string(line);</div> +<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="group__logging.html#gacd5f9588e4976ef45d2ddece37b78003">CGA_LOG_ERROR</a>(<span class="stringliteral">"{}\n"</span>, err);</div> +<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="comment">// In Debug mode, this assert will cause a debugger trap</span></div> +<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="comment">// which is beneficial when debugging errors.</span></div> +<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  assert(<span class="keyword">false</span>);</div> +<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  std::abort();</div> +<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  }</div> +<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> }</div> +<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  </div> +<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="keyword">template</span> <<span class="keyword">typename</span> IntType, <span class="keywordtype">int</span>32_t boundary></div> +<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> __host__ __device__ __forceinline__</div> +<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  IntType</div> +<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="cudautils_8hpp.html#a9ace0fde2c5420f52b40ca77276943ca"> 86</a></span>  <a class="code" href="cudautils_8hpp.html#a9ace0fde2c5420f52b40ca77276943ca">align</a>(<span class="keyword">const</span> IntType& value)</div> +<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> {</div> +<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  static_assert((boundary & (boundary - 1)) == 0, <span class="stringliteral">"Boundary for align must be power of 2"</span>);</div> +<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordflow">return</span> (value + boundary) & ~(boundary - 1);</div> +<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> }</div> +<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  </div> +<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="preprocessor">#ifdef CGA_PROFILING</span></div> +<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="preprocessor">#define CGA_NVTX_RANGE(varname, label) ::claragenomics::cudautils::nvtx_range varname(label)</span></div> +<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> <span class="keyword">class </span>nvtx_range</div> +<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> {</div> +<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keyword">explicit</span> nvtx_range(<span class="keywordtype">char</span> <span class="keyword">const</span>* name)</div> +<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  {</div> +<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  nvtxRangePush(name);</div> +<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  }</div> +<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  </div> +<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  ~nvtx_range()</div> +<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  {</div> +<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  nvtxRangePop();</div> +<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  }</div> +<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> };</div> +<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> <span class="preprocessor">#else</span></div> +<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="preprocessor">#define CGA_NVTX_RANGE(varname, label)</span></div> +<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="preprocessor">#endif // CGA_PROFILING</span></div> +<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  </div> +<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> } <span class="comment">// namespace cudautils</span></div> +<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  </div> +<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1scoped__device__switch.html"> 130</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a></div> +<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> {</div> +<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650"> 136</a></span>  <span class="keyword">explicit</span> <a class="code" href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650">scoped_device_switch</a>(int32_t device_id)</div> +<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  {</div> +<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <a class="code" href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">CGA_CU_CHECK_ERR</a>(cudaGetDevice(&device_id_before_));</div> +<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <a class="code" href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">CGA_CU_CHECK_ERR</a>(cudaSetDevice(device_id));</div> +<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  }</div> +<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  </div> +<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1scoped__device__switch.html#ad17a140b9fc9badff82487e685013125"> 143</a></span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html#ad17a140b9fc9badff82487e685013125">~scoped_device_switch</a>()</div> +<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  {</div> +<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  cudaSetDevice(device_id_before_);</div> +<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  }</div> +<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  </div> +<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a>() = <span class="keyword">delete</span>;</div> +<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a>(<a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a> <span class="keyword">const</span>&) = <span class="keyword">delete</span>;</div> +<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a>& operator=(<a class="code" href="classclaragenomics_1_1scoped__device__switch.html">scoped_device_switch</a> <span class="keyword">const</span>&) = <span class="keyword">delete</span>;</div> +<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  </div> +<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="keyword">private</span>:</div> +<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  int32_t device_id_before_;</div> +<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> };</div> +<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  </div> +<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> } <span class="comment">// namespace claragenomics</span></div> </div><!-- fragment --></div><!-- contents --> -<div class="ttc" id="agroup__cudautils_html_ga161535c48fe399e086ac6277b527fb41"><div class="ttname"><a href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">CGA_CU_CHECK_ERR</a></div><div class="ttdeci">#define CGA_CU_CHECK_ERR(ans)</div><div class="ttdoc">Log on CUDA error in enclosed expression.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:27</div></div> +<div class="ttc" id="agroup__cudautils_html_ga161535c48fe399e086ac6277b527fb41"><div class="ttname"><a href="group__cudautils.html#ga161535c48fe399e086ac6277b527fb41">CGA_CU_CHECK_ERR</a></div><div class="ttdeci">#define CGA_CU_CHECK_ERR(ans)</div><div class="ttdoc">Log on CUDA error in enclosed expression.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:31</div></div> <div class="ttc" id="agroup__logging_html_gacd5f9588e4976ef45d2ddece37b78003"><div class="ttname"><a href="group__logging.html#gacd5f9588e4976ef45d2ddece37b78003">CGA_LOG_ERROR</a></div><div class="ttdeci">#define CGA_LOG_ERROR(...)</div><div class="ttdoc">Log at error level.</div><div class="ttdef"><b>Definition:</b> logging.hpp:164</div></div> -<div class="ttc" id="aclassclaragenomics_1_1scoped__device__switch_html_a41381ff64aeb0750803a315020a13650"><div class="ttname"><a href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650">claragenomics::scoped_device_switch::scoped_device_switch</a></div><div class="ttdeci">scoped_device_switch(int32_t device_id)</div><div class="ttdoc">Constructor.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:101</div></div> -<div class="ttc" id="aclassclaragenomics_1_1scoped__device__switch_html_ad17a140b9fc9badff82487e685013125"><div class="ttname"><a href="classclaragenomics_1_1scoped__device__switch.html#ad17a140b9fc9badff82487e685013125">claragenomics::scoped_device_switch::~scoped_device_switch</a></div><div class="ttdeci">~scoped_device_switch()</div><div class="ttdoc">Destructor switches back to original device ID.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:108</div></div> -<div class="ttc" id="aclassclaragenomics_1_1scoped__device__switch_html"><div class="ttname"><a href="classclaragenomics_1_1scoped__device__switch.html">claragenomics::scoped_device_switch</a></div><div class="ttdoc">A class to switch the CUDA device for the current scope using RAII.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:95</div></div> +<div class="ttc" id="aclassclaragenomics_1_1scoped__device__switch_html_a41381ff64aeb0750803a315020a13650"><div class="ttname"><a href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650">claragenomics::scoped_device_switch::scoped_device_switch</a></div><div class="ttdeci">scoped_device_switch(int32_t device_id)</div><div class="ttdoc">Constructor.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:136</div></div> +<div class="ttc" id="aclassclaragenomics_1_1scoped__device__switch_html_ad17a140b9fc9badff82487e685013125"><div class="ttname"><a href="classclaragenomics_1_1scoped__device__switch.html#ad17a140b9fc9badff82487e685013125">claragenomics::scoped_device_switch::~scoped_device_switch</a></div><div class="ttdeci">~scoped_device_switch()</div><div class="ttdoc">Destructor switches back to original device ID.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:143</div></div> +<div class="ttc" id="aclassclaragenomics_1_1scoped__device__switch_html"><div class="ttname"><a href="classclaragenomics_1_1scoped__device__switch.html">claragenomics::scoped_device_switch</a></div><div class="ttdoc">A class to switch the CUDA device for the current scope using RAII.</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:130</div></div> <div class="ttc" id="alogging_8hpp_html"><div class="ttname"><a href="logging_8hpp.html">logging.hpp</a></div></div> -<div class="ttc" id="agroup__cudautils_html_ga3769a812992df47886894f48f26edf6f"><div class="ttname"><a href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f">claragenomics::cudautils::gpu_assert</a></div><div class="ttdeci">void gpu_assert(cudaError_t code, const char *file, int line)</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:46</div></div> -<div class="ttc" id="acudautils_8hpp_html_a9ace0fde2c5420f52b40ca77276943ca"><div class="ttname"><a href="cudautils_8hpp.html#a9ace0fde2c5420f52b40ca77276943ca">claragenomics::cudautils::align</a></div><div class="ttdeci">__host__ __device__ __forceinline__ IntType align(const IntType &value)</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:82</div></div> +<div class="ttc" id="agroup__cudautils_html_ga3769a812992df47886894f48f26edf6f"><div class="ttname"><a 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@@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/dir_000009_000005.html b/docs/cpp/dir_000009_000005.html new file mode 100644 index 000000000..da5c38bb0 --- /dev/null +++ b/docs/cpp/dir_000009_000005.html @@ -0,0 +1,77 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: common/utils -> logging Relation</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<script 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class="dirtab">Includes file in common/logging</th></tr><tr class="dirtab"><td class="dirtab"><a class="el" href="dir_657c9b9511f57ce884717ee8b069b43d.html">utils</a> / <a class="el" href="cudautils_8hpp.html">cudautils.hpp</a></td><td class="dirtab"><a class="el" href="dir_147746a3e1d59bf3271a44362df8a4c9.html">include</a> / <a class="el" href="dir_eb42830a1028b9a58498a5b4f93061b6.html">claragenomics</a> / <a class="el" href="dir_2e08afdf66b3501ebb3a28ee9bd47f5a.html">logging</a> / <a class="el" href="logging_8hpp.html">logging.hpp</a></td></tr></table></div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/dir_000012_000005.html b/docs/cpp/dir_000012_000005.html new file mode 100644 index 000000000..c4786a2f3 --- /dev/null +++ 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href="dir_8e216217187728c84aa14a4942da12a2.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_657c9b9511f57ce884717ee8b069b43d.html">utils</a></li> </ul> +</div> +</div><!-- top --> +<div class="contents"> +<h3>utils → logging Relation</h3><table class="dirtab"><tr class="dirtab"><th class="dirtab">File in common/utils/include/claragenomics/utils</th><th class="dirtab">Includes file in common/logging</th></tr><tr class="dirtab"><td class="dirtab"><a class="el" href="cudautils_8hpp.html">cudautils.hpp</a></td><td class="dirtab"><a class="el" href="dir_147746a3e1d59bf3271a44362df8a4c9.html">include</a> / <a class="el" href="dir_eb42830a1028b9a58498a5b4f93061b6.html">claragenomics</a> / <a class="el" href="dir_2e08afdf66b3501ebb3a28ee9bd47f5a.html">logging</a> / <a class="el" href="logging_8hpp.html">logging.hpp</a></td></tr></table></div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/dir_00faf102fbd78ece25aa2d8f2597f59b.html b/docs/cpp/dir_00faf102fbd78ece25aa2d8f2597f59b.html index 17386de03..b8afb1951 100644 --- a/docs/cpp/dir_00faf102fbd78ece25aa2d8f2597f59b.html +++ b/docs/cpp/dir_00faf102fbd78ece25aa2d8f2597f59b.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/dir_147746a3e1d59bf3271a44362df8a4c9.html b/docs/cpp/dir_147746a3e1d59bf3271a44362df8a4c9.html index b18d969d0..3cba5faaa 100644 --- a/docs/cpp/dir_147746a3e1d59bf3271a44362df8a4c9.html +++ b/docs/cpp/dir_147746a3e1d59bf3271a44362df8a4c9.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" 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+<div class="dynheader"> +Directory dependency graph for utils:</div> +<div class="dyncontent"> +<div class="center"><img src="dir_85effdddc426fd82e3610be0948fd413_dep.png" border="0" usemap="#dir__85effdddc426fd82e3610be0948fd413__dep" alt="common/utils"/></div> +<map name="dir__85effdddc426fd82e3610be0948fd413__dep" id="dir__85effdddc426fd82e3610be0948fd413__dep"> +<area shape="rect" href="dir_cbd0fd5fcc23422502de88d4fe6e7386.html" title="include" alt="" coords="37,63,109,111"/> +<area shape="rect" href="dir_fd0b9fd7ef60505b59d31114acc22533.html" title="logging" alt="" coords="37,159,109,207"/> +<area shape="rect" href="dir_000010_000005.html" title="1" alt="" coords="78,133,86,147"/> +<area shape="rect" href="dir_85effdddc426fd82e3610be0948fd413.html" alt="" coords="27,52,216,121"/> +<area shape="rect" href="dir_bdd9a5d540de89e9fe90efdfc6973a4f.html" title="common" alt="" coords="16,16,227,132"/> +</map> +</div> </div><!-- contents --> <!-- start footer part --> <hr 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b/docs/cpp/dir_e25067817972d6e3bb7efd580b3302c4.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/dir_e48b4a17d37f1148862a6ed3f83bdb40.html b/docs/cpp/dir_e48b4a17d37f1148862a6ed3f83bdb40.html index 8bba1aeb3..7167dc710 100644 --- a/docs/cpp/dir_e48b4a17d37f1148862a6ed3f83bdb40.html +++ b/docs/cpp/dir_e48b4a17d37f1148862a6ed3f83bdb40.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/dir_eb42830a1028b9a58498a5b4f93061b6.html b/docs/cpp/dir_eb42830a1028b9a58498a5b4f93061b6.html index a324f6f72..6ffb9142b 100644 --- a/docs/cpp/dir_eb42830a1028b9a58498a5b4f93061b6.html +++ b/docs/cpp/dir_eb42830a1028b9a58498a5b4f93061b6.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/dir_f76c88603f4782e2554e1f696f75813e.html b/docs/cpp/dir_f76c88603f4782e2554e1f696f75813e.html index 52e71ec1c..2364189ee 100644 --- a/docs/cpp/dir_f76c88603f4782e2554e1f696f75813e.html +++ b/docs/cpp/dir_f76c88603f4782e2554e1f696f75813e.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/dir_fd0b9fd7ef60505b59d31114acc22533.html b/docs/cpp/dir_fd0b9fd7ef60505b59d31114acc22533.html index 155f7d6f6..442a1ae71 100644 --- a/docs/cpp/dir_fd0b9fd7ef60505b59d31114acc22533.html +++ b/docs/cpp/dir_fd0b9fd7ef60505b59d31114acc22533.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/fasta__parser_8hpp_source.html b/docs/cpp/fasta__parser_8hpp_source.html index 34695c45f..71b9b84ea 100644 --- a/docs/cpp/fasta__parser_8hpp_source.html +++ b/docs/cpp/fasta__parser_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -110,7 +110,7 @@ <div class="line"><a name="l00062"></a><span class="lineno"> 62</span> std::unique_ptr<FastaParser> create_fasta_parser(<span class="keyword">const</span> std::string& fasta_file);</div> <div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  </div> <div class="line"><a name="l00064"></a><span class="lineno"> 64</span> } <span class="comment">// namespace io</span></div> -<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> } <span class="comment">// namespace claragenomicsi</span></div> +<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> } <span class="comment">// namespace claragenomics</span></div> </div><!-- fragment --></div><!-- contents --> <div class="ttc" id="astructclaragenomics_1_1io_1_1FastaSequence_html"><div class="ttname"><a href="structclaragenomics_1_1io_1_1FastaSequence.html">claragenomics::io::FastaSequence</a></div><div class="ttdoc">A structure to hold details of a single FASTA entry.</div><div class="ttdef"><b>Definition:</b> fasta_parser.hpp:21</div></div> <div class="ttc" id="aclassclaragenomics_1_1io_1_1FastaParser_html_a213af5341107ea254176add6dd1dfd2d"><div class="ttname"><a href="classclaragenomics_1_1io_1_1FastaParser.html#a213af5341107ea254176add6dd1dfd2d">claragenomics::io::FastaParser::~FastaParser</a></div><div class="ttdeci">virtual ~FastaParser()=default</div><div class="ttdoc">FastaParser implementations can have custom destructors, so delcare the abstract dtor as default.</div></div> diff --git a/docs/cpp/files.html b/docs/cpp/files.html index 2bfbdbe72..b21fd2c5b 100644 --- a/docs/cpp/files.html +++ b/docs/cpp/files.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -86,26 +86,28 @@ <tr id="row_0_2_0_0_0_0_"><td class="entry"><span style="width:96px;display:inline-block;"> </span><a href="cudautils_8hpp_source.html"><span class="icondoc"></span></a><a class="el" href="cudautils_8hpp.html" target="_self">cudautils.hpp</a></td><td class="desc"></td></tr> <tr id="row_0_2_0_0_0_1_" class="even"><td class="entry"><span style="width:96px;display:inline-block;"> </span><a href="cudaversions_8hpp_source.html"><span class="icondoc"></span></a><b>cudaversions.hpp</b></td><td class="desc"></td></tr> <tr id="row_0_2_0_0_0_2_"><td class="entry"><span style="width:96px;display:inline-block;"> </span><a href="genomeutils_8hpp_source.html"><span class="icondoc"></span></a><b>genomeutils.hpp</b></td><td class="desc"></td></tr> -<tr id="row_0_2_0_0_0_3_" class="even"><td class="entry"><span style="width:96px;display:inline-block;"> </span><a href="mathutils_8hpp_source.html"><span class="icondoc"></span></a><b>mathutils.hpp</b></td><td class="desc"></td></tr> -<tr id="row_0_2_0_0_0_4_"><td class="entry"><span style="width:96px;display:inline-block;"> </span><a href="signed__integer__utils_8hpp_source.html"><span 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class="iconfopen" onclick="toggleFolder('3_')"> </span><a class="el" href="dir_8d2f594888f36d792a9b4a212d391f7f.html" target="_self">cudapoa</a></td><td class="desc"></td></tr> <tr id="row_3_0_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span id="arr_3_0_" class="arrow" onclick="toggleFolder('3_0_')">▼</span><span id="img_3_0_" class="iconfopen" onclick="toggleFolder('3_0_')"> </span><a class="el" href="dir_8613eb7afdfdd11650d28f82119ab8e9.html" target="_self">include</a></td><td class="desc"></td></tr> <tr id="row_3_0_0_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span id="arr_3_0_0_" class="arrow" onclick="toggleFolder('3_0_0_')">▼</span><span id="img_3_0_0_" class="iconfopen" onclick="toggleFolder('3_0_0_')"> </span><a class="el" href="dir_1f71e23d64293220a8931e396f64ac18.html" target="_self">claragenomics</a></td><td class="desc"></td></tr> diff --git a/docs/cpp/functions.html b/docs/cpp/functions.html index e9f7dd0d0..cbd0bc573 100644 --- a/docs/cpp/functions.html +++ b/docs/cpp/functions.