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<a href="xsample04_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">Copyright(c) 2018 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)</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">Licensed under the Apache License, Version 2.0 (the "License");</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">you may not use this file except in compliance with the License.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">You may obtain a copy of the License at</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"></span> </div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> http://www.apache.org/licenses/LICENSE-2.0</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> <span class="comment">Unless required by applicable law or agreed to in writing, software</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">distributed under the License is distributed on an "AS IS" BASIS,</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">See the License for the specific language governing permissions and</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">limitations under the License.</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"></span> </div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">For more information please visit: http://bitmagic.io</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment"></span> </div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">/** \example xsample04.cpp</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment"></span> </div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment"></span> </div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">/*! \file xsample04.cpp</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment"> \brief Example: DNA substring search</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment"></span> </div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">*/</span></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="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#include <sstream></span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#include <chrono></span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor">#include <regex></span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor">#include <time.h></span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#include <stdio.h></span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#include <stdexcept></span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#include <memory></span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <chrono></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <utility></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <algorithm></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <unordered_map></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include "<a class="code" href="bm_8h.html">bm.h</a>"</span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include "<a class="code" href="bmalgo_8h.html">bmalgo.h</a>"</span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include "<a class="code" href="bmserial_8h.html">bmserial.h</a>"</span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include "<a class="code" href="bmaggregator_8h.html">bmaggregator.h</a>"</span></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="preprocessor">#include "bmdbg.h"</span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#include "<a class="code" href="bmtimer_8h.html">bmtimer.h</a>"</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>  </div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keyword">using namespace </span>std;</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> <span class="keyword">static</span></div>
<div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26"> 56</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>()</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> {</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  std::cerr</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  << <span class="stringliteral">"BitMagic DNA Search Sample (c) 2018"</span> << std::endl</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  << <span class="stringliteral">"-fa file-name -- input FASTA file"</span> << std::endl</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  << <span class="stringliteral">"-s hi|lo -- run substring search benchmark"</span> << std::endl</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  << <span class="stringliteral">"-diag -- run diagnostics"</span> << std::endl</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  << <span class="stringliteral">"-timing -- collect timings"</span> << std::endl</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> }</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="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="l00070"></a><span class="lineno"> 70</span> <span class="comment">// Arguments</span></div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="comment">//</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c"> 72</a></span> std::string <a class="code" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a>;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#aa592d3fbead57ca8423ac5caaccada07"> 73</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample04_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#aece8e90d91aaea144d41103f7d2825ee"> 74</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample04_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a4dd1e4b402061691109d356faa4513b5"> 75</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample04_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a"> 76</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a">is_search</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f"> 77</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a> = <span class="keyword">true</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="keyword">static</span></div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a1c6cda197a32141227af69a440929ac6"> 80</a></span> <span class="keywordtype">int</span> <a class="code" href="xsample04_8cpp.html#a1c6cda197a32141227af69a440929ac6">parse_args</a>(<span class="keywordtype">int</span> argc, <span class="keywordtype">char</span> *argv[])</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> {</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 1; i < argc; ++i)</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>  std::string arg = argv[i];</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordflow">if</span> ((arg == <span class="stringliteral">"-h"</span>) || (arg == <span class="stringliteral">"--help"</span>))</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>  <a class="code" href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>();</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  }</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>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-fa"</span> || arg == <span class="stringliteral">"--fa"</span>)</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  {</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  {</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <a class="code" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a> = argv[++i];</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="keywordflow">else</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  {</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  std::cerr << <span class="stringliteral">"Error: -fa requires file name"</span> << std::endl;</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  }</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  }</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">if</span> (arg == <span class="stringliteral">"-diag"</span> || arg == <span class="stringliteral">"--diag"</span> || arg == <span class="stringliteral">"-d"</span> || arg == <span class="stringliteral">"--d"</span>)</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <a class="code" href="xsample04_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-timing"</span> || arg == <span class="stringliteral">"--timing"</span> || arg == <span class="stringliteral">"-t"</span> || arg == <span class="stringliteral">"--t"</span>)</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <a class="code" href="xsample04_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-bench"</span> || arg == <span class="stringliteral">"--bench"</span> || arg == <span class="stringliteral">"-b"</span> || arg == <span class="stringliteral">"--b"</span>)</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <a class="code" href="xsample04_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-search"</span> || arg == <span class="stringliteral">"--search"</span> || arg == <span class="stringliteral">"-s"</span> || arg == <span class="stringliteral">"--s"</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="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a">is_search</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="keywordflow">if</span> (i + 1 < argc)</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>  std::string a = argv[i+1];</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keywordflow">if</span> (a != <span class="stringliteral">"-"</span>)</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  {</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordflow">if</span> (a == <span class="stringliteral">"l"</span> || a == <span class="stringliteral">"lo"</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>  <a