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|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title>BitMagic-C++: xsample04.cpp</title>
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<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">BitMagic-C++
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<div class="header">
<div class="headertitle">
<div class="title">xsample04.cpp</div> </div>
</div><!--header-->
<div class="contents">
<div class="fragment"><div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment">Copyright(c) 2018 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">Licensed under the Apache License, Version 2.0 (the "License");</span></div>
<div class="line"><span class="comment">you may not use this file except in compliance with the License.</span></div>
<div class="line"><span class="comment">You may obtain a copy of the License at</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> http://www.apache.org/licenses/LICENSE-2.0</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">Unless required by applicable law or agreed to in writing, software</span></div>
<div class="line"><span class="comment">distributed under the License is distributed on an "AS IS" BASIS,</span></div>
<div class="line"><span class="comment">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></div>
<div class="line"><span class="comment">See the License for the specific language governing permissions and</span></div>
<div class="line"><span class="comment">limitations under the License.</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">For more information please visit: http://bitmagic.io</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/** \example xsample04.cpp</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/*! \file xsample04.cpp</span></div>
<div class="line"><span class="comment"> \brief Example: DNA substring search</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include <iostream></span></div>
<div class="line"><span class="preprocessor">#include <sstream></span></div>
<div class="line"><span class="preprocessor">#include <chrono></span></div>
<div class="line"><span class="preprocessor">#include <regex></span></div>
<div class="line"><span class="preprocessor">#include <time.h></span></div>
<div class="line"><span class="preprocessor">#include <stdio.h></span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include <stdexcept></span></div>
<div class="line"><span class="preprocessor">#include <memory></span></div>
<div class="line"><span class="preprocessor">#include <vector></span></div>
<div class="line"><span class="preprocessor">#include <chrono></span></div>
<div class="line"><span class="preprocessor">#include <map></span></div>
<div class="line"><span class="preprocessor">#include <utility></span></div>
<div class="line"><span class="preprocessor">#include <algorithm></span></div>
<div class="line"><span class="preprocessor">#include <unordered_map></span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bm_8h.html">bm.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmalgo_8h.html">bmalgo.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmserial_8h.html">bmserial.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmaggregator_8h.html">bmaggregator.h</a>"</span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include "bmdbg.h"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmtimer_8h.html">bmtimer.h</a>"</span></div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="keyword">using namespace </span>std;</div>
<div class="line"> </div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a0"></a><a class="code" href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>()</div>
<div class="line">{</div>
<div class="line"> std::cerr</div>
<div class="line"> << <span class="stringliteral">"BitMagic DNA Search Sample (c) 2018"</span> << std::endl</div>
<div class="line"> << <span class="stringliteral">"-fa file-name -- input FASTA file"</span> << std::endl</div>
<div class="line"> << <span class="stringliteral">"-s hi|lo -- run substring search benchmark"</span> << std::endl</div>
<div class="line"> << <span class="stringliteral">"-diag -- run diagnostics"</span> << std::endl</div>
<div class="line"> << <span class="stringliteral">"-timing -- collect timings"</span> << std::endl</div>
<div class="line"> ;</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="comment">// Arguments</span></div>
<div class="line"><span class="comment">//</span></div>
<div class="line">std::string <a name="a1"></a><a class="code" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a>;</div>
<div class="line"><span class="keywordtype">bool</span> <a name="a2"></a><a class="code" href="xsample04_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a> = <span class="keyword">false</span>;</div>
<div class="line"><span class="keywordtype">bool</span> <a name="a3"></a><a class="code" href="xsample04_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">false</span>;</div>
<div class="line"><span class="keywordtype">bool</span> <a name="a4"></a><a class="code" href="xsample04_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a> = <span class="keyword">false</span>;</div>