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -68,15 +68,25 @@ <h3><a id="index_a"></a>- a -</h3><ul> <li>add_alignment() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">claragenomics::cudaaligner::Aligner</a> </li> +<li>add_edge() +: <a class="el" href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">claragenomics::DirectedGraph</a> +, <a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">claragenomics::UndirectedGraph</a> +</li> <li>add_poa_group() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">claragenomics::cudapoa::Batch</a> </li> +<li>adjacent_nodes_ +: <a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">claragenomics::Graph</a> +</li> <li>align_all() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a8b3c20782b9eaa4c2219fb7ff51772db">claragenomics::cudaaligner::Aligner</a> </li> <li>Anchor() : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#af4dc10f114030a8e3a53f3bad3cd20b2">claragenomics::cudamapper::Anchor</a> </li> +<li>anchors() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">claragenomics::cudamapper::Matcher</a> +</li> </ul> @@ -91,11 +101,17 @@ <h3><a id="index_b"></a>- b -</h3><ul> <h3><a id="index_c"></a>- c -</h3><ul> +<li>cigar_ +: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">claragenomics::cudamapper::Overlap</a> +</li> <li>convert_to_cigar() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">claragenomics::cudaaligner::Alignment</a> </li> <li>create_index() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afc23f3e71c65dc9ed5a9e49cf26ba645">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">claragenomics::cudamapper::Index</a> +</li> +<li>create_matcher() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">claragenomics::cudamapper::Matcher</a> </li> <li>create_sequence() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#a3e4a8fe41b71b13362433360b20115ed">claragenomics::cudamapper::Sequence</a> @@ -107,6 +123,9 @@ <h3><a id="index_d"></a>- d -</h3><ul> <li>data() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#a45c1a69a18ea6f6fd7a45bad6862bbca">claragenomics::cudamapper::Sequence</a> </li> +<li>directed_edge_exists() +: <a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">claragenomics::Graph</a> +</li> <li>direction() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af4b53bc09f5816c3b81fef1c1abf3fc6">claragenomics::cudamapper::SketchElement</a> </li> @@ -114,7 +133,26 @@ <h3><a id="index_d"></a>- d -</h3><ul> : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">claragenomics::cudamapper::SketchElement</a> </li> <li>directions_of_reads() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a407a2466e8740a0f78a3ce876b87352b">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">claragenomics::cudamapper::Index</a> +</li> +</ul> + + +<h3><a id="index_e"></a>- e -</h3><ul> +<li>edge_t +: <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">claragenomics::Graph</a> +</li> +<li>edge_weight_t +: <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">claragenomics::Graph</a> +</li> +<li>edges_ +: <a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">claragenomics::Graph</a> +</li> +<li>edges_to_dot() +: <a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">claragenomics::Graph</a> +</li> +<li>empty_ +: <a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">claragenomics::Graph</a> </li> </ul> @@ -126,6 +164,9 @@ <h3><a id="index_f"></a>- f -</h3><ul> <li>first_element_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a3fca81e893b35e0648977b00f21b7e7e">claragenomics::cudamapper::ArrayBlock</a> </li> +<li>first_occurrence_of_representations() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">claragenomics::cudamapper::Index</a> +</li> <li>format_alignment() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">claragenomics::cudaaligner::Alignment</a> </li> @@ -136,6 +177,9 @@ <h3><a id="index_g"></a>- g -</h3><ul> <li>generate_poa() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">claragenomics::cudapoa::Batch</a> </li> +<li>get_adjacent_nodes() +: <a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">claragenomics::Graph</a> +</li> <li>get_alignment() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">claragenomics::cudaaligner::Alignment</a> </li> @@ -148,14 +192,26 @@ <h3><a id="index_g"></a>- g -</h3><ul> <li>get_consensus() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">claragenomics::cudapoa::Batch</a> </li> +<li>get_edges() +: <a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">claragenomics::Graph</a> +</li> +<li>get_graphs() +: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">claragenomics::cudapoa::Batch</a> +</li> <li>get_msa() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">claragenomics::cudapoa::Batch</a> </li> +<li>get_node_ids() +: <a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">claragenomics::Graph</a> +</li> +<li>get_node_label() +: <a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">claragenomics::Graph</a> +</li> <li>get_num_seqences() : <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a04f6deee5108374fa485487e06e759e5">claragenomics::io::FastaParser</a> </li> <li>get_overlaps() -: <a class="el" href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">claragenomics::cudamapper::Overlapper</a> +: <a class="el" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">claragenomics::cudamapper::Overlapper</a> </li> <li>get_query_sequence() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">claragenomics::cudaaligner::Alignment</a> @@ -189,12 +245,6 @@ <h3><a id="index_m"></a>- m -</h3><ul> <li>maximum_kmer_size() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">claragenomics::cudamapper::Index</a> </li> -<li>maximum_representation() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a69fd1882260a7c55a45fe5e2a092b152">claragenomics::cudamapper::Index</a> -</li> -<li>minimum_representation() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac5036778efd3c83f5bf048174a8ab824">claragenomics::cudamapper::Index</a> -</li> </ul> @@ -203,6 +253,15 @@ <h3><a id="index_n"></a>- n -</h3><ul> : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#ab9663611f0d6c691e40228c5a08cf0e2">claragenomics::cudamapper::Sequence</a> , <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html#aea0664ca6e856203c4b954b519183bec">claragenomics::io::FastaSequence</a> </li> +<li>node_id_t +: <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">claragenomics::Graph</a> +</li> +<li>node_labels_ +: <a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">claragenomics::Graph</a> +</li> +<li>node_labels_to_dot() +: <a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">claragenomics::Graph</a> +</li> <li>num_residues_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">claragenomics::cudamapper::Overlap</a> </li> @@ -213,6 +272,9 @@ <h3><a id="index_n"></a>- n -</h3><ul> <h3><a id="index_o"></a>- o -</h3><ul> +<li>operator()() +: <a class="el" href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61">claragenomics::PairHash</a> +</li> <li>overlap_complete : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">claragenomics::cudamapper::Overlap</a> </li> @@ -224,7 +286,7 @@ <h3><a id="index_p"></a>- p -</h3><ul> : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a0ddea36eed82ea3a9d1fa7ace61051bc">claragenomics::cudamapper::SketchElement</a> </li> <li>positions_in_reads() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5c75f11d1683e4f863f14a4088a36306">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">claragenomics::cudamapper::Index</a> </li> <li>print_paf() : <a class="el" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">claragenomics::cudamapper::Overlapper</a> @@ -247,7 +309,7 @@ <h3><a id="index_q"></a>- q -</h3><ul> , <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">claragenomics::cudamapper::Overlap</a> </li> <li>query_read_name_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ac2baa8c82cbe1ff7475d7a8700a691df">claragenomics::cudamapper::Overlap</a> +: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">claragenomics::cudamapper::Overlap</a> </li> <li>query_start_position_in_read_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">claragenomics::cudamapper::Overlap</a> @@ -256,23 +318,17 @@ <h3><a id="index_q"></a>- q -</h3><ul> <h3><a id="index_r"></a>- r -</h3><ul> -<li>reached_end_of_input() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a4e5b3cf1c41146635ce9d51bbdfe2277">claragenomics::cudamapper::Index</a> -</li> <li>read_id() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af5f2e8fc8df725b336833930baf3cd39">claragenomics::cudamapper::SketchElement</a> </li> -<li>read_id_and_representation_to_sketch_elements() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af8ad540ff0a2a244a35ae846ec745c24">claragenomics::cudamapper::Index</a> -</li> <li>read_id_to_read_length() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af03421436f827e88316c74b0b3af200e">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">claragenomics::cudamapper::Index</a> </li> <li>read_id_to_read_name() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aec3176ac2d5e425b25dec14f411cbfe0">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">claragenomics::cudamapper::Index</a> </li> <li>read_ids() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aac33d8d2aa72bb227326a35f5b452de5">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">claragenomics::cudamapper::Index</a> </li> <li>relative_strand : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">claragenomics::cudamapper::Overlap</a> @@ -280,8 +336,8 @@ <h3><a id="index_r"></a>- r -</h3><ul> <li>representation() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#abb3c8927594ba5f077c4443c229e0730">claragenomics::cudamapper::SketchElement</a> </li> -<li>representation_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a839754dc6ed7d150ae06abf377e39c62">claragenomics::cudamapper::Index::RepresentationToSketchElements</a> +<li>representations() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">claragenomics::cudamapper::Index</a> </li> <li>reset() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">claragenomics::cudaaligner::Aligner</a> @@ -298,11 +354,12 @@ <h3><a id="index_s"></a>- s -</h3><ul> : <a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">claragenomics::cudapoa::Entry</a> , <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html#a9ac5e894fc08745c47b326a7038aa488">claragenomics::io::FastaSequence</a> </li> -<li>sketch_elements_for_representation_and_all_read_ids_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a604d5227c7fe6412e982fb31a1fee549">claragenomics::cudamapper::Index::RepresentationToSketchElements</a> +<li>serialize_to_dot() +: <a class="el" href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">claragenomics::DirectedGraph</a> +, <a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">claragenomics::UndirectedGraph</a> </li> -<li>sketch_elements_for_representation_and_read_id_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a84ff4998d9fec875845a20272d209b30">claragenomics::cudamapper::Index::RepresentationToSketchElements</a> +<li>set_node_label() +: <a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">claragenomics::Graph</a> </li> <li>sync_alignments() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">claragenomics::cudaaligner::Aligner</a> @@ -325,7 +382,7 @@ <h3><a id="index_t"></a>- t -</h3><ul> , <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">claragenomics::cudamapper::Overlap</a> </li> <li>target_read_name_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a8e75cd08ecddc434463ac2e9b748dd6c">claragenomics::cudamapper::Overlap</a> +: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">claragenomics::cudamapper::Overlap</a> </li> <li>target_start_position_in_read_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">claragenomics::cudamapper::Overlap</a> @@ -333,6 +390,16 @@ <h3><a id="index_t"></a>- t -</h3><ul> </ul> +<h3><a id="index_u"></a>- u -</h3><ul> +<li>unique_representations() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">claragenomics::cudamapper::Index</a> +</li> +<li>update_adject_nodes() +: <a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">claragenomics::Graph</a> +</li> +</ul> + + <h3><a id="index_w"></a>- w -</h3><ul> <li>weights : <a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">claragenomics::cudapoa::Entry</a> @@ -344,6 +411,9 @@ <h3><a id="index__7E"></a>- ~ -</h3><ul> <li>~Aligner() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#aaae329eae2ed3e364db643163755e987">claragenomics::cudaaligner::Aligner</a> </li> +<li>~Alignment() +: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">claragenomics::cudaaligner::Alignment</a> +</li> <li>~Batch() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">claragenomics::cudapoa::Batch</a> </li> @@ -353,6 +423,9 @@ <h3><a id="index__7E"></a>- ~ -</h3><ul> <li>~Index() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">claragenomics::cudamapper::Index</a> </li> +<li>~Matcher() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac2f70fb6b1876d0fa81fd8c0189191ab">claragenomics::cudamapper::Matcher</a> +</li> <li>~Overlapper() : <a class="el" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">claragenomics::cudamapper::Overlapper</a> </li> diff --git a/docs/cpp/functions_enum.html b/docs/cpp/functions_enum.html index 607870943..cee4d5e43 100644 --- a/docs/cpp/functions_enum.html +++ b/docs/cpp/functions_enum.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/functions_func.html b/docs/cpp/functions_func.html index 6f4552df0..455fcf75e 100644 --- a/docs/cpp/functions_func.html +++ b/docs/cpp/functions_func.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -68,6 +68,10 @@ <h3><a id="index_a"></a>- a -</h3><ul> <li>add_alignment() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">claragenomics::cudaaligner::Aligner</a> </li> +<li>add_edge() +: <a class="el" href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">claragenomics::DirectedGraph</a> +, <a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">claragenomics::UndirectedGraph</a> +</li> <li>add_poa_group() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">claragenomics::cudapoa::Batch</a> </li> @@ -77,6 +81,9 @@ <h3><a id="index_a"></a>- a -</h3><ul> <li>Anchor() : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#af4dc10f114030a8e3a53f3bad3cd20b2">claragenomics::cudamapper::Anchor</a> </li> +<li>anchors() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">claragenomics::cudamapper::Matcher</a> +</li> </ul> @@ -92,7 +99,10 @@ <h3><a id="index_c"></a>- c -</h3><ul> : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">claragenomics::cudaaligner::Alignment</a> </li> <li>create_index() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afc23f3e71c65dc9ed5a9e49cf26ba645">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">claragenomics::cudamapper::Index</a> +</li> +<li>create_matcher() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">claragenomics::cudamapper::Matcher</a> </li> <li>create_sequence() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#a3e4a8fe41b71b13362433360b20115ed">claragenomics::cudamapper::Sequence</a> @@ -104,11 +114,21 @@ <h3><a id="index_d"></a>- d -</h3><ul> <li>data() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#a45c1a69a18ea6f6fd7a45bad6862bbca">claragenomics::cudamapper::Sequence</a> </li> +<li>directed_edge_exists() +: <a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">claragenomics::Graph</a> +</li> <li>direction() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af4b53bc09f5816c3b81fef1c1abf3fc6">claragenomics::cudamapper::SketchElement</a> </li> <li>directions_of_reads() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a407a2466e8740a0f78a3ce876b87352b">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">claragenomics::cudamapper::Index</a> +</li> +</ul> + + +<h3><a id="index_e"></a>- e -</h3><ul> +<li>edges_to_dot() +: <a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">claragenomics::Graph</a> </li> </ul> @@ -117,6 +137,9 @@ <h3><a id="index_f"></a>- f -</h3><ul> <li>filter_overlaps() : <a class="el" href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">claragenomics::cudamapper::Overlapper</a> </li> +<li>first_occurrence_of_representations() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">claragenomics::cudamapper::Index</a> +</li> <li>format_alignment() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">claragenomics::cudaaligner::Alignment</a> </li> @@ -127,6 +150,9 @@ <h3><a id="index_g"></a>- g -</h3><ul> <li>generate_poa() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">claragenomics::cudapoa::Batch</a> </li> +<li>get_adjacent_nodes() +: <a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">claragenomics::Graph</a> +</li> <li>get_alignment() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">claragenomics::cudaaligner::Alignment</a> </li> @@ -139,14 +165,26 @@ <h3><a id="index_g"></a>- g -</h3><ul> <li>get_consensus() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">claragenomics::cudapoa::Batch</a> </li> +<li>get_edges() +: <a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">claragenomics::Graph</a> +</li> +<li>get_graphs() +: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">claragenomics::cudapoa::Batch</a> +</li> <li>get_msa() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">claragenomics::cudapoa::Batch</a> </li> +<li>get_node_ids() +: <a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">claragenomics::Graph</a> +</li> +<li>get_node_label() +: <a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">claragenomics::Graph</a> +</li> <li>get_num_seqences() : <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a04f6deee5108374fa485487e06e759e5">claragenomics::io::FastaParser</a> </li> <li>get_overlaps() -: <a class="el" href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">claragenomics::cudamapper::Overlapper</a> +: <a class="el" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">claragenomics::cudamapper::Overlapper</a> </li> <li>get_query_sequence() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">claragenomics::cudaaligner::Alignment</a> @@ -173,12 +211,6 @@ <h3><a id="index_m"></a>- m -</h3><ul> <li>maximum_kmer_size() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">claragenomics::cudamapper::Index</a> </li> -<li>maximum_representation() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a69fd1882260a7c55a45fe5e2a092b152">claragenomics::cudamapper::Index</a> -</li> -<li>minimum_representation() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac5036778efd3c83f5bf048174a8ab824">claragenomics::cudamapper::Index</a> -</li> </ul> @@ -186,18 +218,28 @@ <h3><a id="index_n"></a>- n -</h3><ul> <li>name() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#ab9663611f0d6c691e40228c5a08cf0e2">claragenomics::cudamapper::Sequence</a> </li> +<li>node_labels_to_dot() +: <a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">claragenomics::Graph</a> +</li> <li>number_of_reads() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">claragenomics::cudamapper::Index</a> </li> </ul> +<h3><a id="index_o"></a>- o -</h3><ul> +<li>operator()() +: <a class="el" href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61">claragenomics::PairHash</a> +</li> +</ul> + + <h3><a id="index_p"></a>- p -</h3><ul> <li>position_in_read() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a0ddea36eed82ea3a9d1fa7ace61051bc">claragenomics::cudamapper::SketchElement</a> </li> <li>positions_in_reads() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5c75f11d1683e4f863f14a4088a36306">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">claragenomics::cudamapper::Index</a> </li> <li>print_paf() : <a class="el" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">claragenomics::cudamapper::Overlapper</a> @@ -206,27 +248,24 @@ <h3><a id="index_p"></a>- p -</h3><ul> <h3><a id="index_r"></a>- r -</h3><ul> -<li>reached_end_of_input() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a4e5b3cf1c41146635ce9d51bbdfe2277">claragenomics::cudamapper::Index</a> -</li> <li>read_id() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af5f2e8fc8df725b336833930baf3cd39">claragenomics::cudamapper::SketchElement</a> </li> -<li>read_id_and_representation_to_sketch_elements() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af8ad540ff0a2a244a35ae846ec745c24">claragenomics::cudamapper::Index</a> -</li> <li>read_id_to_read_length() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af03421436f827e88316c74b0b3af200e">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">claragenomics::cudamapper::Index</a> </li> <li>read_id_to_read_name() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aec3176ac2d5e425b25dec14f411cbfe0">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">claragenomics::cudamapper::Index</a> </li> <li>read_ids() -: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#aac33d8d2aa72bb227326a35f5b452de5">claragenomics::cudamapper::Index</a> +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">claragenomics::cudamapper::Index</a> </li> <li>representation() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#abb3c8927594ba5f077c4443c229e0730">claragenomics::cudamapper::SketchElement</a> </li> +<li>representations() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">claragenomics::cudamapper::Index</a> +</li> <li>reset() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">claragenomics::cudaaligner::Aligner</a> , <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">claragenomics::cudapoa::Batch</a> @@ -238,16 +277,36 @@ <h3><a id="index_s"></a>- s -</h3><ul> <li>scoped_device_switch() : <a class="el" href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650">claragenomics::scoped_device_switch</a> </li> +<li>serialize_to_dot() +: <a class="el" href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">claragenomics::DirectedGraph</a> +, <a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">claragenomics::UndirectedGraph</a> +</li> +<li>set_node_label() +: <a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">claragenomics::Graph</a> +</li> <li>sync_alignments() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">claragenomics::cudaaligner::Aligner</a> </li> </ul> +<h3><a id="index_u"></a>- u -</h3><ul> +<li>unique_representations() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">claragenomics::cudamapper::Index</a> +</li> +<li>update_adject_nodes() +: <a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">claragenomics::Graph</a> +</li> +</ul> + + <h3><a id="index__7E"></a>- ~ -</h3><ul> <li>~Aligner() : <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#aaae329eae2ed3e364db643163755e987">claragenomics::cudaaligner::Aligner</a> </li> +<li>~Alignment() +: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">claragenomics::cudaaligner::Alignment</a> +</li> <li>~Batch() : <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">claragenomics::cudapoa::Batch</a> </li> @@ -257,6 +316,9 @@ <h3><a id="index__7E"></a>- ~ -</h3><ul> <li>~Index() : <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">claragenomics::cudamapper::Index</a> </li> +<li>~Matcher() +: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac2f70fb6b1876d0fa81fd8c0189191ab">claragenomics::cudamapper::Matcher</a> +</li> <li>~Overlapper() : <a class="el" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">claragenomics::cudamapper::Overlapper</a> </li> diff --git a/docs/cpp/functions_type.html b/docs/cpp/functions_type.html new file mode 100644 index 000000000..71cacd9e1 --- /dev/null +++ b/docs/cpp/functions_type.html @@ -0,0 +1,84 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: Class Members - Typedefs</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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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 --> +<!-- 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="contents"> + <ul> +<li>edge_t +: <a class="el" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">claragenomics::Graph</a> +</li> +<li>edge_weight_t +: <a class="el" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">claragenomics::Graph</a> +</li> +<li>node_id_t +: <a class="el" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">claragenomics::Graph</a> +</li> +</ul> +</div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/functions_vars.html b/docs/cpp/functions_vars.html index cbfede032..a4fcce3f5 100644 --- a/docs/cpp/functions_vars.html +++ b/docs/cpp/functions_vars.