class="code" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  ++i;</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">else</span></div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordflow">if</span> (a == <span class="stringliteral">"h"</span> || a == <span class="stringliteral">"hi"</span>)</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  {</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <a class="code" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  ++i;</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  }</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>  }</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  } <span class="comment">// for i</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordflow">return</span> 0;</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>  </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> <span class="comment">// Global types</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="comment">//</span></div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a24dcda0f03372e9a308e09d98c30b2ed"> 141</a></span> <span class="keyword">typedef</span> std::map<std::string, unsigned> <a class="code" href="xsample04_8cpp.html#a24dcda0f03372e9a308e09d98c30b2ed">freq_map</a>;</div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#acb61f43c97f1f1542bc436dfa56c5f8e"> 142</a></span> <span class="keyword">typedef</span> std::vector<std::pair<unsigned, std::string> > <a class="code" href="xsample04_8cpp.html#acb61f43c97f1f1542bc436dfa56c5f8e">dict_vect</a>;</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  </div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a7967cbddc252672d351b3ddf9d688888"> 144</a></span> <span class="keyword">typedef</span> <a class="code" href="classbm_1_1aggregator.html">bm::aggregator<bm::bvector<></a> > <a class="code" href="xsample04_8cpp.html#a7967cbddc252672d351b3ddf9d688888">aggregator_type</a>;</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  </div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="comment">// ----------------------------------------------------------------------------</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"><a class="line" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc"> 148</a></span> <a class="code" href="classbm_1_1chrono__taker.html#add1676592117ed0eaa2fa6279a71b46a">bm::chrono_taker::duration_map_type</a> <a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</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> <span class="comment">// FASTA format parser</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="keyword">static</span></div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#add74621cca7ebe5386556ba01bc35cd2"> 152</a></span> <span class="keywordtype">int</span> <a class="code" href="xsample04_8cpp.html#add74621cca7ebe5386556ba01bc35cd2">load_FASTA</a>(<span class="keyword">const</span> std::string& fname, std::vector<char>& seq_vect)</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> {</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"1. Parse FASTA"</span>, 1, &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</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>  seq_vect.resize(0);</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  std::ifstream fin(fname.c_str(), std::ios::in);</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">if</span> (!fin.good())</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordflow">return</span> -1;</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  </div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  std::string line;</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; std::getline(fin, line); ++i)</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  {</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">if</span> (line.empty() ||</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  line.front() == <span class="charliteral">'>'</span>)</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordflow">continue</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>  <span class="keywordflow">for</span> (std::string::iterator it = line.begin(); it != line.end(); ++it)</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  seq_vect.push_back(*it);</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  } <span class="comment">// for</span></div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> }</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  </div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  </div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> <span class="comment"></span> </div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> <span class="comment">/**</span></div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span> <span class="comment"> Utility for keeping all DNA finger print vectors and search</span></div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> <span class="comment"> using various techniques</span></div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html"> 180</a></span> <span class="keyword">class </span><a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a></div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> {</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#a1815ea4e87c7c6b84cd7e555a2d8bc48a87a7e916afec9eb45d2d8d2c8e2e5d13"> 183</a></span>  <span class="keyword">enum</span> { eA = 0, eC, eG, <a class="code" href="classDNA__FingerprintScanner.html#a1815ea4e87c7c6b84cd7e555a2d8bc48a87a7e916afec9eb45d2d8d2c8e2e5d13">eT</a>, eN, eEnd };</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  </div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#aac37d48924de403b5baf0e079e40f22c"> 185</a></span>  <a class="code" href="classDNA__FingerprintScanner.html#aac37d48924de403b5baf0e079e40f22c">DNA_FingerprintScanner</a>() {}</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> <span class="comment"></span> </div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> <span class="comment"> /// Build fingerprint bit-vectors from the original sequence</span></div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> <span class="comment"> ///</span></div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#a5ac470fd81df0a04ea1b298a55dba5bb"> 189</a></span> <span class="comment"></span> <span class="keywordtype">void</span> <a class="code" href="classDNA__FingerprintScanner.html#a5ac470fd81df0a04ea1b298a55dba5bb">Build</a>(<span class="keyword">const</span> vector<char>& sequence)</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  {</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="comment">// use bulk insert iterator (faster way to construct a bit-index)</span></div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <a class="code" href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector<>::bulk_insert_iterator</a> iA(m_FPrintBV[eA], <a class="code" href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a>);</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <a class="code" href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector<>::bulk_insert_iterator</a> iC(m_FPrintBV[eC], <a class="code" href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a>);</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <a class="code" href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector<>::bulk_insert_iterator</a> iG(m_FPrintBV[eG], <a class="code" href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a>);</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <a class="code" href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector<>::bulk_insert_iterator</a> iT(m_FPrintBV[eT], <a class="code" href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a>);</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <a class="code" href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector<>::bulk_insert_iterator</a> iN(m_FPrintBV[eN], <a class="code" href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a>);</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  </div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < sequence.size(); ++i)</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  {</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordtype">unsigned</span> pos = unsigned(i);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordflow">switch</span> (sequence[i])</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  {</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordflow">case</span> <span class="charliteral">'A'</span>:</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  iA = pos;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordflow">case</span> <span class="charliteral">'C'</span>:</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  iC = pos;</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keywordflow">case</span> <span class="charliteral">'G'</span>:</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  iG = pos;</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  iT = pos;</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="keywordflow">case</span> <span class="charliteral">'N'</span>:</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  iN = pos;</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordflow">default</span>:</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keywordflow">break</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>  }</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  }</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span> <span class="comment"></span> </div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span> <span class="comment"> /// Return fingerprint bit-vector</span></div>