<div class="line"><span class="keywordtype">bool</span> <a name="a5"></a><a class="code" href="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a">is_search</a> = <span class="keyword">false</span>;</div>
<div class="line"><span class="keywordtype">bool</span> <a name="a6"></a><a class="code" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a> = <span class="keyword">true</span>;</div>
<div class="line"> </div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">int</span> <a name="a7"></a><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">{</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 1; i < argc; ++i)</div>
<div class="line"> {</div>
<div class="line"> std::string arg = argv[i];</div>
<div class="line"> <span class="keywordflow">if</span> ((arg == <span class="stringliteral">"-h"</span>) || (arg == <span class="stringliteral">"--help"</span>))</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>();</div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-fa"</span> || arg == <span class="stringliteral">"--fa"</span>)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a> = argv[++i];</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> {</div>
<div class="line"> std::cerr << <span class="stringliteral">"Error: -fa requires file name"</span> << std::endl;</div>
<div class="line"> <span class="keywordflow">return</span> 1;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">continue</span>;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <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 class="code" href="xsample04_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a> = <span class="keyword">true</span>;</div>
<div class="line"> <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 class="code" href="xsample04_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">true</span>;</div>
<div class="line"> <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 class="code" href="xsample04_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a> = <span class="keyword">true</span>;</div>
<div class="line"> <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"> {</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a">is_search</a> = <span class="keyword">true</span>;</div>
<div class="line"> <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"> {</div>
<div class="line"> std::string a = argv[i+1];</div>
<div class="line"> <span class="keywordflow">if</span> (a != <span class="stringliteral">"-"</span>)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (a == <span class="stringliteral">"l"</span> || a == <span class="stringliteral">"lo"</span>)</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a> = <span class="keyword">false</span>;</div>
<div class="line"> ++i;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> <span class="keywordflow">if</span> (a == <span class="stringliteral">"h"</span> || a == <span class="stringliteral">"hi"</span>)</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#aa3afd260fddf127333599aa96d67aa0f">h_word_set</a> = <span class="keyword">true</span>;</div>
<div class="line"> ++i;</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> } <span class="comment">// for i</span></div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="comment">// Global types</span></div>
<div class="line"><span class="comment">//</span></div>
<div class="line"><span class="keyword">typedef</span> std::map<std::string, unsigned> <a name="a8"></a><a class="code" href="xsample04_8cpp.html#a24dcda0f03372e9a308e09d98c30b2ed">freq_map</a>;</div>
<div class="line"><span class="keyword">typedef</span> std::vector<std::pair<unsigned, std::string> > <a name="a9"></a><a class="code" href="xsample04_8cpp.html#acb61f43c97f1f1542bc436dfa56c5f8e">dict_vect</a>;</div>
<div class="line"> </div>
<div class="line"><span class="keyword">typedef</span> <a name="_a10"></a><a class="code" href="classbm_1_1aggregator.html">bm::aggregator<bm::bvector<></a> > <a name="a11"></a><a class="code" href="xsample04_8cpp.html#a7967cbddc252672d351b3ddf9d688888">aggregator_type</a>;</div>
<div class="line"> </div>
<div class="line"><span class="comment">// ----------------------------------------------------------------------------</span></div>
<div class="line"> </div>
<div class="line"><a class="code" href="classbm_1_1chrono__taker.html#add1676592117ed0eaa2fa6279a71b46a">bm::chrono_taker::duration_map_type</a> <a name="a12"></a><a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>;</div>
<div class="line"> </div>
<div class="line"><span class="comment">// FASTA format parser</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">int</span> <a name="a13"></a><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">{</div>
<div class="line"> <a name="_a14"></a><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"> </div>
<div class="line"> seq_vect.resize(0);</div>
<div class="line"> std::ifstream fin(fname.c_str(), std::ios::in);</div>
<div class="line"> <span class="keywordflow">if</span> (!fin.good())</div>
<div class="line"> <span class="keywordflow">return</span> -1;</div>
<div class="line"> </div>
<div class="line"> std::string line;</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; std::getline(fin, line); ++i)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (line.empty() ||</div>