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -63,9 +63,21 @@ <div class="contents">  <ul> +<li>adjacent_nodes_ +: <a class="el" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">claragenomics::Graph</a> +</li> <li>block_size_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a33ff27afee2ddb07e6fbdda0ff1de229">claragenomics::cudamapper::ArrayBlock</a> </li> +<li>cigar_ +: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">claragenomics::cudamapper::Overlap</a> +</li> +<li>edges_ +: <a class="el" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">claragenomics::Graph</a> +</li> +<li>empty_ +: <a class="el" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">claragenomics::Graph</a> +</li> <li>first_element_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a3fca81e893b35e0648977b00f21b7e7e">claragenomics::cudamapper::ArrayBlock</a> </li> @@ -75,6 +87,9 @@ <li>name : <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html#aea0664ca6e856203c4b954b519183bec">claragenomics::io::FastaSequence</a> </li> +<li>node_labels_ +: <a class="el" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">claragenomics::Graph</a> +</li> <li>num_residues_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">claragenomics::cudamapper::Overlap</a> </li> @@ -95,7 +110,7 @@ , <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">claragenomics::cudamapper::Overlap</a> </li> <li>query_read_name_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ac2baa8c82cbe1ff7475d7a8700a691df">claragenomics::cudamapper::Overlap</a> +: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">claragenomics::cudamapper::Overlap</a> </li> <li>query_start_position_in_read_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">claragenomics::cudamapper::Overlap</a> @@ -103,19 +118,10 @@ <li>relative_strand : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">claragenomics::cudamapper::Overlap</a> </li> -<li>representation_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a839754dc6ed7d150ae06abf377e39c62">claragenomics::cudamapper::Index::RepresentationToSketchElements</a> -</li> <li>seq : <a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">claragenomics::cudapoa::Entry</a> , <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html#a9ac5e894fc08745c47b326a7038aa488">claragenomics::io::FastaSequence</a> </li> -<li>sketch_elements_for_representation_and_all_read_ids_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a604d5227c7fe6412e982fb31a1fee549">claragenomics::cudamapper::Index::RepresentationToSketchElements</a> -</li> -<li>sketch_elements_for_representation_and_read_id_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a84ff4998d9fec875845a20272d209b30">claragenomics::cudamapper::Index::RepresentationToSketchElements</a> -</li> <li>target_end_position_in_read_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">claragenomics::cudamapper::Overlap</a> </li> @@ -130,7 +136,7 @@ , <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">claragenomics::cudamapper::Overlap</a> </li> <li>target_read_name_ -: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a8e75cd08ecddc434463ac2e9b748dd6c">claragenomics::cudamapper::Overlap</a> +: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">claragenomics::cudamapper::Overlap</a> </li> <li>target_start_position_in_read_ : <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">claragenomics::cudamapper::Overlap</a> diff --git a/docs/cpp/genomeutils_8hpp_source.html b/docs/cpp/genomeutils_8hpp_source.html index cf9a1c7f5..155efee94 100644 --- a/docs/cpp/genomeutils_8hpp_source.html +++ b/docs/cpp/genomeutils_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/globals.html b/docs/cpp/globals.html index e7df97139..7d3b47373 100644 --- a/docs/cpp/globals.html +++ b/docs/cpp/globals.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -102,6 +102,9 @@ <li>CGA_LOG_WARN : <a class="el" href="group__logging.html#gaa97f13dd6ae075b35ca3f01a667d9d83">logging.hpp</a> </li> +<li>CGA_NVTX_RANGE +: <a class="el" href="group__cudautils.html#gaded61355db08f1d76bc24edc008d4224">cudautils.hpp</a> +</li> <li>SPDLOG_ACTIVE_LEVEL : <a class="el" href="group__logging.html#gae4fda6f71f35120e2ff48157fca961b5">logging.hpp</a> </li> diff --git a/docs/cpp/globals_defs.html b/docs/cpp/globals_defs.html index ba0529e1a..db866f537 100644 --- a/docs/cpp/globals_defs.html +++ b/docs/cpp/globals_defs.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -102,6 +102,9 @@ <li>CGA_LOG_WARN : <a class="el" href="group__logging.html#gaa97f13dd6ae075b35ca3f01a667d9d83">logging.hpp</a> </li> +<li>CGA_NVTX_RANGE +: <a class="el" href="group__cudautils.html#gaded61355db08f1d76bc24edc008d4224">cudautils.hpp</a> +</li> <li>SPDLOG_ACTIVE_LEVEL : <a class="el" href="group__logging.html#gae4fda6f71f35120e2ff48157fca961b5">logging.hpp</a> </li> diff --git a/docs/cpp/graph_8hpp_source.html b/docs/cpp/graph_8hpp_source.html new file mode 100644 index 000000000..39a2615f4 --- /dev/null +++ b/docs/cpp/graph_8hpp_source.html @@ -0,0 +1,313 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: common/utils/include/claragenomics/utils/graph.hpp Source File</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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><a class="el" href="dir_bdd9a5d540de89e9fe90efdfc6973a4f.html">common</a></li><li class="navelem"><a class="el" href="dir_85effdddc426fd82e3610be0948fd413.html">utils</a></li><li class="navelem"><a class="el" href="dir_cbd0fd5fcc23422502de88d4fe6e7386.html">include</a></li><li class="navelem"><a class="el" href="dir_8e216217187728c84aa14a4942da12a2.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_657c9b9511f57ce884717ee8b069b43d.html">utils</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="headertitle"> +<div class="title">graph.hpp</div> </div> +</div><!--header--> +<div class="contents"> +<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div> +<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.</span></div> +<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">*</span></div> +<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div> +<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">* and proprietary rights in and to this software, related documentation</span></div> +<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">* and any modifications thereto. Any use, reproduction, disclosure or</span></div> +<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">* distribution of this software and related documentation without an express</span></div> +<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div> +<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">*/</span></div> +<div class="line"><a name="l00010"></a><span class="lineno"> 10</span>  </div> +<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#pragma once</span></div> +<div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  </div> +<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <vector></span></div> +<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include <unordered_map></span></div> +<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <unordered_set></span></div> +<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include <cstdint></span></div> +<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include <string></span></div> +<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <iostream></span></div> +<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <sstream></span></div> +<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <algorithm></span></div> +<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  </div> +<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">namespace </span>claragenomics</div> +<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> {</div> +<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  </div> +<div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1PairHash.html"> 27</a></span> <span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1PairHash.html">PairHash</a></div> +<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> {</div> +<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keyword">template</span> <<span class="keyword">class</span> T1, <span class="keyword">class</span> T2></div> +<div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61"> 32</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61">operator()</a>(<span class="keyword">const</span> std::pair<T1, T2>& pair)<span class="keyword"> const</span></div> +<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordtype">size_t</span> hash_1 = std::hash<T1>()(pair.first);</div> +<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordtype">size_t</span> hash_2 = std::hash<T2>()(pair.second);</div> +<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordflow">return</span> hash_1 ^ hash_2;</div> +<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  }</div> +<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> };</div> +<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  </div> +<div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html"> 41</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1Graph.html">Graph</a></div> +<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> {</div> +<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d"> 45</a></span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> = int32_t;</div> +<div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5"> 47</a></span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> = int32_t;</div> +<div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc"> 49</a></span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> = std::pair<node_id_t, node_id_t>;</div> +<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  </div> +<div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb"> 55</a></span>  <span class="keyword">const</span> std::vector<node_id_t>& <a class="code" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">get_adjacent_nodes</a>(<a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node)<span class="keyword"> const</span></div> +<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keyword">auto</span> iter = <a class="code" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a>.find(node);</div> +<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">if</span> (iter != <a class="code" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a>.end())</div> +<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  {</div> +<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordflow">return</span> iter->second;</div> +<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  }</div> +<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordflow">else</span></div> +<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div> +<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">return</span> <a class="code" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">Graph::empty_</a>;</div> +<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  }</div> +<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  }</div> +<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  </div> +<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8"> 71</a></span>  <span class="keyword">const</span> std::vector<node_id_t> <a class="code" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">get_node_ids</a>()<span class="keyword"> const</span></div> +<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  std::vector<node_id_t> nodes;</div> +<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">for</span> (<span class="keyword">auto</span> iter : <a class="code" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a>)</div> +<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  {</div> +<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  nodes.push_back(iter.first);</div> +<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  }</div> +<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  </div> +<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">return</span> nodes;</div> +<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  }</div> +<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  </div> +<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794"> 85</a></span>  <span class="keyword">const</span> std::vector<std::pair<edge_t, edge_weight_t>> <a class="code" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">get_edges</a>()<span class="keyword"> const</span></div> +<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordflow">return</span> {begin(<a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>), end(<a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>)};</div> +<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  }</div> +<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  </div> +<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d"> 94</a></span>  <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">set_node_label</a>(<a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node, <span class="keyword">const</span> std::string& label)</div> +<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  {</div> +<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a>.insert({node, label});</div> +<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  }</div> +<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  </div> +<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// no label is associated or node ID doesn't exist.</span></div> +<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389"> 104</a></span>  std::string <a class="code" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">get_node_label</a>(<a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node)<span class="keyword"> const</span></div> +<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keyword">auto</span> found_node = <a class="code" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a>.find(node);</div> +<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordflow">if</span> (found_node != <a class="code" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a>.end())</div> +<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  {</div> +<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordflow">return</span> found_node->second;</div> +<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  }</div> +<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">else</span></div> +<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  {</div> +<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordflow">return</span> <span class="stringliteral">""</span>;</div> +<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  }</div> +<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  }</div> +<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  </div> +<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="keyword">protected</span>:</div> +<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac"> 122</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a>(<a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</div> +<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  {</div> +<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordflow">return</span> <a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>.find(edge) != <a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>.end();</div> +<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  }</div> +<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  </div> +<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77"> 130</a></span>  <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a>(<a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a> edge)</div> +<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  {</div> +<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keyword">auto</span> find_node = <a class="code" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a>.find(edge.first);</div> +<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">if</span> (find_node == <a class="code" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a>.end())</div> +<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  {</div> +<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a>.insert({edge.first, {edge.second}});</div> +<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  }</div> +<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordflow">else</span></div> +<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  {</div> +<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  find_node->second.push_back(edge.second);</div> +<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  }</div> +<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  }</div> +<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  </div> +<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9"> 146</a></span>  <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a>(std::ostringstream& dot_str)<span class="keyword"> const</span></div> +<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordflow">for</span> (<span class="keyword">auto</span> iter : <a class="code" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a>)</div> +<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  {</div> +<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  dot_str << iter.first << <span class="stringliteral">" [label=\""</span> << iter.second << <span class="stringliteral">"\"];\n"</span>;</div> +<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  }</div> +<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  }</div> +<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  </div> +<div class="line"><a name="l00158"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5"> 158</a></span>  <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a>(std::ostringstream& dot_str, <span class="keyword">const</span> std::string& node_separator)<span class="keyword"> const</span></div> +<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">for</span> (<span class="keyword">auto</span> iter : <a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>)</div> +<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  {</div> +<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>& edge = iter.first;</div> +<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a>& weight = iter.second;</div> +<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  dot_str << edge.first << <span class="stringliteral">" "</span> << node_separator << <span class="stringliteral">" "</span> << edge.second;</div> +<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  dot_str << <span class="stringliteral">" [label=\""</span> << weight << <span class="stringliteral">"\"];\n"</span>;</div> +<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  }</div> +<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  }</div> +<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  </div> +<div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404"> 170</a></span>  std::unordered_map<node_id_t, std::vector<node_id_t>> <a class="code" href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">adjacent_nodes_</a>;</div> +<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  </div> +<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33"> 173</a></span>  std::unordered_map<edge_t, edge_weight_t, PairHash> <a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>;</div> +<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  </div> +<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5"> 176</a></span>  std::unordered_map<node_id_t, std::string> <a class="code" href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">node_labels_</a>;</div> +<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  </div> +<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c"> 179</a></span>  <span class="keyword">const</span> std::vector<node_id_t> <a class="code" href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">empty_</a>;</div> +<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> };</div> +<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  </div> +<div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1DirectedGraph.html"> 183</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1DirectedGraph.html">DirectedGraph</a> : <span class="keyword">public</span> <a class="code" href="classclaragenomics_1_1Graph.html">Graph</a></div> +<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> {</div> +<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">Graph::node_id_t</a>;</div> +<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">Graph::edge_weight_t</a>;</div> +<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">Graph::edge_t</a>;</div> +<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  </div> +<div class="line"><a name="l00198"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371"> 198</a></span>  <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">add_edge</a>(<a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_from, <a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_to, <a class="code" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> weight = 0)</div> +<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  {</div> +<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keyword">auto</span> edge = <a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>(node_id_from, node_id_to);</div> +<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordflow">if</span> (!<a class="code" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a>(edge))</div> +<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  {</div> +<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>.insert({edge, weight});</div> +<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a>(edge);</div> +<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  }</div> +<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  }</div> +<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  </div> +<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3"> 211</a></span>  std::string <a class="code" href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">serialize_to_dot</a>()<span class="keyword"> const</span></div> +<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  std::ostringstream dot_str;</div> +<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  dot_str << <span class="stringliteral">"digraph g {\n"</span>;</div> +<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  </div> +<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="comment">// Get nodel labels, if any.