<div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#a8623c4721c296e6cc065ae6a2ceff980"> 226</a></span> <span class="comment"></span> <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& <a class="code" href="classDNA__FingerprintScanner.html#a8623c4721c296e6cc065ae6a2ceff980">GetVector</a>(<span class="keywordtype">char</span> letter)<span class="keyword"> const</span></div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keywordflow">switch</span> (letter)</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="keywordflow">case</span> <span class="charliteral">'A'</span>:</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="keywordflow">return</span> m_FPrintBV[eA];</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">case</span> <span class="charliteral">'C'</span>:</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="keywordflow">return</span> m_FPrintBV[eC];</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordflow">case</span> <span class="charliteral">'G'</span>:</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordflow">return</span> m_FPrintBV[eG];</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="keywordflow">return</span> m_FPrintBV[eT];</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordflow">case</span> <span class="charliteral">'N'</span>:</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordflow">return</span> m_FPrintBV[eN];</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">default</span>:</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  }</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordflow">throw</span> runtime_error(<span class="stringliteral">"Error. Invalid letter!"</span>);</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="comment"></span> </div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> <span class="comment"> /// Find word strings</span></div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> <span class="comment"> /// using shift + and on fingerprint vectors</span></div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> <span class="comment"> /// (horizontal, non-fused basic method)</span></div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span> <span class="comment"> ///</span></div>
<div class="line"><a name="l00250"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#a35ab54ce8d56bb16f150cffd7c308bab"> 250</a></span> <span class="comment"></span> <span class="keywordtype">void</span> <a class="code" href="classDNA__FingerprintScanner.html#a35ab54ce8d56bb16f150cffd7c308bab">Find</a>(<span class="keyword">const</span> <span class="keywordtype">string</span>& word, vector<unsigned>& res)</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  {</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="keywordflow">if</span> (word.empty())</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv(GetVector(word[0])); <span class="comment">// step 1: copy first vector</span></div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  </div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="comment">// run series of shifts + logical ANDs</span></div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 1; i < word.size(); ++i)</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  {</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  bv.<a class="code" href="classbm_1_1bvector.html#aacf96380ec223d52340a60ec57c8bdbd">shift_right</a>(); <span class="comment">// SHIFT the accumulator bit-vector</span></div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="comment">// get and AND the next fingerprint</span></div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv_mask = GetVector(word[i]);</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  bv &= bv_mask;</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  </div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keyword">auto</span> any = bv.<a class="code" href="classbm_1_1bvector.html#a69729bae3fca407ff1228cf2db761adb">any</a>();</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keywordflow">if</span> (!any)</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</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>  <span class="comment">// translate results from bvector of word ends to result</span></div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordtype">unsigned</span> ws = unsigned(word.size()) - 1;</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  TranslateResults(bv, ws, res);</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"></span> </div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> <span class="comment"> /// This method uses cache blocked aggregator with fused SHIFT+AND kernel</span></div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span> <span class="comment"> ///</span></div>
<div class="line"><a name="l00277"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#a1e7605fd131e0cdf5471a4c335996e8a"> 277</a></span> <span class="comment"></span> <span class="keywordtype">void</span> <a class="code" href="classDNA__FingerprintScanner.html#a1e7605fd131e0cdf5471a4c335996e8a">FindAggFused</a>(<span class="keyword">const</span> <span class="keywordtype">string</span>& word, vector<unsigned>& res)</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  {</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <span class="keywordflow">if</span> (word.empty())</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="comment">// first we setup aggregator, add a group of vectors to be processed</span></div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  m_Agg.reset();</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < word.size(); ++i)</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  {</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv_mask = GetVector(word[i]);</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  m_Agg.add(&bv_mask);</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  }</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  </div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="comment">// now run the whole algorithm to get benefits of cache blocking</span></div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv;</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  m_Agg.combine_shift_right_and(bv);</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  </div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="comment">// translate results from bvector of word ends to result</span></div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="keywordtype">unsigned</span> ws = unsigned(word.size()) - 1;</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  TranslateResults(bv, ws, res);</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  };</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <span class="comment"></span></div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> <span class="comment"> /// Find a set of words in one pass using pipeline</span></div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span> <span class="comment"> /// of aggregators (this is very experimental)</span></div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span> <span class="comment"> ///</span></div>
<div class="line"><a name="l00302"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#abff5b0264b9397cc1137334f2ec2a4b5"> 302</a></span> <span class="comment"></span> <span class="keywordtype">void</span> <a class="code" href="classDNA__FingerprintScanner.html#abff5b0264b9397cc1137334f2ec2a4b5">FindCollection</a>(<span class="keyword">const</span> vector<tuple<string,int> >& words,</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  vector<vector<unsigned>>& hits)</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  {</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  vector<unique_ptr<aggregator_type> > agg_pipeline;</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <span class="keywordtype">unsigned</span> ws = 0;</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  </div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& w : words)</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  {</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  unique_ptr<aggregator_type> agg_ptr(<span class="keyword">new</span> <a class="code" href="xsample04_8cpp.html#a7967cbddc252672d351b3ddf9d688888">aggregator_type</a>());</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  agg_ptr->set_operation(<a class="code" href="classbm_1_1aggregator.html#a90bcc8764cec63d4f135e34db894b4c9a98ce759510d4818b3fc0491c3e269db7">aggregator_type::BM_SHIFT_R_AND</a>);</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  </div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="keyword">const</span> <span class="keywordtype">string</span>& word = get<0>(w);</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < word.size(); ++i)</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  {</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv_mask = GetVector(word[i]);</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  agg_ptr->add(&bv_mask);</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  }</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  </div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  agg_pipeline.emplace_back(agg_ptr.release());</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  ws = unsigned(word.size()) - 1;</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  }</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  </div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="comment">// run the