<div class="line"> line.front() == <span class="charliteral">'>'</span>)</div>
<div class="line"> <span class="keywordflow">continue</span>;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (std::string::iterator it = line.begin(); it != line.end(); ++it)</div>
<div class="line"> seq_vect.push_back(*it);</div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/**</span></div>
<div class="line"><span class="comment"> Utility for keeping all DNA finger print vectors and search</span></div>
<div class="line"><span class="comment"> using various techniques</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">class </span><a name="_a15"></a><a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a></div>
<div class="line">{</div>
<div class="line"><span class="keyword">public</span>:</div>
<div class="line"> <span class="keyword">enum</span> { eA = 0, eC, eG, eT, eN, eEnd };</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a>() {}</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> /// Build fingerprint bit-vectors from the original sequence</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> Build(<span class="keyword">const</span> vector<char>& sequence)</div>
<div class="line"> {</div>
<div class="line"> <span class="comment">// use bulk insert iterator (faster way to construct a bit-index)</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <a name="_a16"></a><a class="code" href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector<>::bulk_insert_iterator</a> iA(m_FPrintBV[eA], <a name="a17"></a><a class="code" href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a>);</div>
<div class="line"> <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 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 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 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"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < sequence.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">unsigned</span> pos = unsigned(i);</div>
<div class="line"> <span class="keywordflow">switch</span> (sequence[i])</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'A'</span>:</div>
<div class="line"> iA = pos;</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'C'</span>:</div>
<div class="line"> iC = pos;</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'G'</span>:</div>
<div class="line"> iG = pos;</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div>
<div class="line"> iT = pos;</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'N'</span>:</div>
<div class="line"> iN = pos;</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> <span class="keywordflow">default</span>:</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> /// Return fingerprint bit-vector</span></div>
<div class="line"><span class="comment"></span> <span class="keyword">const</span> <a name="_a18"></a><a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& GetVector(<span class="keywordtype">char</span> letter)<span class="keyword"> const</span></div>
<div class="line"><span class="keyword"> </span>{</div>
<div class="line"> <span class="keywordflow">switch</span> (letter)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'A'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> m_FPrintBV[eA];</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'C'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> m_FPrintBV[eC];</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'G'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> m_FPrintBV[eG];</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> m_FPrintBV[eT];</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'N'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> m_FPrintBV[eN];</div>
<div class="line"> <span class="keywordflow">default</span>:</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">throw</span> runtime_error(<span class="stringliteral">"Error. Invalid letter!"</span>);</div>
<div class="line"> }</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> /// Find word strings</span></div>
<div class="line"><span class="comment"> /// using shift + and on fingerprint vectors</span></div>
<div class="line"><span class="comment"> /// (horizontal, non-fused basic method)</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> Find(<span class="keyword">const</span> <span class="keywordtype">string</span>& word, vector<unsigned>& res)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (word.empty())</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> <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"> </div>
<div class="line"> <span class="comment">// run series of shifts + logical ANDs</span></div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 1; i < word.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> bv.shift_right(); <span class="comment">// SHIFT the accumulator bit-vector</span></div>
<div class="line"> <span class="comment">// get and AND the next fingerprint</span></div>
<div class="line"> <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"> bv &= bv_mask;</div>
<div class="line"> </div>
<div class="line"> <span class="keyword">auto</span> any = bv.<a name="a19"></a><a class="code" href="classbm_1_1bvector.html#a69729bae3fca407ff1228cf2db761adb">any</a>();</div>