</span></div> +<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a>(dot_str);</div> +<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  </div> +<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="comment">// Get edges.</span></div> +<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a>(dot_str, <span class="stringliteral">"->"</span>);</div> +<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  </div> +<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  dot_str << <span class="stringliteral">"}\n"</span>;</div> +<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="keywordflow">return</span> dot_str.str();</div> +<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  }</div> +<div class="line"><a name="l00225"></a><span class="lineno"> 225</span> };</div> +<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  </div> +<div class="line"><a name="l00228"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1UndirectedGraph.html"> 228</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1UndirectedGraph.html">UndirectedGraph</a> : <span class="keyword">public</span> <a class="code" href="classclaragenomics_1_1Graph.html">Graph</a></div> +<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> {</div> +<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">Graph::node_id_t</a>;</div> +<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">Graph::edge_weight_t</a>;</div> +<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keyword">using</span> <a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">Graph::edge_t</a>;</div> +<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  </div> +<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04"> 243</a></span>  <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">add_edge</a>(<a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_from, <a class="code" href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">node_id_t</a> node_id_to, <a class="code" href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">edge_weight_t</a> weight = 0)</div> +<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  {</div> +<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="keyword">auto</span> edge = <a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>(node_id_from, node_id_to);</div> +<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keyword">auto</span> edge_reversed = <a class="code" href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">edge_t</a>(node_id_to, node_id_from);</div> +<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="keywordflow">if</span> (!<a class="code" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a>(edge) && !<a class="code" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">directed_edge_exists</a>(edge_reversed))</div> +<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  {</div> +<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">edges_</a>.insert({edge, weight});</div> +<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a>(edge);</div> +<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">update_adject_nodes</a>(edge_reversed);</div> +<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  }</div> +<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  }</div> +<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  </div> +<div class="line"><a name="l00258"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f"> 258</a></span>  std::string <a class="code" href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">serialize_to_dot</a>()<span class="keyword"> const</span></div> +<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> <span class="keyword"> </span>{</div> +<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  std::ostringstream dot_str;</div> +<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  dot_str << <span class="stringliteral">"graph g {\n"</span>;</div> +<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  </div> +<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="comment">// Get nodel labels, if any.</span></div> +<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">node_labels_to_dot</a>(dot_str);</div> +<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  </div> +<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="comment">// Get edges.</span></div> +<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="code" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">edges_to_dot</a>(dot_str, <span class="stringliteral">"--"</span>);</div> +<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  </div> +<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  dot_str << <span class="stringliteral">"}\n"</span>;</div> +<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordflow">return</span> dot_str.str();</div> +<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  }</div> +<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> };</div> +<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  </div> +<div class="line"><a name="l00274"></a><span class="lineno"> 274</span> } <span class="comment">// namespace claragenomics</span></div> +</div><!-- fragment --></div><!-- contents --> +<div class="ttc" id="astructclaragenomics_1_1PairHash_html_a46da7ce33ff4cf8a586a0c54b6be1e61"><div class="ttname"><a href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61">claragenomics::PairHash::operator()</a></div><div class="ttdeci">size_t operator()(const std::pair< T1, T2 > &pair) const</div><div class="ttdoc">Operator overload to define hash function.</div><div class="ttdef"><b>Definition:</b> graph.hpp:32</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a88dda0ee0cffa26a188a041593d2fcd5"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">claragenomics::Graph::edges_to_dot</a></div><div class="ttdeci">void edges_to_dot(std::ostringstream &dot_str, const std::string &node_separator) const</div><div class="ttdoc">Serialize edges to dot format.</div><div class="ttdef"><b>Definition:</b> graph.hpp:158</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a1b51bca4b58c9922b375c983415ec0c8"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">claragenomics::Graph::get_node_ids</a></div><div class="ttdeci">const std::vector< node_id_t > get_node_ids() const</div><div class="ttdoc">List all node IDs in the graph.</div><div class="ttdef"><b>Definition:</b> graph.hpp:71</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a8b53264154b5caed266385a007e33404"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a8b53264154b5caed266385a007e33404">claragenomics::Graph::adjacent_nodes_</a></div><div class="ttdeci">std::unordered_map< node_id_t, std::vector< node_id_t > > adjacent_nodes_</div><div class="ttdoc">List of adjacent nodes per node ID.</div><div class="ttdef"><b>Definition:</b> graph.hpp:170</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a4089c636086324cae1f2a2bde56c8b33"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a4089c636086324cae1f2a2bde56c8b33">claragenomics::Graph::edges_</a></div><div class="ttdeci">std::unordered_map< edge_t, edge_weight_t, PairHash > edges_</div><div class="ttdoc">All edges in the graph.</div><div class="ttdef"><b>Definition:</b> graph.hpp:173</div></div> +<div class="ttc" id="aclassclaragenomics_1_1DirectedGraph_html_a7844605760f22a2a60e27c23178497b3"><div class="ttname"><a href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">claragenomics::DirectedGraph::serialize_to_dot</a></div><div class="ttdeci">std::string serialize_to_dot() const</div><div class="ttdoc">Serialize graph structure to dot format.</div><div class="ttdef"><b>Definition:</b> graph.hpp:211</div></div> +<div class="ttc" id="aclassclaragenomics_1_1UndirectedGraph_html_a47c5ee6b9616ab24222526f4dcd1fb04"><div class="ttname"><a href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">claragenomics::UndirectedGraph::add_edge</a></div><div class="ttdeci">void add_edge(node_id_t node_id_from, node_id_t node_id_to, edge_weight_t weight=0)</div><div class="ttdoc">Add undirected edges to graph.</div><div class="ttdef"><b>Definition:</b> graph.hpp:243</div></div> +<div class="ttc" id="aclassclaragenomics_1_1DirectedGraph_html_a85c21aed5db9c7d81cb6003841410371"><div class="ttname"><a href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">claragenomics::DirectedGraph::add_edge</a></div><div class="ttdeci">void add_edge(node_id_t node_id_from, node_id_t node_id_to, edge_weight_t weight=0)</div><div class="ttdoc">Add directed edges to graph.</div><div class="ttdef"><b>Definition:</b> graph.hpp:198</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a1df5a4be1fc2f71130436e9f718e85ac"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">claragenomics::Graph::directed_edge_exists</a></div><div class="ttdeci">bool directed_edge_exists(edge_t edge)</div><div class="ttdoc">Check if a directed edge exists in the grph.</div><div class="ttdef"><b>Definition:</b> graph.hpp:122</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_ada271fc17a3a6e86f5dcc78c4caa729c"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#ada271fc17a3a6e86f5dcc78c4caa729c">claragenomics::Graph::empty_</a></div><div class="ttdeci">const std::vector< node_id_t > empty_</div><div class="ttdoc">An empty list representing no connectivity.</div><div class="ttdef"><b>Definition:</b> graph.hpp:179</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a95ef438f6035c2240bf277645ad27cb9"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">claragenomics::Graph::node_labels_to_dot</a></div><div class="ttdeci">void node_labels_to_dot(std::ostringstream &dot_str) const</div><div class="ttdoc">Serialize node labels to dot format.</div><div class="ttdef"><b>Definition:</b> graph.hpp:146</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a0f9734799fc19b94b0621c956ce5508d"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a0f9734799fc19b94b0621c956ce5508d">claragenomics::Graph::node_id_t</a></div><div class="ttdeci">int32_t node_id_t</div><div class="ttdoc">Typedef for node ID.</div><div class="ttdef"><b>Definition:</b> graph.hpp:45</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_ab52b2707de415931f1990ee338b29eeb"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">claragenomics::Graph::get_adjacent_nodes</a></div><div class="ttdeci">const std::vector< node_id_t > & get_adjacent_nodes(node_id_t node) const</div><div class="ttdoc">Get a list of adjacent nodes to a given node.</div><div class="ttdef"><b>Definition:</b> graph.hpp:55</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a47bd2f14a355fbbd801846b0af305389"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">claragenomics::Graph::get_node_label</a></div><div class="ttdeci">std::string get_node_label(node_id_t node) const</div><div class="ttdoc">Get the label associated with a node.</div><div class="ttdef"><b>Definition:</b> graph.hpp:104</div></div> +<div class="ttc" id="aclassclaragenomics_1_1UndirectedGraph_html_a64b119c6ca6049b081ddde7db3c87e3f"><div class="ttname"><a href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">claragenomics::UndirectedGraph::serialize_to_dot</a></div><div class="ttdeci">std::string serialize_to_dot() const</div><div class="ttdoc">Serialize graph structure to dot format.</div><div class="ttdef"><b>Definition:</b> graph.hpp:258</div></div> +<div class="ttc" id="astructclaragenomics_1_1PairHash_html"><div class="ttname"><a href="structclaragenomics_1_1PairHash.html">claragenomics::PairHash</a></div><div class="ttdef"><b>Definition:</b> graph.hpp:27</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a5da2769d7e5bebd1d74c4899e3aad2c5"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a5da2769d7e5bebd1d74c4899e3aad2c5">claragenomics::Graph::node_labels_</a></div><div class="ttdeci">std::unordered_map< node_id_t, std::string > node_labels_</div><div class="ttdoc">Label per node.</div><div class="ttdef"><b>Definition:</b> graph.hpp:176</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a9861d50dbee863befed15eb8daacff3d"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">claragenomics::Graph::set_node_label</a></div><div class="ttdeci">void set_node_label(node_id_t node, const std::string &label)</div><div class="ttdoc">Add string labels to a node ID.</div><div class="ttdef"><b>Definition:</b> graph.hpp:94</div></div> +<div class="ttc" id="aclassclaragenomics_1_1DirectedGraph_html"><div class="ttname"><a href="classclaragenomics_1_1DirectedGraph.html">claragenomics::DirectedGraph</a></div><div class="ttdoc">DirectedGraph Object representing a directed graph structure.</div><div class="ttdef"><b>Definition:</b> graph.hpp:183</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html"><div class="ttname"><a href="classclaragenomics_1_1Graph.html">claragenomics::Graph</a></div><div class="ttdoc">Object representing a generic graph structure.</div><div class="ttdef"><b>Definition:</b> graph.hpp:41</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a3892123fce03f805e54ce0076e6b68dc"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a3892123fce03f805e54ce0076e6b68dc">claragenomics::Graph::edge_t</a></div><div class="ttdeci">std::pair< node_id_t, node_id_t > edge_t</div><div class="ttdoc">Typedef for edge.</div><div class="ttdef"><b>Definition:</b> graph.hpp:49</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_ac96335c01273c0dd74d2628e7bf38794"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">claragenomics::Graph::get_edges</a></div><div class="ttdeci">const std::vector< std::pair< edge_t, edge_weight_t > > get_edges() const</div><div class="ttdoc">Get a list of all edges in the graph.</div><div class="ttdef"><b>Definition:</b> graph.hpp:85</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_a0043ec8f35f7491c06915c887d31ea77"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">claragenomics::Graph::update_adject_nodes</a></div><div class="ttdeci">void update_adject_nodes(edge_t edge)</div><div class="ttdoc">Update the adjacent nodes based on edge information.</div><div class="ttdef"><b>Definition:</b> graph.hpp:130</div></div> +<div class="ttc" id="aclassclaragenomics_1_1Graph_html_ad5388bf7676b6e35a6e62c034e2993b5"><div class="ttname"><a href="classclaragenomics_1_1Graph.html#ad5388bf7676b6e35a6e62c034e2993b5">claragenomics::Graph::edge_weight_t</a></div><div class="ttdeci">int32_t edge_weight_t</div><div class="ttdoc">Tpyedef for edge weight.</div><div class="ttdef"><b>Definition:</b> graph.hpp:47</div></div> +<div class="ttc" id="aclassclaragenomics_1_1UndirectedGraph_html"><div class="ttname"><a href="classclaragenomics_1_1UndirectedGraph.html">claragenomics::UndirectedGraph</a></div><div class="ttdoc">UndirectedGraph Object representing an undirected graph structure.</div><div class="ttdef"><b>Definition:</b> graph.hpp:228</div></div> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/graph_legend.html b/docs/cpp/graph_legend.html new file mode 100644 index 000000000..b9f463dfd --- /dev/null +++ b/docs/cpp/graph_legend.html @@ -0,0 +1,137 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: Graph Legend</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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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 --> +<!-- 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">Graph Legend</div> </div> +</div><!--header--> +<div class="contents"> +<p>This page explains how to interpret the graphs that are generated by doxygen.</p> +<p>Consider the following example: </p><div class="fragment"><div class="line">/*! Invisible class because of truncation */</div> +<div class="line">class Invisible { };</div> +<div class="line"> </div> +<div class="line">/*! Truncated class, inheritance relation is hidden */</div> +<div class="line">class Truncated : public Invisible { };</div> +<div class="line"> </div> +<div class="line">/* Class not documented with doxygen comments */</div> +<div class="line">class Undocumented { };</div> +<div class="line"> </div> +<div class="line">/*! Class that is inherited using public inheritance */</div> +<div class="line">class PublicBase : public Truncated { };</div> +<div class="line"> </div> +<div class="line">/*! A template class */</div> +<div class="line">template<class T> class Templ { };</div> +<div class="line"> </div> +<div class="line">/*! Class that is inherited using protected inheritance */</div> +<div class="line">class ProtectedBase { };</div> +<div class="line"> </div> +<div class="line">/*! Class that is inherited using private inheritance */</div> +<div class="line">class PrivateBase { };</div> +<div class="line"> </div> +<div class="line">/*! Class that is used by the Inherited class */</div> +<div class="line">class Used { };</div> +<div class="line"> </div> +<div class="line">/*! Super class that inherits a number of other classes */</div> +<div class="line">class Inherited : public PublicBase,</div> +<div class="line"> protected ProtectedBase,</div> +<div class="line"> private PrivateBase,</div> +<div class="line"> public Undocumented,</div> +<div class="line"> public Templ<int></div> +<div class="line">{</div> +<div class="line"> private:</div> +<div class="line"> Used *m_usedClass;</div> +<div class="line">};</div> +</div><!-- fragment --><p> This will result in the following graph:</p> +<center><img src="graph_legend.png" alt="" class="inline"/></center><p>The boxes in the above graph have the following meaning: </p> +<ul> +<li> +A filled gray box represents the struct or class for which the graph is generated. </li> +<li> +A box with a black border denotes a documented struct or class. </li> +<li> +A box with a gray border denotes an undocumented struct or class. </li> +<li> +A box with a red border denotes a documented struct or class forwhich not all inheritance/containment relations are shown. A graph is truncated if it does not fit within the specified boundaries. </li> +</ul> +<p>The arrows have the following meaning: </p> +<ul> +<li> +A dark blue arrow is used to visualize a public inheritance relation between two classes. </li> +<li> +A dark green arrow is used for protected inheritance. </li> +<li> +A dark red arrow is used for private inheritance. </li> +<li> +A purple dashed arrow is used if a class is contained or used by another class. The arrow is labelled with the variable(s) through which the pointed class or struct is accessible. </li> +<li> +A yellow dashed arrow denotes a relation between a template instance and the template class it was instantiated from. 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id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -78,6 +78,9 @@ <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td></tr> <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences. <a href="classclaragenomics_1_1cudamapper_1_1Index.html#details">More...</a><br /></td></tr> <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">claragenomics::cudamapper::Matcher</a></td></tr> +<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> - base matcher. <a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#details">More...</a><br /></td></tr> +<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></td></tr> <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html">claragenomics::cudamapper::Sequence</a></td></tr> @@ -93,9 +96,9 @@ virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">claragenomics::cudamapper::Overlapper::~Overlapper</a> ()=default</td></tr> <tr class="memdesc:ga569c8855bdf9806d3747b26fc7e98975"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor for <a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a>. <br /></td></tr> <tr class="separator:ga569c8855bdf9806d3747b26fc7e98975"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:ga5498f3d8b5eff6481c67fdf0a049c300"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">claragenomics::cudamapper::Overlapper::get_overlaps</a> (std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> > &overlaps, std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> > &anchors, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &index)=0</td></tr> -<tr class="memdesc:ga5498f3d8b5eff6481c67fdf0a049c300"><td class="mdescLeft"> </td><td class="mdescRight">returns overlaps for a set of reads <a href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">More...</a><br /></td></tr> -<tr class="separator:ga5498f3d8b5eff6481c67fdf0a049c300"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">claragenomics::cudamapper::Overlapper::get_overlaps</a> (std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> > &overlaps, thrust::device_vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> > &anchors, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &index_query, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &index_target)=0</td></tr> +<tr class="memdesc:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="mdescLeft"> </td><td class="mdescRight">returns overlaps for a set of reads <a href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">More...