pipeline</span></div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <a class="code" href="group__setalgo.html#gab95bf57beb1b63e172642fe4f2fda6dd">bm::aggregator_pipeline_execute</a><<a class="code" href="xsample04_8cpp.html#a7967cbddc252672d351b3ddf9d688888">aggregator_type</a>,</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  vector<unique_ptr<aggregator_type> >::iterator>(agg_pipeline.begin(), agg_pipeline.end());</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  </div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <span class="comment">// convert the results</span></div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < agg_pipeline.size(); ++i)</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  {</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keyword">const</span> <a class="code" href="classbm_1_1aggregator.html">aggregator_type</a>* agg_ptr = agg_pipeline[i].get();</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <span class="keyword">auto</span> bv = agg_ptr-><a class="code" href="classbm_1_1aggregator.html#ab2db2624b3bfb9ae9575a53daeb99e7a">get_target</a>();</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  vector<unsigned> res;</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  res.reserve(12000);</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  TranslateResults(*bv, ws, res);</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  hits.emplace_back(res);</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  }</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  }</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  </div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span> <span class="comment"></span> </div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span> <span class="comment"> /// Translate search results vector using (word size) left shift</span></div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> <span class="comment"> ///</span></div>
<div class="line"><a name="l00344"></a><span class="lineno"><a class="line" href="classDNA__FingerprintScanner.html#a8fa67c59e26693e801129c2eae97075c"> 344</a></span> <span class="comment"></span> <span class="keywordtype">void</span> <a class="code" href="classDNA__FingerprintScanner.html#a8fa67c59e26693e801129c2eae97075c">TranslateResults</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv,</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordtype">unsigned</span> left_shift,</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  vector<unsigned>& res)</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  {</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <a class="code" href="classbm_1_1bvector_1_1enumerator.html">bm::bvector<>::enumerator</a> en = bv.<a class="code" href="classbm_1_1bvector.html#a86b939f3aed555dc073e8c26e9efea71">first</a>();</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordflow">for</span> (; en.<a class="code" href="classbm_1_1bvector_1_1iterator__base.html#a3f6af7f5b46c0219b28916187d302c43">valid</a>(); ++en)</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  {</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keyword">auto</span> pos = *en;</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  res.push_back(pos - left_shift);</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  }</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  }</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  </div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> m_FPrintBV[eEnd];</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <a class="code" href="classbm_1_1aggregator.html">aggregator_type</a> m_Agg;</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> };</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  </div>
<div class="line"><a name="l00361"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a45d62a2dc44b10c0ec50341b488d320f"> 361</a></span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> <a class="code" href="xsample04_8cpp.html#a45d62a2dc44b10c0ec50341b488d320f">WORD_SIZE</a> = 28;</div>
<div class="line"><a name="l00362"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e"> 362</a></span> <span class="keyword">using</span> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> = vector<unsigned>;</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span> <span class="comment"></span> </div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span> <span class="comment">/// generate the most frequent words of specified length from the input sequence</span></div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span> <span class="comment">///</span></div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> <span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><a name="l00367"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#afc650d5b1927c328a678f8bb0a39ac9f"> 367</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample04_8cpp.html#afc650d5b1927c328a678f8bb0a39ac9f">generate_kmers</a>(vector<tuple<string,int>>& top_words,</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  vector<tuple<string,int>>& lo_words,</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  <span class="keyword">const</span> vector<char>& data,</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordtype">size_t</span> N,</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keywordtype">unsigned</span> word_size)</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span> {</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  cout << <span class="stringliteral">"k-mer generation... "</span> << endl;</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  </div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  top_words.clear();</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  lo_words.clear();</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  </div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="keywordflow">if</span> (data.size() < word_size)</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  </div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keywordtype">size_t</span> end_pos = data.size() - word_size;</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  <span class="keywordtype">size_t</span> i = 0;</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  map<string, int> words;</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  <span class="keywordflow">while</span> (i < end_pos)</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  {</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="keywordtype">string</span> s(&data[i], word_size);</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  <span class="keywordflow">if</span> (s.find(<span class="charliteral">'N'</span>) == string::npos)</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  words[s] += 1;</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  i += word_size;</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <span class="keywordflow">if</span> (i % 10000 == 0)</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  {</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  cout << <span class="stringliteral">"\r"</span> << i << <span class="stringliteral">"/"</span> << end_pos << flush;</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  }</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  }</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  </div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  cout << endl << <span class="stringliteral">"Picking k-mer samples..."</span> << flush;</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  </div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  multimap<int,string, greater<int>> dst;</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  for_each(words.begin(), words.end(), [&](<span class="keyword">const</span> std::pair<string,int>& p)</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  {</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  dst.emplace(p.second, p.first);</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  });</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  {</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  <span class="keyword">auto</span> it = dst.begin();</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> count = 0; count < N && it !=dst.end(); ++it,++count)</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  top_words.emplace_back(it->second, it->first);</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  }</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  </div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  {</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keyword">auto</span> it = dst.rbegin();</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> count = 0; count < N && it !