<div class="line"> <span class="keywordflow">if</span> (!any)</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// translate results from bvector of word ends to result</span></div>
<div class="line"> <span class="keywordtype">unsigned</span> ws = unsigned(word.size()) - 1;</div>
<div class="line"> TranslateResults(bv, ws, res);</div>
<div class="line"> };</div>
<div class="line"> </div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> /// This method uses cache blocked aggregator with fused SHIFT+AND kernel</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> FindAggFused(<span class="keyword">const</span> <span class="keywordtype">string</span>& word, vector<unsigned>& res)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (word.empty())</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> <span class="comment">// first we setup aggregator, add a group of vectors to be processed</span></div>
<div class="line"> m_Agg.reset();</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < word.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> <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"> m_Agg.add(&bv_mask);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// now run the whole algorithm to get benefits of cache blocking</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv;</div>
<div class="line"> m_Agg.combine_shift_right_and(bv);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// translate results from bvector of word ends to result</span></div>
<div class="line"> <span class="keywordtype">unsigned</span> ws = unsigned(word.size()) - 1;</div>
<div class="line"> TranslateResults(bv, ws, res);</div>
<div class="line"> };</div>
<div class="line"> <span class="comment"></span></div>
<div class="line"><span class="comment"> /// Find a set of words in one pass using pipeline</span></div>
<div class="line"><span class="comment"> /// of aggregators (this is very experimental)</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> FindCollection(<span class="keyword">const</span> vector<tuple<string,int> >& words,</div>
<div class="line"> vector<vector<unsigned>>& hits)</div>
<div class="line"> {</div>
<div class="line"> vector<unique_ptr<aggregator_type> > agg_pipeline;</div>
<div class="line"> <span class="keywordtype">unsigned</span> ws = 0;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& w : words)</div>
<div class="line"> {</div>
<div class="line"> 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"> agg_ptr->set_operation(<a name="a20"></a><a class="code" href="classbm_1_1aggregator.html#a90bcc8764cec63d4f135e34db894b4c9a98ce759510d4818b3fc0491c3e269db7">aggregator_type::BM_SHIFT_R_AND</a>);</div>
<div class="line"> </div>
<div class="line"> <span class="keyword">const</span> <span class="keywordtype">string</span>& word = get<0>(w);</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < word.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> <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"> agg_ptr->add(&bv_mask);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> agg_pipeline.emplace_back(agg_ptr.release());</div>
<div class="line"> ws = unsigned(word.size()) - 1;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// run the pipeline</span></div>
<div class="line"> <a name="a21"></a><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"> vector<unique_ptr<aggregator_type> >::iterator>(agg_pipeline.begin(), agg_pipeline.end());</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// convert the results</span></div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < agg_pipeline.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">const</span> <a name="_a22"></a><a class="code" href="classbm_1_1aggregator.html">aggregator_type</a>* agg_ptr = agg_pipeline[i].get();</div>
<div class="line"> <span class="keyword">auto</span> bv = agg_ptr-><a name="a23"></a><a class="code" href="classbm_1_1aggregator.html#ab2db2624b3bfb9ae9575a53daeb99e7a">get_target</a>();</div>
<div class="line"> vector<unsigned> res;</div>
<div class="line"> res.reserve(12000);</div>
<div class="line"> TranslateResults(*bv, ws, res);</div>
<div class="line"> hits.emplace_back(res);</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"><span class="keyword">protected</span>:</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> /// Translate search results vector using (word size) left shift</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> TranslateResults(<span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv,</div>
<div class="line"> <span class="keywordtype">unsigned</span> left_shift,</div>
<div class="line"> vector<unsigned>& res)</div>
<div class="line"> {</div>
<div class="line"> <a name="_a24"></a><a class="code" href="classbm_1_1bvector_1_1enumerator.html">bm::bvector<>::enumerator</a> en = bv.<a name="a25"></a><a class="code" href="classbm_1_1bvector.html#a86b939f3aed555dc073e8c26e9efea71">first</a>();</div>
<div class="line"> <span class="keywordflow">for</span> (; en.<a name="a26"></a><a class="code" href="classbm_1_1bvector_1_1iterator__base.html#a3f6af7f5b46c0219b28916187d302c43">valid</a>(); ++en)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> pos = *en;</div>