</a><br /></td></tr> +<tr class="separator:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:ga54fedd97206ad1691f7b9d9966d01371"><td class="memItemLeft" align="right" valign="top"><a id="ga54fedd97206ad1691f7b9d9966d01371"></a> static void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">claragenomics::cudamapper::Overlapper::print_paf</a> (const std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> > &overlaps)</td></tr> <tr class="memdesc:ga54fedd97206ad1691f7b9d9966d01371"><td class="mdescLeft"> </td><td class="mdescRight">prints overlaps to stdout in <a href="https://github.com/lh3/miniasm/blob/master/PAF.md">PAF format</a> <br /></td></tr> @@ -166,8 +169,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#ga3e5732f34489315ec8d1ef8 </div> </div> -<a id="ga5498f3d8b5eff6481c67fdf0a049c300"></a> -<h2 class="memtitle"><span class="permalink"><a href="#ga5498f3d8b5eff6481c67fdf0a049c300">◆ </a></span>get_overlaps()</h2> +<a id="gab0e3be4a9442dfb2b7952fb473e591a3"></a> +<h2 class="memtitle"><span class="permalink"><a href="#gab0e3be4a9442dfb2b7952fb473e591a3">◆ </a></span>get_overlaps()</h2> <div class="memitem"> <div class="memproto"> @@ -184,14 +187,20 @@ <h2 class="memtitle"><span class="permalink"><a href="#ga5498f3d8b5eff6481c67fdf <tr> <td class="paramkey"></td> <td></td> - <td class="paramtype">std::vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> > & </td> + <td class="paramtype">thrust::device_vector< <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> > & </td> <td class="paramname"><em>anchors</em>, </td> </tr> <tr> <td class="paramkey"></td> <td></td> <td class="paramtype">const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> & </td> - <td class="paramname"><em>index</em> </td> + <td class="paramname"><em>index_query</em>, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype">const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> & </td> + <td class="paramname"><em>index_target</em> </td> </tr> <tr> <td></td> @@ -211,7 +220,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#ga5498f3d8b5eff6481c67fdf <table class="params"> <tr><td class="paramname">overlaps</td><td>Output vector into which generated overlaps will be placed </td></tr> <tr><td class="paramname">anchors</td><td>vector of anchor objects. Does not need to be ordered </td></tr> - <tr><td class="paramname">index</td><td>representation index for reads </td></tr> + <tr><td class="paramname">index_query</td><td>representation index for reads </td></tr> + <tr><td class="paramname">index_target</td><td></td></tr> </table> </dd> </dl> diff --git a/docs/cpp/group__cudapoa.html b/docs/cpp/group__cudapoa.html index 8b4c8ffba..b10a9615c 100644 --- a/docs/cpp/group__cudapoa.html +++ b/docs/cpp/group__cudapoa.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/group__cudautils.html b/docs/cpp/group__cudautils.html index 1323a016c..b9d2c2d3c 100644 --- a/docs/cpp/group__cudautils.html +++ b/docs/cpp/group__cudautils.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -63,12 +63,19 @@ <div class="header"> <div class="summary"> +<a href="#define-members">Macros</a> | <a href="#func-members">Functions</a> </div> <div class="headertitle"> <div class="title">Internal CUDA utilities package</div> </div> </div><!--header--> <div class="contents"> <table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="define-members"></a> +Macros</h2></td></tr> +<tr class="memitem:gaded61355db08f1d76bc24edc008d4224"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudautils.html#gaded61355db08f1d76bc24edc008d4224">CGA_NVTX_RANGE</a>(varname, label)</td></tr> +<tr class="memdesc:gaded61355db08f1d76bc24edc008d4224"><td class="mdescLeft"> </td><td class="mdescRight">Dummy implementation for CGA_NVTX_RANGE macro. <a href="group__cudautils.html#gaded61355db08f1d76bc24edc008d4224">More...</a><br /></td></tr> +<tr class="separator:gaded61355db08f1d76bc24edc008d4224"><td class="memSeparator" colspan="2"> </td></tr> +</table><table class="memberdecls"> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a> Functions</h2></td></tr> <tr class="memitem:ga3769a812992df47886894f48f26edf6f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f">claragenomics::cudautils::gpu_assert</a> (cudaError_t code, const char *file, int line)</td></tr> @@ -100,6 +107,43 @@ <h2 class="memtitle"><span class="permalink"><a href="#ga161535c48fe399e086ac627 </div><!-- fragment --> <p>Log on CUDA error in enclosed expression. </p> +</div> +</div> +<a id="gaded61355db08f1d76bc24edc008d4224"></a> +<h2 class="memtitle"><span class="permalink"><a href="#gaded61355db08f1d76bc24edc008d4224">◆ </a></span>CGA_NVTX_RANGE</h2> + +<div class="memitem"> +<div class="memproto"> + <table class="memname"> + <tr> + <td class="memname">#define CGA_NVTX_RANGE</td> + <td>(</td> + <td class="paramtype"> </td> + <td class="paramname">varname, </td> + </tr> + <tr> + <td class="paramkey"></td> + <td></td> + <td class="paramtype"> </td> + <td class="paramname">label </td> + </tr> + <tr> + <td></td> + <td>)</td> + <td></td><td></td> + </tr> + </table> +</div><div class="memdoc"> + +<p>Dummy implementation for CGA_NVTX_RANGE macro. </p> +<dl class="params"><dt>Parameters</dt><dd> + <table class="params"> + <tr><td class="paramname">varname</td><td>Unused variable </td></tr> + <tr><td class="paramname">label</td><td>Unused variable </td></tr> + </table> + </dd> +</dl> + </div> </div> <h2 class="groupheader">Function Documentation</h2> @@ -155,7 +199,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#ga3769a812992df47886894f4 </div> </div> </div><!-- contents --> -<div class="ttc" id="agroup__cudautils_html_ga3769a812992df47886894f48f26edf6f"><div class="ttname"><a href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f">claragenomics::cudautils::gpu_assert</a></div><div class="ttdeci">void gpu_assert(cudaError_t code, const char *file, int line)</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:46</div></div> +<div class="ttc" id="agroup__cudautils_html_ga3769a812992df47886894f48f26edf6f"><div class="ttname"><a href="group__cudautils.html#ga3769a812992df47886894f48f26edf6f">claragenomics::cudautils::gpu_assert</a></div><div class="ttdeci">void gpu_assert(cudaError_t code, const char *file, int line)</div><div class="ttdef"><b>Definition:</b> cudautils.hpp:50</div></div> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> Generated by  <a href="http://www.doxygen.org/index.html"> diff --git a/docs/cpp/group__logging.html b/docs/cpp/group__logging.html index 68ed2c5d6..7e4eb975e 100644 --- a/docs/cpp/group__logging.html +++ b/docs/cpp/group__logging.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/hierarchy.html b/docs/cpp/hierarchy.html new file mode 100644 index 000000000..60d1819eb --- /dev/null +++ b/docs/cpp/hierarchy.html @@ -0,0 +1,102 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: Class Hierarchy</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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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 --> +<!-- 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">Class Hierarchy</div> </div> +</div><!--header--> +<div class="contents"> +<div class="textblock"> +<p><a href="inherits.html">Go to the graphical class hierarchy</a></p> +This inheritance list is sorted roughly, but not completely, alphabetically:</div><div class="directory"> +<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span>]</div><table class="directory"> +<tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html" target="_self">claragenomics::cudaaligner::Aligner</a></td><td class="desc"></td></tr> +<tr id="row_1_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html" target="_self">claragenomics::cudaaligner::Alignment</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html" title="Alignment - Object encapsulating an alignment between 2 string.">Alignment</a> - Object encapsulating an alignment between 2 string </td></tr> +<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html" target="_self">claragenomics::cudamapper::Anchor</a></td><td class="desc"></td></tr> +<tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html" target="_self">claragenomics::cudamapper::ArrayBlock</a></td><td class="desc"></td></tr> +<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html" target="_self">claragenomics::cudapoa::Batch</a></td><td class="desc"></td></tr> +<tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html" target="_self">claragenomics::cudapoa::Entry</a></td><td class="desc">A structure to represent a sequence entry </td></tr> +<tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html" target="_self">claragenomics::io::FastaParser</a></td><td class="desc"></td></tr> +<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html" target="_self">claragenomics::io::FastaSequence</a></td><td class="desc">A structure to hold details of a single FASTA entry </td></tr> +<tr id="row_8_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_8_" class="arrow" onclick="toggleFolder('8_')">▼</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1Graph.html" target="_self">claragenomics::Graph</a></td><td class="desc">Object representing a generic graph structure </td></tr> +<tr id="row_8_0_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1DirectedGraph.html" target="_self">claragenomics::DirectedGraph</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1DirectedGraph.html" title="DirectedGraph Object representing a directed graph structure.">DirectedGraph</a> Object representing a directed graph structure </td></tr> +<tr id="row_8_1_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1UndirectedGraph.html" target="_self">claragenomics::UndirectedGraph</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1UndirectedGraph.html" title="UndirectedGraph Object representing an undirected graph structure.">UndirectedGraph</a> Object representing an undirected graph structure </td></tr> +<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" target="_self">claragenomics::cudamapper::Index</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences </td></tr> +<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" target="_self">claragenomics::cudamapper::Matcher</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> - base matcher </td></tr> +<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html" target="_self">claragenomics::cudamapper::Overlap</a></td><td class="desc"></td></tr> +<tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html" target="_self">claragenomics::cudamapper::Overlapper</a></td><td class="desc"></td></tr> +<tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structclaragenomics_1_1PairHash.html" target="_self">claragenomics::PairHash</a></td><td class="desc"></td></tr> +<tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1scoped__device__switch.html" target="_self">claragenomics::scoped_device_switch</a></td><td class="desc">A class to switch the CUDA device for the current scope using RAII </td></tr> +<tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html" target="_self">claragenomics::cudamapper::Sequence</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html" title="Sequence - represents an individual read (name, DNA nucleotides etc)">Sequence</a> - represents an individual read (name, DNA nucleotides etc) </td></tr> +<tr id="row_16_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html" target="_self">claragenomics::cudamapper::SketchElement</a></td><td class="desc"><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html" title="SketchElement - Contains integer representation, position, direction and read id of a kmer.">SketchElement</a> - Contains integer representation, position, direction and read id of a kmer </td></tr> +</table> +</div><!-- directory --> +</div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/index.html b/docs/cpp/index.html index 00bc52878..43a6f8149 100644 --- a/docs/cpp/index.html +++ b/docs/cpp/index.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -79,10 +79,28 @@ <h2><a class="anchor" id="autotoc_md2"></a> <h2><a class="anchor" id="autotoc_md3"></a> cudaaligner</h2> <p>The <code>cudaaligner</code> package provides GPU-accelerated global alignment.</p> -<h1><a class="anchor" id="autotoc_md4"></a> +<h2><a class="anchor" id="autotoc_md4"></a> +cudamapper</h2> +<p><b>Note</b> cudamapper is still in pre-alpha stage and should be considered experimental.</p> +<p>The <code>cudamapper</code> package provides minimizer-based GPU-accelerated approximate mapping. <code>cudamapper</code> outputs mappings in the PAF format and is currently optimised for all-vs-all long read (ONT, Pacific Biosciences) sequences.</p> +<p>To run all-vs all overlaps use the following command:</p> +<p><code>cudamapper in.fasta in.fasta</code></p> +<p>A query fasta can be mapped to a reference as follows:</p> +<p><code>cudamapper query.fasta target.fasta</code></p> +<h3><a class="anchor" id="autotoc_md5"></a> +cudamapper usage information</h3> +<p>To access more information about running cudamapper, run <code>cudamapper --help</code>.</p> +<h1><a class="anchor" id="autotoc_md6"></a> Clone Clara Genomics Analysis</h1> +<h2><a class="anchor" id="autotoc_md7"></a> +Latest released version</h2> +<p>This will clone the repo to the <code>master</code> branch, which contains code for latest released version and hot-fixes.</p> +<div class="fragment"><div class="line">git clone --recursive -b master git@github.com:clara-genomics/ClaraGenomicsAnalysis.git</div> +</div><!-- fragment --><h2><a class="anchor" id="autotoc_md8"></a> +Latest development version</h2> +<p>This will clone the repo to the default branch, which is set to be the latest development branch. This branch is subject to change frequently as features and bug fixes are pushed.</p> <div class="fragment"><div class="line">git clone --recursive git@github.com:clara-genomics/ClaraGenomicsAnalysis.git</div> -</div><!-- fragment --><h1><a class="anchor" id="autotoc_md5"></a> +</div><!-- fragment --><h1><a class="anchor" id="autotoc_md9"></a> System Requirements</h1> <p>Minimum requirements -</p> <ol type="1"> @@ -92,45 +110,46 @@ <h1><a class="anchor" id="autotoc_md4"></a> <li>Python 3.6.7+</li> <li>htslib 1.9+ (<a href="https://github.com/samtools/htslib,">https://github.com/samtools/htslib,</a> also requires <code>zlib1g-dev</code>, <code>libbz2-dev</code> and <code>liblzma-dev</code> to be installed on Ubuntu)</li> </ol> -<h1><a class="anchor" id="autotoc_md6"></a> +<h1><a class="anchor" id="autotoc_md10"></a> Clara Genomics Analysis Setup</h1> -<h2><a class="anchor" id="autotoc_md7"></a> +<h2><a class="anchor" id="autotoc_md11"></a> Build</h2> <p>To build Clara Genomics Analysis -</p> <div class="fragment"><div class="line">mkdir build</div> <div class="line">cd build</div> <div class="line">cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=install</div> <div class="line">make -j install</div> -</div><!-- fragment --><h2><a class="anchor" id="autotoc_md8"></a> +</div><!-- fragment --><h2><a class="anchor" id="autotoc_md12"></a> Install</h2> <p>To install the SDK -</p> <div class="fragment"><div class="line">make install</div> -</div><!-- fragment --><h2><a class="anchor" id="autotoc_md9"></a> +</div><!-- fragment --><h2><a class="anchor" id="autotoc_md13"></a> Package generation</h2> <p>Package generation puts the libraries, headers and binaries built by the <code>make</code> command above into a <code>.deb</code>/<code>.rpm</code> for portability and easy installation. The package generation itself doesn't guarantee any cross-platform compatibility.</p> <p>It is recommended that a separate build and packaging be performed for each distribution and CUDA version that needs to be supported.</p> <p>The type of package (deb vs rpm) is determined automatically based on the platform the code is being run on. To generate a package for the SDK -</p> <div class="fragment"><div class="line">make package</div> -</div><!-- fragment --><h1><a class="anchor" id="autotoc_md10"></a> +</div><!-- fragment --><h1><a class="anchor" id="autotoc_md14"></a> Enable Unit Tests</h1> <p>To enable unit tests, add <code>-Dcga_enable_tests=ON</code> to the <code>cmake</code> command in the build step.</p> <p>This builds GTest based unit tests for all applicable modules, and installs them under <code>${CMAKE_INSTALL_PREFIX}/tests</code>. These tests are standalone binaries and can be executed directly. e.g.</p> <div class="fragment"><div class="line">cd $INSTALL_DIR</div> <div class="line">./tests/cudapoatests</div> -</div><!-- fragment --><h1><a class="anchor" id="autotoc_md11"></a> +</div><!-- fragment --><h1><a class="anchor" id="autotoc_md15"></a> Enable Benchmarks</h1> <p>To enable benchmarks, add <code>-Dcga_enable_benchmarks=ON</code> to the <code>cmake</code> command in the build step.</p> <p>This builds Google Benchmark based microbenchmarks for applicable modules. The built benchmarks are installed under <code>${CMAKE_INSTALL_PREFIX}/benchmarks/<module></code> and can be run directly.</p> <p>e.g. </p><div class="fragment"><div class="line">#INSTALL_DIR/benchmarks/cudapoa/multibatch</div> </div><!-- fragment --><p>A description of each of the benchmarks is present in a README under the module's benchmark folder.</p> -<h1><a class="anchor" id="autotoc_md12"></a> +<h1><a class="anchor" id="autotoc_md16"></a> Enable Doc Generation</h1> -<p>To enable document generation for Clara Genomics Analysis, please install <code>Doxygen</code> on your system. Once <code>Doxygen</code> has been installed, run the following to build documents.</p> +<p>To enable document generation for Clara Genomics Analysis, please install <code>Doxygen</code> on your system. Once<code>Doxygen</code> has been installed, run the following to build documents.</p> <div class="fragment"><div class="line">make docs</div> </div><!-- fragment --><p>Docs are also generated as part of the default <code>all</code> target when <code>Doxygen</code> is available on the system.</p> -<h1><a class="anchor" id="autotoc_md13"></a> +<p>To disable documentation generation add <code>-Dcga_generate_docs=OFF</code> to the <code>cmake</code> command in the <a href="#build">build step</a>.</p> +<h1><a class="anchor" id="autotoc_md17"></a> Code Formatting</h1> -<h2><a class="anchor" id="autotoc_md14"></a> +<h2><a class="anchor" id="autotoc_md18"></a> C++ / CUDA</h2> <p>Clara Genomics Analysis makes use of <code>clang-format</code> to format it's source and header files. To make use of auto-formatting, <code>clang-format</code> would have to be installed from the LLVM package (for latest builds, best to refer to <a href="http://releases.llvm.org/download.html">http://releases.llvm.org/download.html</a>).</p> <p>Once <code>clang-format</code> has been installed, make sure the binary is in your path.</p> @@ -139,10 +158,21 @@ <h2><a class="anchor" id="autotoc_md14"></a> <div class="fragment"><div class="line">make format</div> </div><!-- fragment --><p>To check if files are correct formatted, run the following in your build directory.</p> <div class="fragment"><div class="line">make check-format</div> -</div><!-- fragment --><h2><a class="anchor" id="autotoc_md15"></a> +</div><!-- fragment --><h2><a class="anchor" id="autotoc_md19"></a> Python</h2> <p>Clara Genomics Analysis follows the PEP-8 style guidelines for all its Python code. The automated CI system for Clara Genomics Analysis run <code>flake8</code> to check the style.</p> <p>To run style check manually, simply run the following from the top level folder. </p><div class="fragment"><div class="line">flake8 pyclaragenomics/</div> +</div><!-- fragment --><h1><a class="anchor" id="autotoc_md20"></a> +Running CI Tests Locally</h1> +<p>Please note, your git repository will be mounted to the container, any untracked files will be removed from it. Before executing the CI locally, stash or add them to the index.</p> +<p>Requirements:</p><ol type="1"> +<li>docker (<a href="https://docs.docker.com/install/linux/docker-ce/ubuntu/">https://docs.docker.com/install/linux/docker-ce/ubuntu/</a>)</li> +<li>nvidia-docker (<a href="https://github.com/NVIDIA/nvidia-docker">https://github.com/NVIDIA/nvidia-docker</a>)</li> +<li>nvidia-container-runtime (<a href="https://github.com/NVIDIA/nvidia-container-runtime">https://github.com/NVIDIA/nvidia-container-runtime</a>)</li> +</ol> +<p>Run the following command to execute the CI build steps inside a container locally: </p><div class="fragment"><div class="line">bash ci/local/build.sh -r <ClaraGenomicsAnalysis repo path></div> +</div><!-- fragment --><p> ci/local/build.sh script was adapted from <a href="https://github.com/rapidsai/cudf/tree/branch-0.11/ci/local">rapidsai/cudf</a></p> +<p>The default docker image is <b>clara-genomics-base:cuda10.0-ubuntu16.04-gcc5-py3.7</b>. Other images from <a href="https://hub.docker.com/r/gpuci/clara-genomics-base/tags">gpuci/clara-genomics-base</a> repository can be used instead, by using -i argument </p><div class="fragment"><div class="line">bash ci/local/build.sh -r <ClaraGenomicsAnalysis repo path> -i gpuci/clara-genomics-base:cuda10.0-ubuntu18.04-gcc7-py3.6</div> </div><!-- fragment --> </div></div><!-- PageDoc --> </div><!-- contents --> <!