=dst.rend(); ++it, ++count)</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  lo_words.emplace_back(it->second, it->first);</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  }</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  </div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  cout << <span class="stringliteral">"OK"</span> << endl;</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span> }</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span> <span class="comment"></span> </div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span> <span class="comment">/// 2-way string matching</span></div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span> <span class="comment">///</span></div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span> <span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><a name="l00421"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#ad5e2b9cf1214f70b8b60fdd248da5703"> 421</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample04_8cpp.html#ad5e2b9cf1214f70b8b60fdd248da5703">find_word_2way</a>(vector<char>& data,</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keyword">const</span> <span class="keywordtype">char</span>* word, <span class="keywordtype">unsigned</span> word_size,</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a>& r)</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span> {</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  <span class="keywordflow">if</span> (data.size() < word_size)</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  </div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="keywordtype">size_t</span> i = 0;</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  <span class="keywordtype">size_t</span> end_pos = data.size() - word_size;</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  <span class="keywordflow">while</span> (i < end_pos)</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  {</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keywordtype">bool</span> found = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = i, k = 0, l = word_size - 1; l > k; ++j, ++k, --l)</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  {</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  <span class="keywordflow">if</span> (data[j] != word[k] || data[i + l] != word[l])</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  {</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  found = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  }</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  }</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  r.push_back(<span class="keywordtype">unsigned</span>(i));</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  ++i;</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  }</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span> }</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span> <span class="comment"></span> </div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span> <span class="comment">/// Find all words in one pass (cache coherent algorithm)</span></div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span> <span class="comment">/// (variation of 2-way string matching for collection search)</span></div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span> <span class="comment">///</span></div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span> <span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><a name="l00451"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a0591c5d1e9537ed3993e1e753b178f2c"> 451</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample04_8cpp.html#a0591c5d1e9537ed3993e1e753b178f2c">find_words</a>(<span class="keyword">const</span> vector<char>& data,</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  vector<const char*> words,</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordtype">unsigned</span> word_size,</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  vector<vector<unsigned>>& hits)</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span> {</div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <span class="keywordflow">if</span> (data.size() < word_size)</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  </div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="keywordtype">size_t</span> i = 0;</div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="keywordtype">size_t</span> end_pos = data.size() - word_size;</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <span class="keywordtype">size_t</span> words_size = words.size();</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  <span class="keywordflow">while</span> (i < end_pos)</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  {</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> idx = 0; idx < words_size; ++idx)</div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  {</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keyword">auto</span>& word = words[idx];</div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <span class="keywordtype">bool</span> found = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = i, k = 0, l = word_size - 1; l > k; ++j, ++k, --l)</div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  {</div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  <span class="keywordflow">if</span> (data[j] != word[k] || data[i + l] != word[l])</div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  {</div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  found = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  }</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  } <span class="comment">// for</span></div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  {</div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  hits[idx].push_back(<span class="keywordtype">unsigned</span>(i));</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  }</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  } <span class="comment">// for</span></div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  ++i;</div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  } <span class="comment">// while</span></div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span> }</div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  </div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span> <span class="comment"></span> </div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span> <span class="comment">/// Check search result match</span></div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span> <span class="comment">///</span></div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span> <span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><a name="l00490"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f"> 490</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(<span class="keyword">const</span> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a>& h1, <span class="keyword">const</span> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a>& h2)</div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span> {</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  <span class="keywordflow">if</span> (h1.size() != h2.size())</div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  {</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  cerr << <span class="stringliteral">"size1 = "</span> << h1.size() << <span class="stringliteral">" size2 = "</span> << h2.size() << endl;</div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  }</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < h1.size(); ++i)</div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  {</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  <span class="keywordflow">if</span> (h1[i] != h2[i])</div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  }</div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span> }</div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  </div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  </div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  </div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span>  </div>
<div class="line"><a name="l00508"></a><span class="lineno"><a class="line" href="xsample04_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97"> 508</a></span> <span class="keywordtype">int</span> <a class="code" href="xsample04_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a>(<span class="keywordtype">int</span> argc, <span class="keywordtype">char</span> *argv[])</div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span> {</div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  <span class="keywordflow">if</span> (argc < 3)</div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  {</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  <a class="code" href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>();</div>
<div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  }</div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  </div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  std::vector<char> seq_vect;</div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  </div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  {</div>
<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  <span class="keyword">auto</span> ret = <a class="code" href="xsample04_8cpp.html#a1c6cda197a32141227af69a440929ac6">parse_args</a>(argc, argv);</div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <span class="keywordflow">if</span> (ret != 0)</div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <span class="keywordflow">return</span> ret;</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  </div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  <a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a> idx;</div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  </div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a>.empty())</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  {</div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  <span class="keyword">auto</span> res = <a class="code" href="xsample04_8cpp.html#add74621cca7ebe5386556ba01bc35cd2">load_FASTA</a>(<a class="code" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a>, seq_vect);</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="keywordflow">if</span> (res != 0)</div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span>  <span class="keywordflow">return</span> res;</div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  std::cout << <span class="stringliteral">"FASTA sequence size="</span> << seq_vect.size() << std::endl;</div>