<div class="line"> res.push_back(pos - left_shift);</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"><span class="keyword">private</span>:</div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> m_FPrintBV[eEnd];</div>
<div class="line"> <a class="code" href="classbm_1_1aggregator.html">aggregator_type</a> m_Agg;</div>
<div class="line">};</div>
<div class="line"> </div>
<div class="line"><span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> <a name="a27"></a><a class="code" href="xsample04_8cpp.html#a45d62a2dc44b10c0ec50341b488d320f">WORD_SIZE</a> = 28;</div>
<div class="line"><span class="keyword">using</span> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> = vector<unsigned>;</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// generate the most frequent words of specified length from the input sequence</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a28"></a><a class="code" href="xsample04_8cpp.html#afc650d5b1927c328a678f8bb0a39ac9f">generate_kmers</a>(vector<tuple<string,int>>& top_words,</div>
<div class="line"> vector<tuple<string,int>>& lo_words,</div>
<div class="line"> <span class="keyword">const</span> vector<char>& data,</div>
<div class="line"> <span class="keywordtype">size_t</span> N,</div>
<div class="line"> <span class="keywordtype">unsigned</span> word_size)</div>
<div class="line">{</div>
<div class="line"> cout << <span class="stringliteral">"k-mer generation... "</span> << endl;</div>
<div class="line"> </div>
<div class="line"> top_words.clear();</div>
<div class="line"> lo_words.clear();</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (data.size() < word_size)</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">size_t</span> end_pos = data.size() - word_size;</div>
<div class="line"> <span class="keywordtype">size_t</span> i = 0;</div>
<div class="line"> map<string, int> words;</div>
<div class="line"> <span class="keywordflow">while</span> (i < end_pos)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">string</span> s(&data[i], word_size);</div>
<div class="line"> <span class="keywordflow">if</span> (s.find(<span class="charliteral">'N'</span>) == string::npos)</div>
<div class="line"> words[s] += 1;</div>
<div class="line"> i += word_size;</div>
<div class="line"> <span class="keywordflow">if</span> (i % 10000 == 0)</div>
<div class="line"> {</div>
<div class="line"> cout << <span class="stringliteral">"\r"</span> << i << <span class="stringliteral">"/"</span> << end_pos << flush;</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> cout << endl << <span class="stringliteral">"Picking k-mer samples..."</span> << flush;</div>
<div class="line"> </div>
<div class="line"> multimap<int,string, greater<int>> dst;</div>
<div class="line"> for_each(words.begin(), words.end(), [&](<span class="keyword">const</span> std::pair<string,int>& p)</div>
<div class="line"> {</div>
<div class="line"> dst.emplace(p.second, p.first);</div>
<div class="line"> });</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> it = dst.begin();</div>
<div class="line"> <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> count = 0; count < N && it !=dst.end(); ++it,++count)</div>
<div class="line"> top_words.emplace_back(it->second, it->first);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> it = dst.rbegin();</div>
<div class="line"> <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> count = 0; count < N && it !=dst.rend(); ++it, ++count)</div>
<div class="line"> lo_words.emplace_back(it->second, it->first);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> cout << <span class="stringliteral">"OK"</span> << endl;</div>
<div class="line">}</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// 2-way string matching</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a29"></a><a class="code" href="xsample04_8cpp.html#ad5e2b9cf1214f70b8b60fdd248da5703">find_word_2way</a>(vector<char>& data,</div>
<div class="line"> <span class="keyword">const</span> <span class="keywordtype">char</span>* word, <span class="keywordtype">unsigned</span> word_size,</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a>& r)</div>
<div class="line">{</div>
<div class="line"> <span class="keywordflow">if</span> (data.size() < word_size)</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">size_t</span> i = 0;</div>
<div class="line"> <span class="keywordtype">size_t</span> end_pos = data.size() - word_size;</div>
<div class="line"> <span class="keywordflow">while</span> (i < end_pos)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">bool</span> found = <span class="keyword">true</span>;</div>
<div class="line"> <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"> {</div>
<div class="line"> <span class="keywordflow">if</span> (data[j] != word[k] || data[i + l] != word[l])</div>
<div class="line"> {</div>
<div class="line"> found = <span class="keyword">false</span>;</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">if</span> (found)</div>
<div class="line"> r.push_back(<span class="keywordtype">unsigned</span>(i));</div>
<div class="line"> ++i;</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Find all words in one pass (cache coherent algorithm)</span></div>