-- start footer part --> diff --git a/docs/cpp/index_8hpp_source.html b/docs/cpp/index_8hpp_source.html index fb97627b0..0b60a83c4 100644 --- a/docs/cpp/index_8hpp_source.html +++ b/docs/cpp/index_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -85,83 +85,74 @@ <div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <memory></span></div> <div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include <string></span></div> <div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <vector></span></div> -<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include "claragenomics/cudamapper/sketch_element.hpp"</span></div> -<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include "claragenomics/cudamapper/types.hpp"</span></div> -<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include "claragenomics/io/fasta_parser.hpp"</span></div> +<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include <claragenomics/cudamapper/sketch_element.hpp></span></div> +<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include <claragenomics/cudamapper/types.hpp></span></div> +<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <claragenomics/io/fasta_parser.hpp></span></div> <div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  </div> -<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="keyword">namespace </span>claragenomics</div> -<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> {</div> -<div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  </div> -<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="keyword">namespace </span>cudamapper</div> -<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> {</div> -<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  </div> -<div class="line"><a name="l00029"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Index.html"> 29</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a></div> -<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> {</div> -<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keyword">public</span>:</div> -<div class="line"><a name="l00033"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html"> 33</a></span>  <span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html">RepresentationToSketchElements</a></div> -<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  {</div> -<div class="line"><a name="l00036"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a839754dc6ed7d150ae06abf377e39c62"> 36</a></span>  representation_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a839754dc6ed7d150ae06abf377e39c62">representation_</a>;</div> -<div class="line"><a name="l00038"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a84ff4998d9fec875845a20272d209b30"> 38</a></span>  <a class="code" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html">ArrayBlock</a> <a class="code" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a84ff4998d9fec875845a20272d209b30">sketch_elements_for_representation_and_read_id_</a>;</div> -<div class="line"><a name="l00040"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a604d5227c7fe6412e982fb31a1fee549"> 40</a></span>  <a class="code" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html">ArrayBlock</a> <a class="code" href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a604d5227c7fe6412e982fb31a1fee549">sketch_elements_for_representation_and_all_read_ids_</a>;</div> -<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  };</div> -<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  </div> -<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">~Index</a>() = <span class="keywordflow">default</span>;</div> -<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  </div> -<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<position_in_read_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5c75f11d1683e4f863f14a4088a36306">positions_in_reads</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  </div> -<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<read_id_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#aac33d8d2aa72bb227326a35f5b452de5">read_ids</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  </div> -<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<SketchElement::DirectionOfRepresentation>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a407a2466e8740a0f78a3ce876b87352b">directions_of_reads</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <thrust/device_vector.h></span></div> +<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  </div> +<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">namespace </span>claragenomics</div> +<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> {</div> +<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  </div> +<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">namespace </span>cudamapper</div> +<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> {</div> +<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  </div> +<div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Index.html"> 31</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a></div> +<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> {</div> +<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">~Index</a>() = <span class="keywordflow">default</span>;</div> +<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  </div> +<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> thrust::device_vector<representation_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">representations</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  </div> +<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> thrust::device_vector<read_id_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">read_ids</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  </div> +<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> thrust::device_vector<position_in_read_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">positions_in_reads</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  </div> +<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> thrust::device_vector<SketchElement::DirectionOfRepresentation>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">directions_of_reads</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  </div> +<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::string& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">read_id_to_read_name</a>(<span class="keyword">const</span> read_id_t read_id) <span class="keyword">const</span> = 0;</div> <div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  </div> -<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">virtual</span> std::uint64_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">number_of_reads</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> thrust::device_vector<representation_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">unique_representations</a>() <span class="keyword">const</span> = 0;</div> <div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  </div> -<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<std::string>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#aec3176ac2d5e425b25dec14f411cbfe0">read_id_to_read_name</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> thrust::device_vector<std::uint32_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">first_occurrence_of_representations</a>() <span class="keyword">const</span> = 0;</div> <div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  </div> -<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<std::uint32_t>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#af03421436f827e88316c74b0b3af200e">read_id_to_read_length</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  </div> -<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">virtual</span> std::uint64_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac5036778efd3c83f5bf048174a8ab824">minimum_representation</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  </div> -<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keyword">virtual</span> std::uint64_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a69fd1882260a7c55a45fe5e2a092b152">maximum_representation</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  </div> -<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<std::vector<RepresentationToSketchElements>>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#af8ad540ff0a2a244a35ae846ec745c24">read_id_and_representation_to_sketch_elements</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> std::uint32_t& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">read_id_to_read_length</a>(<span class="keyword">const</span> read_id_t read_id) <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  </div> +<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keyword">virtual</span> std::uint64_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">number_of_reads</a>() <span class="keyword">const</span> = 0;</div> +<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  </div> +<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919"> 77</a></span>  <span class="keyword">static</span> uint64_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">maximum_kmer_size</a>()</div> +<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  {</div> +<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">return</span> <span class="keyword">sizeof</span>(representation_t) * 8 / 2;</div> +<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  }</div> <div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  </div> -<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">static</span> std::unique_ptr<Index></div> -<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#acb29a3ba1a493f706a3ec25bc290b30a">create_index</a>(<span class="keyword">const</span> std::vector<io::FastaParser*>& parsers, <span class="keyword">const</span> std::uint64_t kmer_size, <span class="keyword">const</span> std::uint64_t window_size, <span class="keyword">const</span> std::vector<std::pair<std::uint64_t, std::uint64_t>>& ranges);</div> -<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  </div> -<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a4e5b3cf1c41146635ce9d51bbdfe2277">reached_end_of_input</a>() <span class="keyword">const</span> = 0;</div> -<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  </div> -<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keyword">static</span> std::unique_ptr<Index> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#acb29a3ba1a493f706a3ec25bc290b30a">create_index</a>();</div> +<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keyword">static</span> std::unique_ptr<Index></div> +<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">create_index</a>(<span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1io_1_1FastaParser.html">io::FastaParser</a>& parser,</div> +<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keyword">const</span> read_id_t first_read_id,</div> +<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">const</span> read_id_t past_the_last_read_id,</div> +<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keyword">const</span> std::uint64_t kmer_size,</div> +<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keyword">const</span> std::uint64_t window_size,</div> +<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keyword">const</span> <span class="keywordtype">bool</span> hash_representations = <span class="keyword">true</span>);</div> +<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> };</div> <div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  </div> -<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919"> 103</a></span>  <span class="keyword">static</span> uint64_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">maximum_kmer_size</a>()</div> -<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  {</div> -<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordflow">return</span> <span class="keyword">sizeof</span>(representation_t) * 8 / 2;</div> -<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  }</div> -<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> };</div> -<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  </div> -<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  </div> -<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> } <span class="comment">// namespace cudamapper</span></div> -<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  </div> -<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> } <span class="comment">// namespace claragenomics</span></div> +<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  </div> +<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> } <span class="comment">// namespace cudamapper</span></div> +<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  </div> +<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> } <span class="comment">// namespace claragenomics</span></div> </div><!-- fragment --></div><!-- contents --> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a69fd1882260a7c55a45fe5e2a092b152"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a69fd1882260a7c55a45fe5e2a092b152">claragenomics::cudamapper::Index::maximum_representation</a></div><div class="ttdeci">virtual std::uint64_t maximum_representation() const =0</div><div class="ttdoc">maximum possible representation</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_aac33d8d2aa72bb227326a35f5b452de5"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#aac33d8d2aa72bb227326a35f5b452de5">claragenomics::cudamapper::Index::read_ids</a></div><div class="ttdeci">virtual const std::vector< read_id_t > & read_ids() const =0</div><div class="ttdoc">returns an array of reads ids for sketch elements</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements_html_a839754dc6ed7d150ae06abf377e39c62"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a839754dc6ed7d150ae06abf377e39c62">claragenomics::cudamapper::Index::RepresentationToSketchElements::representation_</a></div><div class="ttdeci">representation_t representation_</div><div class="ttdoc">representation</div><div class="ttdef"><b>Definition:</b> index.hpp:36</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_ac5036778efd3c83f5bf048174a8ab824"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac5036778efd3c83f5bf048174a8ab824">claragenomics::cudamapper::Index::minimum_representation</a></div><div class="ttdeci">virtual std::uint64_t minimum_representation() const =0</div><div class="ttdoc">minimum possible representation</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements_html_a604d5227c7fe6412e982fb31a1fee549"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a604d5227c7fe6412e982fb31a1fee549">claragenomics::cudamapper::Index::RepresentationToSketchElements::sketch_elements_for_representation_and_all_read_ids_</a></div><div class="ttdeci">ArrayBlock sketch_elements_for_representation_and_all_read_ids_</div><div class="ttdoc">pointer to all sketch elements with that representation in all reads</div><div class="ttdef"><b>Definition:</b> index.hpp:40</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_acb29a3ba1a493f706a3ec25bc290b30a"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#acb29a3ba1a493f706a3ec25bc290b30a">claragenomics::cudamapper::Index::create_index</a></div><div class="ttdeci">static std::unique_ptr< Index > create_index()</div><div class="ttdoc">creates an empty Index</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></div><div class="ttdoc">Index - manages mapping of (k,w)-kmer-representation and all its occurences.</div><div class="ttdef"><b>Definition:</b> index.hpp:29</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_afcaccc9f9526d9c66280eca17ff3a4ac"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">claragenomics::cudamapper::Index::~Index</a></div><div class="ttdeci">virtual ~Index()=default</div><div class="ttdoc">Virtual destructor for Index.</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a5cfe03b47850170ec64d61d2dbef0401"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">claragenomics::cudamapper::Index::read_ids</a></div><div class="ttdeci">virtual const thrust::device_vector< read_id_t > & read_ids() const =0</div><div class="ttdoc">returns an array of reads ids for sketch elements</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a876d5e82f9fc36f481854f7d84e5fc80"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">claragenomics::cudamapper::Index::representations</a></div><div class="ttdeci">virtual const thrust::device_vector< representation_t > & representations() const =0</div><div class="ttdoc">returns an array of representations of sketch elements</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></div><div class="ttdoc">Index - manages mapping of (k,w)-kmer-representation and all its occurences.</div><div class="ttdef"><b>Definition:</b> index.hpp:31</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_afcaccc9f9526d9c66280eca17ff3a4ac"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">claragenomics::cudamapper::Index::~Index</a></div><div class="ttdeci">virtual ~Index()=default</div><div class="ttdoc">Virtual destructor.</div></div> <div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_ac9e936ae3809c82894a22a5ddb6bb937"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">claragenomics::cudamapper::Index::number_of_reads</a></div><div class="ttdeci">virtual std::uint64_t number_of_reads() const =0</div><div class="ttdoc">returns number of reads in input data</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1ArrayBlock_html"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html">claragenomics::cudamapper::ArrayBlock</a></div><div class="ttdef"><b>Definition:</b> types.hpp:25</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements_html_a84ff4998d9fec875845a20272d209b30"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html#a84ff4998d9fec875845a20272d209b30">claragenomics::cudamapper::Index::RepresentationToSketchElements::sketch_elements_for_representation_and_read_id_</a></div><div class="ttdeci">ArrayBlock sketch_elements_for_representation_and_read_id_</div><div class="ttdoc">pointer to all sketch elements for that representation in some read (no need to save which one)</div><div class="ttdef"><b>Definition:</b> index.hpp:38</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_af8ad540ff0a2a244a35ae846ec745c24"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#af8ad540ff0a2a244a35ae846ec745c24">claragenomics::cudamapper::Index::read_id_and_representation_to_sketch_elements</a></div><div class="ttdeci">virtual const std::vector< std::vector< RepresentationToSketchElements > > & read_id_and_representation_to_sketch_elements() const =0</div><div class="ttdoc">For each read_id (outer vector) returns a vector in which each element contains a representation from...</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_aec3176ac2d5e425b25dec14f411cbfe0"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#aec3176ac2d5e425b25dec14f411cbfe0">claragenomics::cudamapper::Index::read_id_to_read_name</a></div><div class="ttdeci">virtual const std::vector< std::string > & read_id_to_read_name() const =0</div><div class="ttdoc">returns mapping of internal read id that goes from 0 to number_of_reads-1 to actual read name from th...</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a4e5b3cf1c41146635ce9d51bbdfe2277"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a4e5b3cf1c41146635ce9d51bbdfe2277">claragenomics::cudamapper::Index::reached_end_of_input</a></div><div class="ttdeci">virtual bool reached_end_of_input() const =0</div><div class="ttdoc">Returns whether there are any more reads to process in the reads file (e.g FASTA file)</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_af9247d4b637615bf5912acc57b27b919"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">claragenomics::cudamapper::Index::maximum_kmer_size</a></div><div class="ttdeci">static uint64_t maximum_kmer_size()</div><div class="ttdoc">Return the maximum kmer length allowable. This is just the size of the representation in bits divided...</div><div class="ttdef"><b>Definition:</b> index.hpp:103</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a407a2466e8740a0f78a3ce876b87352b"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a407a2466e8740a0f78a3ce876b87352b">claragenomics::cudamapper::Index::directions_of_reads</a></div><div class="ttdeci">virtual const std::vector< SketchElement::DirectionOfRepresentation > & directions_of_reads() const =0</div><div class="ttdoc">returns an array of directions in which sketch elements were read</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_af03421436f827e88316c74b0b3af200e"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#af03421436f827e88316c74b0b3af200e">claragenomics::cudamapper::Index::read_id_to_read_length</a></div><div class="ttdeci">virtual const std::vector< std::uint32_t > & read_id_to_read_length() const =0</div><div class="ttdoc">returns mapping of internal read id that goes from 0 to read lengths for that read</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements_html"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Index_1_1RepresentationToSketchElements.html">claragenomics::cudamapper::Index::RepresentationToSketchElements</a></div><div class="ttdoc">RepresentationToSketchElements - representation, pointer to section of data arrays with sketch elemen...</div><div class="ttdef"><b>Definition:</b> index.hpp:33</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a5c75f11d1683e4f863f14a4088a36306"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5c75f11d1683e4f863f14a4088a36306">claragenomics::cudamapper::Index::positions_in_reads</a></div><div class="ttdeci">virtual const std::vector< position_in_read_t > & positions_in_reads() const =0</div><div class="ttdoc">returns an array of starting positions of sketch elements in their reads</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a59186cdd6dbfd21baeb07e80bd4354d4"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">claragenomics::cudamapper::Index::read_id_to_read_length</a></div><div class="ttdeci">virtual const std::uint32_t & read_id_to_read_length(const read_id_t read_id) const =0</div><div class="ttdoc">returns read length for the read with the gived read_id</div></div> +<div class="ttc" id="aclassclaragenomics_1_1io_1_1FastaParser_html"><div class="ttname"><a href="classclaragenomics_1_1io_1_1FastaParser.html">claragenomics::io::FastaParser</a></div><div class="ttdef"><b>Definition:</b> fasta_parser.hpp:31</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_ac59d309eeb226592a96622fec2b307fd"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">claragenomics::cudamapper::Index::read_id_to_read_name</a></div><div class="ttdeci">virtual const std::string & read_id_to_read_name(const read_id_t read_id) const =0</div><div class="ttdoc">returns read name of read with the given read_id</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a66e5d024befc410221610f454eff7183"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">claragenomics::cudamapper::Index::positions_in_reads</a></div><div class="ttdeci">virtual const thrust::device_vector< position_in_read_t > & positions_in_reads() const =0</div><div class="ttdoc">returns an array of starting positions of sketch elements in their reads</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a47c3cb89daa4076243dd5977acfb7ccf"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">claragenomics::cudamapper::Index::create_index</a></div><div class="ttdeci">static std::unique_ptr< Index > create_index(const io::FastaParser &parser, const read_id_t first_read_id, const read_id_t past_the_last_read_id, const std::uint64_t kmer_size, const std::uint64_t window_size, const bool hash_representations=true)</div><div class="ttdoc">generates a mapping of (k,w)-kmer-representation to all of its occurrences for one or more sequences</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_af9247d4b637615bf5912acc57b27b919"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">claragenomics::cudamapper::Index::maximum_kmer_size</a></div><div class="ttdeci">static uint64_t maximum_kmer_size()</div><div class="ttdoc">Return the maximum kmer length allowable.