<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  </div>
<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  {</div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"2. Build DNA index"</span>, 1, &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  idx.<a class="code" href="classDNA__FingerprintScanner.html#a5ac470fd81df0a04ea1b298a55dba5bb">Build</a>(seq_vect);</div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  }</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  }</div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  </div>
<div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  </div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  <span class="keywordflow">if</span> (<a class="code" href="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a">is_search</a>)</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  {</div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span>  vector<tuple<string,int> > h_words;</div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  vector<tuple<string,int> > l_words;</div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  </div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  vector<tuple<string,int>>& words = <a class="code" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a> ? h_words : l_words;</div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  </div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  <span class="comment">// generate search sets for benchmarking</span></div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  <a class="code" href="xsample04_8cpp.html#afc650d5b1927c328a678f8bb0a39ac9f">generate_kmers</a>(h_words, l_words, seq_vect, 25, <a class="code" href="xsample04_8cpp.html#a45d62a2dc44b10c0ec50341b488d320f">WORD_SIZE</a>);</div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  </div>
<div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  </div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  vector<THitList> word_hits;</div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  vector<THitList> word_hits_agg;</div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  </div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  <span class="comment">// search all words in one pass and</span></div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  <span class="comment">// store results in list of hits according to the order of words</span></div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  <span class="comment">// (this method uses memory proximity</span></div>
<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  <span class="comment">// of searched words to maximize CPU cache hit rate)</span></div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  </div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  {</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  vector<const char*> word_list;</div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& w : words)</div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  {</div>
<div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  word_list.push_back(get<0>(w).c_str());</div>
<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  }</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  word_hits.resize(words.size());</div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  for_each(word_hits.begin(), word_hits.end(), [](<a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a>& ht) {</div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  ht.reserve(12000);</div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  });</div>
<div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  </div>
<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"6. String search 2-way single pass"</span>,</div>
<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  <span class="keywordtype">unsigned</span>(words.size()), &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  <a class="code" href="xsample04_8cpp.html#a0591c5d1e9537ed3993e1e753b178f2c">find_words</a>(seq_vect, word_list, <span class="keywordtype">unsigned</span>(<a class="code" href="xsample04_8cpp.html#a45d62a2dc44b10c0ec50341b488d320f">WORD_SIZE</a>), word_hits);</div>
<div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  }</div>
<div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  </div>
<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <span class="comment">// collection search, runs all hits at once</span></div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  {</div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"7. Aggregated search single pass"</span>,</div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordtype">unsigned</span>(words.size()), &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  </div>
<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  idx.<a class="code" href="classDNA__FingerprintScanner.html#abff5b0264b9397cc1137334f2ec2a4b5">FindCollection</a>(words, word_hits_agg);</div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  }</div>
<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  </div>
<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  <span class="comment">// a few variants of word-by-word searches</span></div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> word_idx = 0; word_idx < words.size(); ++ word_idx)</div>
<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  {</div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  <span class="keyword">auto</span>& word = get<0>(words[word_idx]);</div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> hits1;</div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  </div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  {</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"3. String search 2-way"</span>, 1, &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  <a class="code" href="xsample04_8cpp.html#ad5e2b9cf1214f70b8b60fdd248da5703">find_word_2way</a>(seq_vect,</div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  word.c_str(), <span class="keywordtype">unsigned</span>(word.size()),</div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  hits1);</div>
<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  }</div>
<div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> hits2;</div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  {</div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"4. Search with bvector SHIFT+AND"</span>, 1, &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  idx.<a class="code" href="classDNA__FingerprintScanner.html#a35ab54ce8d56bb16f150cffd7c308bab">Find</a>(word, hits2);</div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  }</div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> hits4;</div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  {</div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"5. Search with aggregator fused SHIFT+AND"</span>, 1, &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  idx.<a class="code" href="classDNA__FingerprintScanner.html#a1e7605fd131e0cdf5471a4c335996e8a">FindAggFused</a>(word, hits4);</div>
<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  }</div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  </div>
<div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  <span class="comment">// check correctness</span></div>
<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(hits1, hits2)</div>
<div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  || !<a class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(hits2, hits4))</div>
<div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  {</div>
<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  cout << <span class="stringliteral">"Mismatch ERROR for: "</span> << word << endl;</div>
<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  }</div>
<div class="line"><a name="l00615"></a><span class="lineno"> 615</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(word_hits[word_idx], hits1)</div>
<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  || !<a class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(word_hits_agg[word_idx], hits1))</div>
<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  {</div>
<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  cout << <span class="stringliteral">"Sigle pass mismatch ERROR for: "</span> << word << endl;</div>
<div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  }</div>
<div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  {</div>
<div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  cout << word_idx << <span class="stringliteral">": "</span> << word << <span class="stringliteral">": "</span> << hits1.size() << <span class="stringliteral">" hits "</span> << endl;</div>
<div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  }</div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  }</div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  </div>
<div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  }</div>
<div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  </div>
<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  <span class="keywordflow">if</span> (<a class="code" href="xsample04_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a>) <span class="comment">// print all collected timings</span></div>
<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  {</div>
<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  std::cout << std::endl << <span class="stringliteral">"Performance:"</span> << std::endl;</div>