<div class="line"><span class="comment">/// (variation of 2-way string matching for collection search)</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a30"></a><a class="code" href="xsample04_8cpp.html#a0591c5d1e9537ed3993e1e753b178f2c">find_words</a>(<span class="keyword">const</span> vector<char>& data,</div>
<div class="line"> vector<const char*> words,</div>
<div class="line"> <span class="keywordtype">unsigned</span> word_size,</div>
<div class="line"> vector<vector<unsigned>>& hits)</div>
<div class="line">{</div>
<div class="line"> <span class="keywordflow">if</span> (data.size() < word_size)</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">size_t</span> i = 0;</div>
<div class="line"> <span class="keywordtype">size_t</span> end_pos = data.size() - word_size;</div>
<div class="line"> <span class="keywordtype">size_t</span> words_size = words.size();</div>
<div class="line"> <span class="keywordflow">while</span> (i < end_pos)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> idx = 0; idx < words_size; ++idx)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span>& word = words[idx];</div>
<div class="line"> <span class="keywordtype">bool</span> found = <span class="keyword">true</span>;</div>
<div class="line"> <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"> {</div>
<div class="line"> <span class="keywordflow">if</span> (data[j] != word[k] || data[i + l] != word[l])</div>
<div class="line"> {</div>
<div class="line"> found = <span class="keyword">false</span>;</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> }</div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> <span class="keywordflow">if</span> (found)</div>
<div class="line"> {</div>
<div class="line"> hits[idx].push_back(<span class="keywordtype">unsigned</span>(i));</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> }</div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> ++i;</div>
<div class="line"> } <span class="comment">// while</span></div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Check search result match</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">bool</span> <a name="a31"></a><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">{</div>
<div class="line"> <span class="keywordflow">if</span> (h1.size() != h2.size())</div>
<div class="line"> {</div>
<div class="line"> cerr << <span class="stringliteral">"size1 = "</span> << h1.size() << <span class="stringliteral">" size2 = "</span> << h2.size() << endl;</div>
<div class="line"> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < h1.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (h1[i] != h2[i])</div>
<div class="line"> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="keywordtype">int</span> <a name="a32"></a><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">{</div>
<div class="line"> <span class="keywordflow">if</span> (argc < 3)</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>();</div>
<div class="line"> <span class="keywordflow">return</span> 1;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> std::vector<char> seq_vect;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">try</span></div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> ret = <a class="code" href="xsample04_8cpp.html#a1c6cda197a32141227af69a440929ac6">parse_args</a>(argc, argv);</div>
<div class="line"> <span class="keywordflow">if</span> (ret != 0)</div>
<div class="line"> <span class="keywordflow">return</span> ret;</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a> idx;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (!<a class="code" href="xsample04_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a>.empty())</div>
<div class="line"> {</div>
<div class="line"> <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"> <span class="keywordflow">if</span> (res != 0)</div>
<div class="line"> <span class="keywordflow">return</span> res;</div>
<div class="line"> std::cout << <span class="stringliteral">"FASTA sequence size="</span> << seq_vect.size() << std::endl;</div>
<div class="line"> </div>
<div class="line"> {</div>
<div class="line"> <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"> idx.<a name="a33"></a><a class="code" href="classDNA__FingerprintScanner.html#a5ac470fd81df0a04ea1b298a55dba5bb">Build</a>(seq_vect);</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (<a class="code" href="xsample04_8cpp.html#a2c4a694dfd3f687d8cc845046ae5c30a">is_search</a>)</div>
<div class="line"> {</div>
<div class="line"> vector<tuple<string,int> > h_words;</div>
<div class="line"> vector<tuple<string,int> > l_words;</div>
<div class="line"> </div>
<div class="line"> 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"> </div>
<div class="line"> <span class="comment">// generate search sets for benchmarking</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <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"> </div>
<div class="line"> </div>
<div class="line"> vector<THitList> word_hits;</div>
<div class="line"> vector<THitList> word_hits_agg;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// search all words in one pass and</span></div>
<div class="line"> <span class="comment">// store results in list of hits according to the order of words</span></div>
<div class="line"> <span class="comment">// (this method uses memory proximity</span></div>