</div><div class="ttdef"><b>Definition:</b> index.hpp:77</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_a5824f352fd89f69c9acc14430a3aa6cd"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">claragenomics::cudamapper::Index::directions_of_reads</a></div><div class="ttdeci">virtual const thrust::device_vector< SketchElement::DirectionOfRepresentation > & directions_of_reads() const =0</div><div class="ttdoc">returns an array of directions in which sketch elements were read</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_af44999c8852d5915d585c55a1a95c74a"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">claragenomics::cudamapper::Index::unique_representations</a></div><div class="ttdeci">virtual const thrust::device_vector< representation_t > & unique_representations() const =0</div><div class="ttdoc">returns an array where each representation is recorder only once, sorted by representation</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html_af4f69a9003fedb9ca11665d5faa43bff"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">claragenomics::cudamapper::Index::first_occurrence_of_representations</a></div><div class="ttdeci">virtual const thrust::device_vector< std::uint32_t > & first_occurrence_of_representations() const =0</div><div class="ttdoc">returns first occurrence of corresponding representation from unique_representations() in data arrays</div></div> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> Generated by  <a href="http://www.doxygen.org/index.html"> diff --git a/docs/cpp/inherit_graph_0.map b/docs/cpp/inherit_graph_0.map new file mode 100644 index 000000000..3fa168578 --- /dev/null +++ b/docs/cpp/inherit_graph_0.map @@ -0,0 +1,3 @@ +<map id="Graphical Class Hierarchy" name="Graphical Class 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b/docs/cpp/logging_8hpp.html index 0d359cd13..a5db7a556 100644 --- a/docs/cpp/logging_8hpp.html +++ b/docs/cpp/logging_8hpp.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -76,6 +76,25 @@ <div class="contents"> <div class="textblock"><code>#include <claragenomics/utils/cudaversions.hpp></code><br /> <code>#include <spdlog/spdlog.h></code><br /> +</div><div class="textblock"><div class="dynheader"> +Include dependency graph for logging.hpp:</div> +<div class="dyncontent"> +<div class="center"><img src="logging_8hpp__incl.png" border="0" usemap="#common_2logging_2include_2claragenomics_2logging_2logging_8hpp" alt=""/></div> +<map name="common_2logging_2include_2claragenomics_2logging_2logging_8hpp" id="common_2logging_2include_2claragenomics_2logging_2logging_8hpp"> +<area shape="rect" title=" " alt="" coords="65,5,227,61"/> +<area shape="rect" href="cudaversions_8hpp_source.html" title=" " alt="" coords="5,109,140,151"/> +<area shape="rect" title=" " alt="" coords="164,117,277,143"/> +</map> +</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="logging_8hpp__dep__incl.png" border="0" usemap="#common_2logging_2include_2claragenomics_2logging_2logging_8hppdep" alt=""/></div> +<map name="common_2logging_2include_2claragenomics_2logging_2logging_8hppdep" id="common_2logging_2include_2claragenomics_2logging_2logging_8hppdep"> +<area shape="rect" title=" " alt="" coords="5,5,168,61"/> +<area shape="rect" href="cudautils_8hpp.html" title=" " alt="" coords="14,109,159,165"/> +</map> +</div> </div> <p><a href="logging_8hpp_source.html">Go to the source code of this file.</a></p> <table class="memberdecls"> diff --git 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id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/matcher_8hpp_source.html b/docs/cpp/matcher_8hpp_source.html new file mode 100644 index 000000000..4e1ec6c40 --- /dev/null +++ b/docs/cpp/matcher_8hpp_source.html @@ -0,0 +1,123 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: cudamapper/include/claragenomics/cudamapper/matcher.hpp Source File</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<script type="text/javascript" src="jquery.js"></script> +<script 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+<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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><a class="el" href="dir_2312589fb962dec58b1579fafe6a300a.html">cudamapper</a></li><li class="navelem"><a class="el" href="dir_46ada5e69ffe047ce1b425fcb02bc946.html">include</a></li><li class="navelem"><a class="el" href="dir_00faf102fbd78ece25aa2d8f2597f59b.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_5d9177f36fbce0c085b11d352d248d8a.html">cudamapper</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="headertitle"> +<div class="title">matcher.hpp</div> </div> +</div><!--header--> +<div class="contents"> +<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div> +<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.</span></div> +<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">*</span></div> +<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div> +<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">* and proprietary rights in and to this software, related documentation</span></div> +<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">* and any modifications thereto. Any use, reproduction, disclosure or</span></div> +<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">* distribution of this software and related documentation without an express</span></div> +<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div> +<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">*/</span></div> +<div class="line"><a name="l00010"></a><span class="lineno"> 10</span>  </div> +<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#pragma once</span></div> +<div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  </div> +<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <memory></span></div> +<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include <thrust/device_vector.h></span></div> +<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <claragenomics/cudamapper/index.hpp></span></div> +<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  </div> +<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="keyword">namespace </span>claragenomics</div> +<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> {</div> +<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  </div> +<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="keyword">namespace </span>cudamapper</div> +<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> {</div> +<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  </div> +<div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Matcher.html"> 26</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">Matcher</a></div> +<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> {</div> +<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac2f70fb6b1876d0fa81fd8c0189191ab">~Matcher</a>() = <span class="keywordflow">default</span>;</div> +<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  </div> +<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keyword">virtual</span> thrust::device_vector<Anchor>& <a class="code" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">anchors</a>() = 0;</div> +<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  </div> +<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keyword">static</span> std::unique_ptr<Matcher> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">create_matcher</a>(<span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>& query_index,</div> +<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>& target_index);</div> +<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> };</div> +<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  </div> +<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  </div> +<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> } <span class="comment">// namespace cudamapper</span></div> +<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  </div> +<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> } <span class="comment">// namespace claragenomics</span></div> +</div><!-- fragment --></div><!-- contents --> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></div><div class="ttdoc">Index - manages mapping of (k,w)-kmer-representation and all its occurences.</div><div class="ttdef"><b>Definition:</b> index.hpp:31</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Matcher_html_ac2f70fb6b1876d0fa81fd8c0189191ab"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac2f70fb6b1876d0fa81fd8c0189191ab">claragenomics::cudamapper::Matcher::~Matcher</a></div><div class="ttdeci">virtual ~Matcher()=default</div><div class="ttdoc">Virtual destructor.</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Matcher_html_ae65a1507ddf1bf2aa046fc0eacfea752"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">claragenomics::cudamapper::Matcher::create_matcher</a></div><div class="ttdeci">static std::unique_ptr< Matcher > create_matcher(const Index &query_index, const Index &target_index)</div><div class="ttdoc">Creates a Matcher object.</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Matcher_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Matcher.html">claragenomics::cudamapper::Matcher</a></div><div class="ttdoc">Matcher - base matcher.</div><div class="ttdef"><b>Definition:</b> matcher.hpp:26</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Matcher_html_ac3de5ba06b0c7ef0329caf71ae98f2d2"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">claragenomics::cudamapper::Matcher::anchors</a></div><div class="ttdeci">virtual thrust::device_vector< Anchor > & anchors()=0</div><div class="ttdoc">returns anchors</div></div> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/mathutils_8hpp_source.html b/docs/cpp/mathutils_8hpp_source.html index 624a9fb59..b9b43ab6f 100644 --- a/docs/cpp/mathutils_8hpp_source.html +++ b/docs/cpp/mathutils_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/menudata.js b/docs/cpp/menudata.js index 31b184868..76c3d6218 100644 --- a/docs/cpp/menudata.js +++ b/docs/cpp/menudata.js @@ -26,12 +26,14 @@ var menudata={children:[ {text:"Classes",url:"annotated.html",children:[ {text:"Class List",url:"annotated.html"}, {text:"Class Index",url:"classes.html"}, +{text:"Class Hierarchy",url:"inherits.html"}, {text:"Class Members",url:"functions.html",children:[ {text:"All",url:"functions.html",children:[ {text:"a",url:"functions.html#index_a"}, {text:"b",url:"functions.html#index_b"}, {text:"c",url:"functions.html#index_c"}, {text:"d",url:"functions.html#index_d"}, +{text:"e",url:"functions.html#index_e"}, {text:"f",url:"functions.html#index_f"}, {text:"g",url:"functions.html#index_g"}, {text:"l",url:"functions.html#index_l"}, @@ -43,6 +45,7 @@ var menudata={children:[ {text:"r",url:"functions.html#index_r"}, {text:"s",url:"functions.html#index_s"}, {text:"t",url:"functions.html#index_t"}, +{text:"u",url:"functions.html#index_u"}, {text:"w",url:"functions.html#index_w"}, {text:"~",url:"functions.html#index__7E"}]}, {text:"Functions",url:"functions_func.html",children:[ @@ -50,15 +53,19 @@ var menudata={children:[ {text:"b",url:"functions_func.html#index_b"}, {text:"c",url:"functions_func.html#index_c"}, {text:"d",url:"functions_func.html#index_d"}, +{text:"e",url:"functions_func.html#index_e"}, {text:"f",url:"functions_func.html#index_f"}, {text:"g",url:"functions_func.html#index_g"}, {text:"m",url:"functions_func.html#index_m"}, {text:"n",url:"functions_func.html#index_n"}, +{text:"o",url:"functions_func.html#index_o"}, {text:"p",url:"functions_func.html#index_p"}, {text:"r",url:"functions_func.html#index_r"}, {text:"s",url:"functions_func.html#index_s"}, +{text:"u",url:"functions_func.html#index_u"}, {text:"~",url:"functions_func.html#index__7E"}]}, {text:"Variables",url:"functions_vars.html"}, +{text:"Typedefs",url:"functions_type.html"}, {text:"Enumerations",url:"functions_enum.html"}]}]}, {text:"Files",url:"files.html",children:[ {text:"File List",url:"files.html"}, diff --git a/docs/cpp/modules.html b/docs/cpp/modules.html index 48c59a7ce..f1f253e24 100644 --- a/docs/cpp/modules.html +++ b/docs/cpp/modules.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/overlapper_8hpp_source.html b/docs/cpp/overlapper_8hpp_source.html index 16fa4f1e8..5aabd26aa 100644 --- a/docs/cpp/overlapper_8hpp_source.html +++ b/docs/cpp/overlapper_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -82,36 +82,40 @@ <div class="line"><a name="l00010"></a><span class="lineno"> 10</span>  </div> <div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#pragma once</span></div> <div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  </div> -<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include "index.hpp"</span></div> -<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "types.hpp"</span></div> -<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  </div> -<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="keyword">namespace </span>claragenomics</div> -<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> {</div> -<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  </div> -<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">namespace </span>cudamapper</div> -<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> {</div> -<div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  </div> -<div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html"> 26</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a></div> -<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> {</div> -<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="keyword">public</span>:</div> -<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">~Overlapper</a>() = <span class="keywordflow">default</span>;</div> -<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  </div> -<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">get_overlaps</a>(std::vector<Overlap>& overlaps, std::vector<Anchor>& anchors, <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>& index) = 0;</div> -<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  </div> -<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">print_paf</a>(<span class="keyword">const</span> std::vector<Overlap>& overlaps);</div> -<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  </div> -<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">filter_overlaps</a>(std::vector<Overlap>& filtered_overlaps, <span class="keyword">const</span> std::vector<Overlap>& overlaps, <span class="keywordtype">size_t</span> min_residues = 5,</div> -<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordtype">size_t</span> min_overlap_len = 0);</div> -<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> };</div> -<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="comment">//}</span></div> -<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> } <span class="comment">// namespace cudamapper</span></div> -<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  </div> -<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> } <span class="comment">// namespace claragenomics</span></div> +<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <thrust/device_vector.h></span></div> +<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "index.hpp"</span></div> +<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include "types.hpp"</span></div> +<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  </div> +<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="keyword">namespace </span>claragenomics</div> +<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> {</div> +<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  </div> +<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="keyword">namespace </span>cudamapper</div> +<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> {</div> +<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  </div> +<div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html"> 27</a></span> <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a></div> +<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> {</div> +<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">public</span>:</div> +<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keyword">virtual</span> <a class="code" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">~Overlapper</a>() = <span class="keywordflow">default</span>;</div> +<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  </div> +<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">get_overlaps</a>(std::vector<Overlap>& overlaps,</div> +<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  thrust::device_vector<Anchor>& anchors,</div> +<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>& index_query,</div> +<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>& index_target) = 0;</div> +<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  </div> +<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">print_paf</a>(<span class="keyword">const</span> std::vector<Overlap>& overlaps);</div> +<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  </div> +<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">filter_overlaps</a>(std::vector<Overlap>& filtered_overlaps, <span class="keyword">const</span> std::vector<Overlap>& overlaps, <span class="keywordtype">size_t</span> min_residues = 5,</div> +<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordtype">size_t</span> min_overlap_len = 0);</div> +<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> };</div> +<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="comment">//}</span></div> +<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> } <span class="comment">// namespace cudamapper</span></div> +<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  </div> +<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> } <span class="comment">// namespace claragenomics</span></div> </div><!-- fragment --></div><!-- contents --> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></div><div class="ttdoc">Index - manages mapping of (k,w)-kmer-representation and all its occurences.</div><div class="ttdef"><b>Definition:</b> index.hpp:29</div></div> -<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Overlapper_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></div><div class="ttdef"><b>Definition:</b> overlapper.hpp:26</div></div> +<div class="ttc" id="agroup__cudamapper_html_gab0e3be4a9442dfb2b7952fb473e591a3"><div class="ttname"><a href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">claragenomics::cudamapper::Overlapper::get_overlaps</a></div><div class="ttdeci">virtual void get_overlaps(std::vector< Overlap > &overlaps, thrust::device_vector< Anchor > &anchors, const Index &index_query, const Index &index_target)=0</div><div class="ttdoc">returns overlaps for a set of reads</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></div><div class="ttdoc">Index - manages mapping of (k,w)-kmer-representation and all its occurences.</div><div class="ttdef"><b>Definition:</b> index.hpp:31</div></div> +<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Overlapper_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></div><div class="ttdef"><b>Definition:</b> overlapper.hpp:27</div></div> <div class="ttc" id="agroup__cudamapper_html_ga54fedd97206ad1691f7b9d9966d01371"><div class="ttname"><a href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">claragenomics::cudamapper::Overlapper::print_paf</a></div><div class="ttdeci">static void print_paf(const std::vector< Overlap > &overlaps)</div><div class="ttdoc">prints overlaps to stdout in PAF format</div></div> -<div class="ttc" id="agroup__cudamapper_html_ga5498f3d8b5eff6481c67fdf0a049c300"><div class="ttname"><a href="group__cudamapper.html#ga5498f3d8b5eff6481c67fdf0a049c300">claragenomics::cudamapper::Overlapper::get_overlaps</a></div><div class="ttdeci">virtual void get_overlaps(std::vector< Overlap > &overlaps, std::vector< Anchor > &anchors, const Index &index)=0</div><div class="ttdoc">returns overlaps for a set of reads</div></div> <div class="ttc" id="agroup__cudamapper_html_ga3e5732f34489315ec8d1ef8b82ccea5c"><div class="ttname"><a href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">claragenomics::cudamapper::Overlapper::filter_overlaps</a></div><div class="ttdeci">static void filter_overlaps(std::vector< Overlap > &filtered_overlaps, const std::vector< Overlap > &overlaps, size_t min_residues=5, size_t min_overlap_len=0)</div><div class="ttdoc">removes overlaps which are unlikely to be true overlaps</div></div> <div class="ttc" 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b/docs/cpp/sequence_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/signed__integer__utils_8hpp_source.html b/docs/cpp/signed__integer__utils_8hpp_source.html index cfe663d8b..73af9cf9d 100644 --- a/docs/cpp/signed__integer__utils_8hpp_source.html +++ b/docs/cpp/signed__integer__utils_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/sketch__element_8hpp_source.html b/docs/cpp/sketch__element_8hpp_source.html index 91f4d1908..f84101239 100644 --- a/docs/cpp/sketch__element_8hpp_source.html +++ b/docs/cpp/sketch__element_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -84,7 +84,7 @@ <div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  </div> <div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <cstdint></span></div> <div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include <memory></span></div> -<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include "claragenomics/cudamapper/types.hpp"</span></div> +<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <claragenomics/cudamapper/types.hpp></span></div> <div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  </div> <div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="keyword">namespace </span>claragenomics</div> <div class="line"><a name="l00018"></a><span class="lineno"> 18</span> {</div> diff --git a/docs/cpp/stringutils_8hpp_source.html b/docs/cpp/stringutils_8hpp_source.html index 9f022eb4d..886df7407 100644 --- a/docs/cpp/stringutils_8hpp_source.html +++ b/docs/cpp/stringutils_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1PairHash-members.html b/docs/cpp/structclaragenomics_1_1PairHash-members.html new file mode 100644 index 000000000..f46f26af9 --- /dev/null +++ b/docs/cpp/structclaragenomics_1_1PairHash-members.html @@ -0,0 +1,85 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: Member 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="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">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="structclaragenomics_1_1PairHash.html">PairHash</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="headertitle"> +<div class="title">claragenomics::PairHash Member List</div> </div> +</div><!