<div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  <a class="code" href="classbm_1_1chrono__taker.html#a30b45453d952d14afe56c29087970899">bm::chrono_taker::print_duration_map</a>(<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>, <a class="code" href="classbm_1_1chrono__taker.html#a9a41e5f2fe48ba472fd77a1dbd86457da86a293fae2205928a132bdf4e1b69996">bm::chrono_taker::ct_all</a>);</div>
<div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  }</div>
<div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  }</div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  <span class="keywordflow">catch</span> (std::exception& ex)</div>
<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  {</div>
<div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  std::cerr << <span class="stringliteral">"Error:"</span> << ex.what() << std::endl;</div>
<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  }</div>
<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  </div>
<div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00642"></a><span class="lineno"> 642</span> }</div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="abmaggregator_8h_html"><div class="ttname"><a href="bmaggregator_8h.html">bmaggregator.h</a></div><div class="ttdoc">Algorithms for fast aggregation of N bvectors.</div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html"><div class="ttname"><a href="classbm_1_1chrono__taker.html">bm::chrono_taker</a></div><div class="ttdoc">Utility class to collect performance measurements and statistics.</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00039">bmtimer.h:39</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_afc650d5b1927c328a678f8bb0a39ac9f"><div class="ttname"><a href="xsample04_8cpp.html#afc650d5b1927c328a678f8bb0a39ac9f">generate_kmers</a></div><div class="ttdeci">static void generate_kmers(vector< tuple< string, int >> &top_words, vector< tuple< string, int >> &lo_words, const vector< char > &data, size_t N, unsigned word_size)</div><div class="ttdoc">generate the most frequent words of specified length from the input sequence</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00367">xsample04.cpp:367</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a35ab54ce8d56bb16f150cffd7c308bab"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a35ab54ce8d56bb16f150cffd7c308bab">DNA_FingerprintScanner::Find</a></div><div class="ttdeci">void Find(const string &word, vector< unsigned > &res)</div><div class="ttdoc">Find word strings using shift + and on fingerprint vectors (horizontal, non-fused basic method)</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00250">xsample04.cpp:250</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_a69729bae3fca407ff1228cf2db761adb"><div class="ttname"><a href="classbm_1_1bvector.html#a69729bae3fca407ff1228cf2db761adb">bm::bvector::any</a></div><div class="ttdeci">bool any() const BMNOEXCEPT</div><div class="ttdoc">Returns true if any bits in this bitset are set, and otherwise returns false.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l02244">bm.h:2244</a></div></div>
<div class="ttc" id="agroup__bvector_html_gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e"><div class="ttname"><a href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a></div><div class="ttdeci">@ BM_SORTED</div><div class="ttdoc">input set is sorted (ascending order)</div><div class="ttdef"><b>Definition:</b> <a href="bmconst_8h_source.html#l00191">bmconst.h:191</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a5ac470fd81df0a04ea1b298a55dba5bb"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a5ac470fd81df0a04ea1b298a55dba5bb">DNA_FingerprintScanner::Build</a></div><div class="ttdeci">void Build(const vector< char > &sequence)</div><div class="ttdoc">Build fingerprint bit-vectors from the original sequence.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00189">xsample04.cpp:189</a></div></div>
<div class="ttc" id="aclassbm_1_1aggregator_html"><div class="ttname"><a href="classbm_1_1aggregator.html">bm::aggregator</a></div><div class="ttdoc">Algorithms for fast aggregation of a group of bit-vectors.</div><div class="ttdef"><b>Definition:</b> <a href="bmaggregator_8h_source.html#l00058">bmaggregator.h:58</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_1_1enumerator_html"><div class="ttname"><a href="classbm_1_1bvector_1_1enumerator.html">bm::bvector::enumerator</a></div><div class="ttdoc">Constant iterator designed to enumerate "ON" bits.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00599">bm.h:599</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a1815ea4e87c7c6b84cd7e555a2d8bc48a87a7e916afec9eb45d2d8d2c8e2e5d13"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a1815ea4e87c7c6b84cd7e555a2d8bc48a87a7e916afec9eb45d2d8d2c8e2e5d13">DNA_FingerprintScanner::eT</a></div><div class="ttdeci">@ eT</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00183">xsample04.cpp:183</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html"><div class="ttname"><a href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a></div><div class="ttdoc">Utility for keeping all DNA finger print vectors and search using various techniques.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00180">xsample04.cpp:180</a></div></div>
<div class="ttc" id="aclassbm_1_1aggregator_html_ab2db2624b3bfb9ae9575a53daeb99e7a"><div class="ttname"><a href="classbm_1_1aggregator.html#ab2db2624b3bfb9ae9575a53daeb99e7a">bm::aggregator::get_target</a></div><div class="ttdeci">const bvector_type * get_target() const</div><div class="ttdef"><b>Definition:</b> <a href="bmaggregator_8h_source.html#l00326">bmaggregator.h:326</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_abff5b0264b9397cc1137334f2ec2a4b5"><div class="ttname"><a href="classDNA__FingerprintScanner.html#abff5b0264b9397cc1137334f2ec2a4b5">DNA_FingerprintScanner::FindCollection</a></div><div class="ttdeci">void FindCollection(const vector< tuple< string, int > > &words, vector< vector< unsigned >> &hits)</div><div class="ttdoc">Find a set of words in one pass using pipeline of aggregators (this is very experimental)</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00302">xsample04.cpp:302</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_aece8e90d91aaea144d41103f7d2825ee"><div class="ttname"><a href="xsample04_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a></div><div class="ttdeci">bool is_timing</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00074">xsample04.cpp:74</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a8fa67c59e26693e801129c2eae97075c"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a8fa67c59e26693e801129c2eae97075c">DNA_FingerprintScanner::TranslateResults</a></div><div class="ttdeci">void TranslateResults(const bm::bvector<> &bv, unsigned left_shift, vector< unsigned > &res)</div><div class="ttdoc">Translate search results vector using (word size) left shift.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00344">xsample04.cpp:344</a></div></div>
<div class="ttc" id="abmalgo_8h_html"><div class="ttname"><a href="bmalgo_8h.html">bmalgo.h</a></div><div class="ttdoc">Algorithms for bvector<> (main include)</div></div>
<div class="ttc" id="axsample04_8cpp_html_a81962ff36a3740bd2a6a458b74e57e26"><div class="ttname"><a href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a></div><div class="ttdeci">static void show_help()</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00056">xsample04.cpp:56</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a7967cbddc252672d351b3ddf9d688888"><div class="ttname"><a href="xsample04_8cpp.html#a7967cbddc252672d351b3ddf9d688888">aggregator_type</a></div><div class="ttdeci">bm::aggregator< bm::bvector<> > aggregator_type</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00144">xsample04.cpp:144</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_aac37d48924de403b5baf0e079e40f22c"><div class="ttname"><a href="classDNA__FingerprintScanner.html#aac37d48924de403b5baf0e079e40f22c">DNA_FingerprintScanner::DNA_FingerprintScanner</a></div><div class="ttdeci">DNA_FingerprintScanner()</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00185">xsample04.cpp:185</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_aa592d3fbead57ca8423ac5caaccada07"><div class="ttname"><a href="xsample04_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a></div><div class="ttdeci">bool is_diag</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00073">xsample04.cpp:73</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a0591c5d1e9537ed3993e1e753b178f2c"><div class="ttname"><a href="xsample04_8cpp.html#a0591c5d1e9537ed3993e1e753b178f2c">find_words</a></div><div class="ttdeci">static void find_words(const vector< char > &data, vector< const char * > words, unsigned word_size, vector< vector< unsigned >> &hits)</div><div class="ttdoc">Find all words in one pass (cache coherent algorithm) (variation of 2-way string matching for collect...</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00451">xsample04.cpp:451</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html"><div class="ttname"><a href="classbm_1_1bvector.html">bm::bvector<></a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a24dcda0f03372e9a308e09d98c30b2ed"><div class="ttname"><a href="xsample04_8cpp.html#a24dcda0f03372e9a308e09d98c30b2ed">freq_map</a></div><div class="ttdeci">std::map< std::string, unsigned > freq_map</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00141">xsample04.cpp:141</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_1_1iterator__base_html_a3f6af7f5b46c0219b28916187d302c43"><div class="ttname"><a href="classbm_1_1bvector_1_1iterator__base.html#a3f6af7f5b46c0219b28916187d302c43">bm::bvector::iterator_base::valid</a></div><div class="ttdeci">bool valid() const BMNOEXCEPT</div><div class="ttdoc">Checks if iterator is still valid. Analog of != 0 comparison for pointers.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00280">bm.h:280</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a6cb51d150528a5d2d87acb3e88f450bc"><div class="ttname"><a href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a></div><div class="ttdeci">bm::chrono_taker::duration_map_type timing_map</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00148">xsample04.cpp:148</a></div></div>