<div class="line"> <span class="comment">// of searched words to maximize CPU cache hit rate)</span></div>
<div class="line"> </div>
<div class="line"> {</div>
<div class="line"> vector<const char*> word_list;</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& w : words)</div>
<div class="line"> {</div>
<div class="line"> word_list.push_back(get<0>(w).c_str());</div>
<div class="line"> }</div>
<div class="line"> word_hits.resize(words.size());</div>
<div class="line"> for_each(word_hits.begin(), word_hits.end(), [](<a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a>& ht) {</div>
<div class="line"> ht.reserve(12000);</div>
<div class="line"> });</div>
<div class="line"> </div>
<div class="line"> <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"> <span class="keywordtype">unsigned</span>(words.size()), &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> <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"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// collection search, runs all hits at once</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> {</div>
<div class="line"> <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"> <span class="keywordtype">unsigned</span>(words.size()), &<a class="code" href="xsample04_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> </div>
<div class="line"> idx.<a name="a34"></a><a class="code" href="classDNA__FingerprintScanner.html#abff5b0264b9397cc1137334f2ec2a4b5">FindCollection</a>(words, word_hits_agg);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// a few variants of word-by-word searches</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> word_idx = 0; word_idx < words.size(); ++ word_idx)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span>& word = get<0>(words[word_idx]);</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> hits1;</div>
<div class="line"> </div>
<div class="line"> {</div>
<div class="line"> <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 class="code" href="xsample04_8cpp.html#ad5e2b9cf1214f70b8b60fdd248da5703">find_word_2way</a>(seq_vect,</div>
<div class="line"> word.c_str(), <span class="keywordtype">unsigned</span>(word.size()),</div>
<div class="line"> hits1);</div>
<div class="line"> }</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> hits2;</div>
<div class="line"> {</div>
<div class="line"> <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"> idx.<a name="a35"></a><a class="code" href="classDNA__FingerprintScanner.html#a35ab54ce8d56bb16f150cffd7c308bab">Find</a>(word, hits2);</div>
<div class="line"> }</div>
<div class="line"> <a class="code" href="xsample04_8cpp.html#a20a9f23a3245391824c91b2f3b43e09e">THitList</a> hits4;</div>
<div class="line"> {</div>
<div class="line"> <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"> idx.<a name="a36"></a><a class="code" href="classDNA__FingerprintScanner.html#a1e7605fd131e0cdf5471a4c335996e8a">FindAggFused</a>(word, hits4);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// check correctness</span></div>
<div class="line"> <span class="keywordflow">if</span> (!<a class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(hits1, hits2)</div>
<div class="line"> || !<a class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(hits2, hits4))</div>
<div class="line"> {</div>
<div class="line"> cout << <span class="stringliteral">"Mismatch ERROR for: "</span> << word << endl;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> <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 class="code" href="xsample04_8cpp.html#a83cc2d037a5af2472ec8218eea2e567f">hitlist_compare</a>(word_hits_agg[word_idx], hits1))</div>
<div class="line"> {</div>
<div class="line"> cout << <span class="stringliteral">"Sigle pass mismatch ERROR for: "</span> << word << endl;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> {</div>
<div class="line"> cout << word_idx << <span class="stringliteral">": "</span> << word << <span class="stringliteral">": "</span> << hits1.size() << <span class="stringliteral">" hits "</span> << endl;</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <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"> {</div>
<div class="line"> std::cout << std::endl << <span class="stringliteral">"Performance:"</span> << std::endl;</div>
<div class="line"> <a name="a37"></a><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 name="a38"></a><a class="code" href="classbm_1_1chrono__taker.html#a9a41e5f2fe48ba472fd77a1dbd86457da86a293fae2205928a132bdf4e1b69996">bm::chrono_taker::ct_all</a>);</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">catch</span> (std::exception& ex)</div>
<div class="line"> {</div>
<div class="line"> std::cerr << <span class="stringliteral">"Error:"</span> << ex.what() << std::endl;</div>
<div class="line"> <span class="keywordflow">return</span> 1;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line">}</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"><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="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="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="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="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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