--header--> +<div class="contents"> + +<p>This is the complete list of members for <a class="el" href="structclaragenomics_1_1PairHash.html">claragenomics::PairHash</a>, including all inherited members.</p> +<table class="directory"> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61">operator()</a>(const std::pair< T1, T2 > &pair) const</td><td class="entry"><a class="el" href="structclaragenomics_1_1PairHash.html">claragenomics::PairHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> +</table></div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/structclaragenomics_1_1PairHash.html b/docs/cpp/structclaragenomics_1_1PairHash.html new file mode 100644 index 000000000..f79f05cea --- /dev/null +++ b/docs/cpp/structclaragenomics_1_1PairHash.html @@ -0,0 +1,100 @@ +<!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 1.8.16"/> +<meta name="viewport" content="width=device-width, initial-scale=1"/> +<title>ClaraGenomicsAnalysis: claragenomics::PairHash Struct 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 style="height: 56px;"> + <td id="projectalign" style="padding-left: 0.5em;"> + <div id="projectname">ClaraGenomicsAnalysis +  <span id="projectnumber">0.4.0</span> + </div> + </td> + </tr> + </tbody> +</table> +</div> +<!-- end header part --> +<!-- Generated by Doxygen 1.8.16 --> +<script type="text/javascript"> +/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&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&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> +<!-- 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 id="nav-path" class="navpath"> + <ul> +<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="structclaragenomics_1_1PairHash.html">PairHash</a></li> </ul> +</div> +</div><!-- top --> +<div class="header"> + <div class="summary"> +<a href="#pub-methods">Public Member Functions</a> | +<a href="structclaragenomics_1_1PairHash-members.html">List of all members</a> </div> + <div class="headertitle"> +<div class="title">claragenomics::PairHash Struct Reference</div> </div> +</div><!--header--> +<div class="contents"> + +<p><code>#include <<a class="el" href="graph_8hpp_source.html">graph.hpp</a>></code></p> +<table class="memberdecls"> +<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> +Public Member Functions</h2></td></tr> +<tr class="memitem:a46da7ce33ff4cf8a586a0c54b6be1e61"><td class="memTemplParams" colspan="2"><a id="a46da7ce33ff4cf8a586a0c54b6be1e61"></a> +template<class T1 , class T2 > </td></tr> +<tr class="memitem:a46da7ce33ff4cf8a586a0c54b6be1e61"><td class="memTemplItemLeft" align="right" valign="top">size_t </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61">operator()</a> (const std::pair< T1, T2 > &pair) const</td></tr> +<tr class="memdesc:a46da7ce33ff4cf8a586a0c54b6be1e61"><td class="mdescLeft"> </td><td class="mdescRight">Operator overload to define hash function. <br /></td></tr> +<tr class="separator:a46da7ce33ff4cf8a586a0c54b6be1e61"><td class="memSeparator" colspan="2"> </td></tr> +</table> +<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> +<div class="textblock"><p>Hash function for a pair </p> +</div><hr/>The documentation for this struct was generated from the following file:<ul> +<li>common/utils/include/claragenomics/utils/<a class="el" href="graph_8hpp_source.html">graph.hpp</a></li> +</ul> +</div><!-- contents --> +<!-- start footer part --> +<hr class="footer"/><address class="footer"><small> +Generated by  <a href="http://www.doxygen.org/index.html"> +<img class="footer" src="doxygen.png" alt="doxygen"/> +</a> 1.8.16 +</small></address> +</body> +</html> diff --git a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor-members.html b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor-members.html index 7ed4b62d6..8b86bb709 100644 --- a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor-members.html +++ b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor.html b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor.html index 908ab2fe8..7191f1de4 100644 --- a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor.html +++ b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Anchor.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock-members.html b/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock-members.html index 175b259a5..8dcf89da5 100644 --- a/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock-members.html +++ b/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock.html b/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock.html index 4027b4739..b22a5913d 100644 --- a/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock.html +++ b/docs/cpp/structclaragenomics_1_1cudamapper_1_1ArrayBlock.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap-members.html b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap-members.html index 69743aae3..09502440e 100644 --- a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap-members.html +++ b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -73,19 +73,20 @@ <p>This is the complete list of members for <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a>, including all inherited members.</p> <table class="directory"> - <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">num_residues_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">overlap_complete</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224">query_end_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">query_length_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">query_read_id_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ac2baa8c82cbe1ff7475d7a8700a691df">query_read_name_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">query_start_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">relative_strand</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">target_end_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11">target_length_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">target_read_id_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a8e75cd08ecddc434463ac2e9b748dd6c">target_read_name_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> - <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">target_start_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">cigar_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">num_residues_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">overlap_complete</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224">query_end_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">query_length_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">query_read_id_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">query_read_name_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">query_start_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">relative_strand</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">target_end_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11">target_length_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">target_read_id_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr class="even"><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">target_read_name_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> + <tr><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">target_start_position_in_read_</a></td><td class="entry"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></td><td class="entry"></td></tr> </table></div><!-- contents --> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> diff --git a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap.html b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap.html index 07b258df1..8791fc816 100644 --- a/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap.html +++ b/docs/cpp/structclaragenomics_1_1cudamapper_1_1Overlap.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -102,14 +102,14 @@ position_in_read_t </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">target_end_position_in_read_</a></td></tr> <tr class="memdesc:ad4721b3555a83acb588c54dc369f7797"><td class="mdescLeft"> </td><td class="mdescRight">end position in the target <br /></td></tr> <tr class="separator:ad4721b3555a83acb588c54dc369f7797"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:ac2baa8c82cbe1ff7475d7a8700a691df"><td class="memItemLeft" align="right" valign="top"><a id="ac2baa8c82cbe1ff7475d7a8700a691df"></a> -std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ac2baa8c82cbe1ff7475d7a8700a691df">query_read_name_</a></td></tr> -<tr class="memdesc:ac2baa8c82cbe1ff7475d7a8700a691df"><td class="mdescLeft"> </td><td class="mdescRight">query read name (e.g from FASTA) <br /></td></tr> -<tr class="separator:ac2baa8c82cbe1ff7475d7a8700a691df"><td class="memSeparator" colspan="2"> </td></tr> -<tr class="memitem:a8e75cd08ecddc434463ac2e9b748dd6c"><td class="memItemLeft" align="right" valign="top"><a id="a8e75cd08ecddc434463ac2e9b748dd6c"></a> -std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a8e75cd08ecddc434463ac2e9b748dd6c">target_read_name_</a></td></tr> -<tr class="memdesc:a8e75cd08ecddc434463ac2e9b748dd6c"><td class="mdescLeft"> </td><td class="mdescRight">target read name (e.g from FASTA) <br /></td></tr> -<tr class="separator:a8e75cd08ecddc434463ac2e9b748dd6c"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:a7d37018aff3304bbe75b2d612b55c057"><td class="memItemLeft" align="right" valign="top"><a id="a7d37018aff3304bbe75b2d612b55c057"></a> +char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">query_read_name_</a> = 0</td></tr> +<tr class="memdesc:a7d37018aff3304bbe75b2d612b55c057"><td class="mdescLeft"> </td><td class="mdescRight">query read name (e.g from FASTA) <br /></td></tr> +<tr class="separator:a7d37018aff3304bbe75b2d612b55c057"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:afcb7e39abf2761899ff1abb3c95b82ca"><td class="memItemLeft" align="right" valign="top"><a id="afcb7e39abf2761899ff1abb3c95b82ca"></a> +char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">target_read_name_</a> = 0</td></tr> +<tr class="memdesc:afcb7e39abf2761899ff1abb3c95b82ca"><td class="mdescLeft"> </td><td class="mdescRight">target read name (e.g from FASTA) <br /></td></tr> +<tr class="separator:afcb7e39abf2761899ff1abb3c95b82ca"><td class="memSeparator" colspan="2"> </td></tr> <tr class="memitem:a1c0b9bac9b2e15f70c60fcdae9728fd7"><td class="memItemLeft" align="right" valign="top"><a id="a1c0b9bac9b2e15f70c60fcdae9728fd7"></a> RelativeStrand </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">relative_strand</a></td></tr> <tr class="memdesc:a1c0b9bac9b2e15f70c60fcdae9728fd7"><td class="mdescLeft"> </td><td class="mdescRight">Relative strand: Forward ("+") or Reverse("-") <br /></td></tr> @@ -130,6 +130,10 @@ bool </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">overlap_complete</a> = false</td></tr> <tr class="memdesc:a31d4f58b24a2e3fc57b5bca803827360"><td class="mdescLeft"> </td><td class="mdescRight">Whether the overlap is considered valid by the generating overlapper. <br /></td></tr> <tr class="separator:a31d4f58b24a2e3fc57b5bca803827360"><td class="memSeparator" colspan="2"> </td></tr> +<tr class="memitem:ad9b3ed3f91b4979afb6198cea2d77e54"><td class="memItemLeft" align="right" valign="top"><a id="ad9b3ed3f91b4979afb6198cea2d77e54"></a> +char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">cigar_</a> = 0</td></tr> +<tr class="memdesc:ad9b3ed3f91b4979afb6198cea2d77e54"><td class="mdescLeft"> </td><td class="mdescRight">CIGAR string for alignment of mapped section. <br /></td></tr> +<tr class="separator:ad9b3ed3f91b4979afb6198cea2d77e54"><td class="memSeparator" colspan="2"> </td></tr> </table> <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> <div class="textblock"><p><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> - represents one overlap between two substrings</p> diff --git a/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry-members.html b/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry-members.html index 9a98fd8f8..77548f782 100644 --- a/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry-members.html +++ b/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry.html b/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry.html index 36b997c50..6ce862c1b 100644 --- a/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry.html +++ b/docs/cpp/structclaragenomics_1_1cudapoa_1_1Entry.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence-members.html b/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence-members.html index 84f99580f..ba9233c73 100644 --- a/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence-members.html +++ b/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence-members.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence.html b/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence.html index 667a914d9..b414099d2 100644 --- a/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence.html +++ b/docs/cpp/structclaragenomics_1_1io_1_1FastaSequence.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> diff --git a/docs/cpp/types_8hpp_source.html b/docs/cpp/types_8hpp_source.html index b9e48e48d..7f865cf11 100644 --- a/docs/cpp/types_8hpp_source.html +++ b/docs/cpp/types_8hpp_source.html @@ -22,7 +22,7 @@ <tr style="height: 56px;"> <td id="projectalign" style="padding-left: 0.5em;"> <div id="projectname">ClaraGenomicsAnalysis -  <span id="projectnumber">0.3.0</span> +  <span id="projectnumber">0.4.0</span> </div> </td> </tr> @@ -132,20 +132,22 @@ <div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c"> 86</a></span>  position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">target_start_position_in_read_</a>;</div> <div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224"> 88</a></span>  position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224">query_end_position_in_read_</a>;</div> <div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797"> 90</a></span>  position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">target_end_position_in_read_</a>;</div> -<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ac2baa8c82cbe1ff7475d7a8700a691df"> 92</a></span>  std::string <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ac2baa8c82cbe1ff7475d7a8700a691df">query_read_name_</a>;</div> -<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a8e75cd08ecddc434463ac2e9b748dd6c"> 94</a></span>  std::string <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a8e75cd08ecddc434463ac2e9b748dd6c">target_read_name_</a>;</div> +<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057"> 92</a></span>  <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">query_read_name_</a> = 0;</div> +<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca"> 94</a></span>  <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">target_read_name_</a> = 0;</div> <div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7"> 96</a></span>  RelativeStrand <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">relative_strand</a>;</div> <div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d"> 98</a></span>  std::uint32_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">num_residues_</a> = 0;</div> <div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b"> 100</a></span>  std::uint32_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">query_length_</a> = 0;</div> <div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11"> 102</a></span>  std::uint32_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11">target_length_</a> = 0;</div> <div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360"> 104</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">overlap_complete</a> = <span class="keyword">false</span>;</div> -<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> } <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a>;</div> -<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> } <span class="comment">// namespace cudamapper</span></div> -<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  </div> -<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> } <span class="comment">// namespace claragenomics</span></div> +<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54"> 106</a></span>  <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">cigar_</a> = 0;</div> +<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> } <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a>;</div> +<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  </div> +<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> } <span class="comment">// namespace cudamapper</span></div> +<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  </div> +<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> } <span class="comment">// namespace claragenomics</span></div> </div><!-- fragment --></div><!-- contents --> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a7677cc8d0aa20fc788b57f85905e051b"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">claragenomics::cudamapper::Overlap::query_length_</a></div><div class="ttdeci">std::uint32_t query_length_</div><div class="ttdoc">Length of query sequence.</div><div class="ttdef"><b>Definition:</b> types.hpp:100</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a8e75cd08ecddc434463ac2e9b748dd6c"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a8e75cd08ecddc434463ac2e9b748dd6c">claragenomics::cudamapper::Overlap::target_read_name_</a></div><div class="ttdeci">std::string target_read_name_</div><div class="ttdoc">target read name (e.g from FASTA)</div><div class="ttdef"><b>Definition:</b> types.hpp:94</div></div> +<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_ad9b3ed3f91b4979afb6198cea2d77e54"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">claragenomics::cudamapper::Overlap::cigar_</a></div><div class="ttdeci">char * cigar_</div><div class="ttdoc">CIGAR string for alignment of mapped section.</div><div class="ttdef"><b>Definition:</b> types.hpp:106</div></div> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_ab3594748a49ae4472ca28a03b05ddb7d"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">claragenomics::cudamapper::Overlap::num_residues_</a></div><div class="ttdeci">std::uint32_t num_residues_</div><div class="ttdoc">Number of residues (e.g anchors) between the two reads.</div><div class="ttdef"><b>Definition:</b> types.hpp:98</div></div> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a3d98a09e4ccd8bda66cb09a72adaf1fc"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">claragenomics::cudamapper::Overlap::query_read_id_</a></div><div class="ttdeci">read_id_t query_read_id_</div><div class="ttdoc">internal read ID for query</div><div class="ttdef"><b>Definition:</b> types.hpp:80</div></div> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_a3c79e476eae0672a9a941e0980b6dcc3"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#a3c79e476eae0672a9a941e0980b6dcc3">claragenomics::cudamapper::Anchor::query_read_id_</a></div><div class="ttdeci">read_id_t query_read_id_</div><div class="ttdoc">read ID of query</div><div class="ttdef"><b>Definition:</b> types.hpp:64</div></div> @@ -164,8 +166,9 @@ <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_ad58b2a619bd71c37c337ed44e45b4d23"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ad58b2a619bd71c37c337ed44e45b4d23">claragenomics::cudamapper::Anchor::target_position_in_read_</a></div><div class="ttdeci">position_in_read_t target_position_in_read_</div><div class="ttdoc">position of second sketch element in target_read_id_</div><div class="ttdef"><b>Definition:</b> types.hpp:70</div></div> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1ArrayBlock_html_a33ff27afee2ddb07e6fbdda0ff1de229"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a33ff27afee2ddb07e6fbdda0ff1de229">claragenomics::cudamapper::ArrayBlock::block_size_</a></div><div class="ttdeci">std::uint32_t block_size_</div><div class="ttdoc">number of elements of the block</div><div class="ttdef"><b>Definition:</b> types.hpp:30</div></div> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a1c0b9bac9b2e15f70c60fcdae9728fd7"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">claragenomics::cudamapper::Overlap::relative_strand</a></div><div class="ttdeci">RelativeStrand relative_strand</div><div class="ttdoc">Relative strand: Forward ("+") or Reverse("-")</div><div class="ttdef"><b>Definition:</b> types.hpp:96</div></div> -<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_ac2baa8c82cbe1ff7475d7a8700a691df"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ac2baa8c82cbe1ff7475d7a8700a691df">claragenomics::cudamapper::Overlap::query_read_name_</a></div><div class="ttdeci">std::string query_read_name_</div><div class="ttdoc">query read name (e.g from FASTA)</div><div class="ttdef"><b>Definition:</b> types.hpp:92</div></div> +<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a7d37018aff3304bbe75b2d612b55c057"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">claragenomics::cudamapper::Overlap::query_read_name_</a></div><div class="ttdeci">char * query_read_name_</div><div class="ttdoc">query read name (e.g from FASTA)</div><div class="ttdef"><b>Definition:</b> types.hpp:92</div></div> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></div><div class="ttdef"><b>Definition:</b> types.hpp:77</div></div> +<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_afcb7e39abf2761899ff1abb3c95b82ca"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">claragenomics::cudamapper::Overlap::target_read_name_</a></div><div class="ttdeci">char * target_read_name_</div><div class="ttdoc">target read name (e.g from FASTA)</div><div class="ttdef"><b>Definition:</b> types.hpp:94</div></div> <div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_ae9ae1af9e2feaea69ebde6b165966cec"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ae9ae1af9e2feaea69ebde6b165966cec">claragenomics::cudamapper::Anchor::target_read_id_</a></div><div class="ttdeci">read_id_t target_read_id_</div><div class="ttdoc">read ID of target</div><div class="ttdef"><b>Definition:</b> types.hpp:66</div></div> <!-- start footer part --> <hr class="footer"/><address class="footer"><small>