<div class="ttc" id="abmtimer_8h_html"><div class="ttname"><a href="bmtimer_8h.html">bmtimer.h</a></div><div class="ttdoc">Timing utilities for benchmarking (internal)</div></div>
<div class="ttc" id="axsample04_8cpp_html_a2c4a694dfd3f687d8cc845046ae5c30a"><div class="ttname"><a href="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a">is_search</a></div><div class="ttdeci">bool is_search</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00076">xsample04.cpp:76</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_a9a41e5f2fe48ba472fd77a1dbd86457da86a293fae2205928a132bdf4e1b69996"><div class="ttname"><a href="classbm_1_1chrono__taker.html#a9a41e5f2fe48ba472fd77a1dbd86457da86a293fae2205928a132bdf4e1b69996">bm::chrono_taker::ct_all</a></div><div class="ttdeci">@ ct_all</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00060">bmtimer.h:60</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a9988650f5c236d5a70e710498d62904c"><div class="ttname"><a href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a></div><div class="ttdeci">std::string ifa_name</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00072">xsample04.cpp:72</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a4dd1e4b402061691109d356faa4513b5"><div class="ttname"><a href="xsample04_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a></div><div class="ttdeci">bool is_bench</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00075">xsample04.cpp:75</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_acb61f43c97f1f1542bc436dfa56c5f8e"><div class="ttname"><a href="xsample04_8cpp.html#acb61f43c97f1f1542bc436dfa56c5f8e">dict_vect</a></div><div class="ttdeci">std::vector< std::pair< unsigned, std::string > > dict_vect</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00142">xsample04.cpp:142</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a1c6cda197a32141227af69a440929ac6"><div class="ttname"><a href="xsample04_8cpp.html#a1c6cda197a32141227af69a440929ac6">parse_args</a></div><div class="ttdeci">static int parse_args(int argc, char *argv[])</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00080">xsample04.cpp:80</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_aa3afd260fddf127333599aa96d67aa0f"><div class="ttname"><a href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a></div><div class="ttdeci">bool h_word_set</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00077">xsample04.cpp:77</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_aacf96380ec223d52340a60ec57c8bdbd"><div class="ttname"><a href="classbm_1_1bvector.html#aacf96380ec223d52340a60ec57c8bdbd">bm::bvector::shift_right</a></div><div class="ttdeci">bool shift_right()</div><div class="ttdoc">Shift right by 1 bit, fill with zero return carry out.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l04360">bm.h:4360</a></div></div>
<div class="ttc" id="agroup__setalgo_html_gab95bf57beb1b63e172642fe4f2fda6dd"><div class="ttname"><a href="group__setalgo.html#gab95bf57beb1b63e172642fe4f2fda6dd">bm::aggregator_pipeline_execute</a></div><div class="ttdeci">void aggregator_pipeline_execute(It first, It last)</div><div class="ttdoc">Experimental method ro run multiple aggregators in sync.</div><div class="ttdef"><b>Definition:</b> <a href="bmaggregator_8h_source.html#l00481">bmaggregator.h:481</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a1e7605fd131e0cdf5471a4c335996e8a"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a1e7605fd131e0cdf5471a4c335996e8a">DNA_FingerprintScanner::FindAggFused</a></div><div class="ttdeci">void FindAggFused(const string &word, vector< unsigned > &res)</div><div class="ttdoc">This method uses cache blocked aggregator with fused SHIFT+AND kernel.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00277">xsample04.cpp:277</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_add1676592117ed0eaa2fa6279a71b46a"><div class="ttname"><a href="classbm_1_1chrono__taker.html#add1676592117ed0eaa2fa6279a71b46a">bm::chrono_taker::duration_map_type</a></div><div class="ttdeci">std::map< std::string, statistics > duration_map_type</div><div class="ttdoc">test name to duration map</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00065">bmtimer.h:65</a></div></div>
<div class="ttc" id="abmserial_8h_html"><div class="ttname"><a href="bmserial_8h.html">bmserial.h</a></div><div class="ttdoc">Serialization / compression of bvector<>. Set theoretical operations on compressed BLOBs.</div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_a30b45453d952d14afe56c29087970899"><div class="ttname"><a href="classbm_1_1chrono__taker.html#a30b45453d952d14afe56c29087970899">bm::chrono_taker::print_duration_map</a></div><div class="ttdeci">static void print_duration_map(const duration_map_type &dmap, format fmt=ct_time)</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00127">bmtimer.h:127</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a83cc2d037a5af2472ec8218eea2e567f"><div class="ttname"><a href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a></div><div class="ttdeci">static bool hitlist_compare(const THitList &h1, const THitList &h2)</div><div class="ttdoc">Check search result match.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00490">xsample04.cpp:490</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_add74621cca7ebe5386556ba01bc35cd2"><div class="ttname"><a href="xsample04_8cpp.html#add74621cca7ebe5386556ba01bc35cd2">load_FASTA</a></div><div class="ttdeci">static int load_FASTA(const std::string &fname, std::vector< char > &seq_vect)</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00152">xsample04.cpp:152</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a20a9f23a3245391824c91b2f3b43e09e"><div class="ttname"><a href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a></div><div class="ttdeci">vector< unsigned > THitList</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00362">xsample04.cpp:362</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a0ddf1224851353fc92bfbff6f499fa97"><div class="ttname"><a href="xsample04_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a></div><div class="ttdeci">int main(int argc, char *argv[])</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00508">xsample04.cpp:508</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_a86b939f3aed555dc073e8c26e9efea71"><div class="ttname"><a href="classbm_1_1bvector.html#a86b939f3aed555dc073e8c26e9efea71">bm::bvector::first</a></div><div class="ttdeci">enumerator first() const</div><div class="ttdoc">Returns enumerator pointing on the first non-zero bit.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l01770">bm.h:1770</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_1_1bulk__insert__iterator_html"><div class="ttname"><a href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector::bulk_insert_iterator</a></div><div class="ttdoc">Output iterator iterator designed to set "ON" bits based on input sequence of integers.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00461">bm.h:461</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_ad5e2b9cf1214f70b8b60fdd248da5703"><div class="ttname"><a href="xsample04_8cpp.html#ad5e2b9cf1214f70b8b60fdd248da5703">find_word_2way</a></div><div class="ttdeci">static void find_word_2way(vector< char > &data, const char *word, unsigned word_size, THitList &r)</div><div class="ttdoc">2-way string matching</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00421">xsample04.cpp:421</a></div></div>
<div class="ttc" id="aclassbm_1_1aggregator_html_a90bcc8764cec63d4f135e34db894b4c9a98ce759510d4818b3fc0491c3e269db7"><div class="ttname"><a href="classbm_1_1aggregator.html#a90bcc8764cec63d4f135e34db894b4c9a98ce759510d4818b3fc0491c3e269db7">bm::aggregator< bm::bvector<> >::BM_SHIFT_R_AND</a></div><div class="ttdeci">@ BM_SHIFT_R_AND</div><div class="ttdef"><b>Definition:</b> <a href="bmaggregator_8h_source.html#l00079">bmaggregator.h:79</a></div></div>
<div class="ttc" id="abm_8h_html"><div class="ttname"><a href="bm_8h.html">bm.h</a></div><div class="ttdoc">Compressed bit-vector bvector<> container, set algebraic methods, traversal iterators.</div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a8623c4721c296e6cc065ae6a2ceff980"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a8623c4721c296e6cc065ae6a2ceff980">DNA_FingerprintScanner::GetVector</a></div><div class="ttdeci">const bm::bvector & GetVector(char letter) const</div><div class="ttdoc">Return fingerprint bit-vector.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00226">xsample04.cpp:226</a></div></div>
<div class="ttc" id="axsample04_8cpp_html_a45d62a2dc44b10c0ec50341b488d320f"><div class="ttname"><a href="xsample04_8cpp.html#a45d62a2dc44b10c0ec50341b488d320f">WORD_SIZE</a></div><div class="ttdeci">static const size_t WORD_SIZE</div><div class="ttdef"><b>Definition:</b> <a href="xsample04_8cpp_source.html#l00361">xsample04.cpp:361</a></div></div>
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