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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++: xsample04a.cpp</title>
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<div id="projectname">BitMagic-C++
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<div class="header">
<div class="headertitle">
<div class="title">xsample04a.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 xsample04a.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 xsample04a.cpp</span></div>
<div class="line"><span class="comment"> \brief Example: DNA index construction</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 <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"> </div>
<div class="line"><span class="preprocessor">#include <future></span></div>
<div class="line"><span class="preprocessor">#include <thread></span></div>
<div class="line"><span class="preprocessor">#include <mutex></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"> </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="xsample04a_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 Index Build 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">"-j number -- number of parallel jobs to run"</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="xsample04a_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a>;</div>
<div class="line"><span class="keywordtype">bool</span> <a name="a2"></a><a class="code" href="xsample04a_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">false</span>;</div>
<div class="line"><span class="keywordtype">unsigned</span> <a name="a3"></a><a class="code" href="xsample04a_8cpp.html#aeb19f159bbe1dcac8757cbf6b8c9a334">parallel_jobs</a> = 4;</div>
<div class="line"> </div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">int</span> <a name="a4"></a><a class="code" href="xsample04a_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="xsample04a_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>();</div>
<div class="line"> <span class="keywordflow">return</span> 0;</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="xsample04a_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"> <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-j"</span> || arg == <span class="stringliteral">"--j"</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="xsample04a_8cpp.html#aeb19f159bbe1dcac8757cbf6b8c9a334">parallel_jobs</a> = unsigned(::atoi(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: -j requires number of jobs"</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">"-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="xsample04a_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">true</span>;</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"> </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="a5"></a><a class="code" href="xsample04a_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="a6"></a><a class="code" href="xsample04a_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="_a7"></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="xsample04a_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="_a8"></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"> <a name="_a9"></a><a class="code" href="classbm_1_1bvector_1_1insert__iterator.html">bm::bvector<>::insert_iterator</a> iA = m_FPrintBV[eA].inserter();</div>
<div class="line"> <a class="code" href="classbm_1_1bvector_1_1insert__iterator.html">bm::bvector<>::insert_iterator</a> iC = m_FPrintBV[eC].inserter();</div>
<div class="line"> <a class="code" href="classbm_1_1bvector_1_1insert__iterator.html">bm::bvector<>::insert_iterator</a> iG = m_FPrintBV[eG].inserter();</div>
<div class="line"> <a class="code" href="classbm_1_1bvector_1_1insert__iterator.html">bm::bvector<>::insert_iterator</a> iT = m_FPrintBV[eT].inserter();</div>
<div class="line"> <a class="code" href="classbm_1_1bvector_1_1insert__iterator.html">bm::bvector<>::insert_iterator</a> iN = m_FPrintBV[eN].inserter();</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"> /// Build index using bulk insert iterator</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> BuildBulk(<span class="keyword">const</span> vector<char>& sequence)</div>
<div class="line"> {</div>
<div class="line"> <a name="_a10"></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="a11"></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"> </div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> /// Build fingerprint bit-vectors using bulk insert iterator and parallel</span></div>
<div class="line"><span class="comment"> /// processing</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> BuildParallel(<span class="keyword">const</span> vector<char>& sequence, <span class="keywordtype">unsigned</span> threads)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">struct </span>Func</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a>* target_idx;</div>
<div class="line"> <span class="keyword">const</span> std::vector<char>* src_sequence;</div>
<div class="line"> </div>
<div class="line"> Func(<a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a>* idx, <span class="keyword">const</span> vector<char>& src) </div>
<div class="line"> : target_idx(idx), src_sequence(&src) {}</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">void</span> operator() (<span class="keywordtype">size_t</span> from, <span class="keywordtype">size_t</span> to)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">const</span> vector<char>& sequence = *src_sequence;</div>
<div class="line"> <a name="_a12"></a><a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bvA, bvT, bvG, bvC, bvN;</div>
<div class="line"> </div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="classbm_1_1bvector_1_1bulk__insert__iterator.html">bm::bvector<>::bulk_insert_iterator</a> iA(bvA, <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(bvC, <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(bvG, <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(bvT, <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(bvN, <a class="code" href="group__bvector.html#gga04a7a7cda4bf04cd107e198b3b1e4ed8a78505da4a29a1a7e3381d9d28d41953e">bm::BM_SORTED</a>);</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = from; i < sequence.size() && (i < to); ++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"> } <span class="comment">// for</span></div>
<div class="line"> <span class="comment">// Bulk insert iterator keeps an buffer, which has to be</span></div>
<div class="line"> <span class="comment">// flushed, before all bits appear in the target vector</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> iA.flush();</div>
<div class="line"> iC.flush();</div>
<div class="line"> iT.flush();</div>
<div class="line"> iG.flush();</div>
<div class="line"> iN.flush();</div>
<div class="line"> }</div>
<div class="line"> <span class="comment">// merge results of parallel processing back to index</span></div>
<div class="line"> target_idx-><a name="a13"></a><a class="code" href="classDNA__FingerprintScanner.html#a745f01367c2d7ba05c7595c187b42b61">MergeVector</a>(<span class="charliteral">'A'</span>, bvA);</div>
<div class="line"> target_idx-><a class="code" href="classDNA__FingerprintScanner.html#a745f01367c2d7ba05c7595c187b42b61">MergeVector</a>(<span class="charliteral">'T'</span>, bvT);</div>
<div class="line"> target_idx-><a class="code" href="classDNA__FingerprintScanner.html#a745f01367c2d7ba05c7595c187b42b61">MergeVector</a>(<span class="charliteral">'G'</span>, bvG);</div>
<div class="line"> target_idx-><a class="code" href="classDNA__FingerprintScanner.html#a745f01367c2d7ba05c7595c187b42b61">MergeVector</a>(<span class="charliteral">'C'</span>, bvC);</div>
<div class="line"> target_idx-><a class="code" href="classDNA__FingerprintScanner.html#a745f01367c2d7ba05c7595c187b42b61">MergeVector</a>(<span class="charliteral">'N'</span>, bvN);</div>
<div class="line"> }</div>
<div class="line"> };</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (threads <= 1)</div>
<div class="line"> {</div>
<div class="line"> BuildBulk(sequence);</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// Create parallel async tasks running on a range of source sequence</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> std::vector<std::future<void> > futures;</div>
<div class="line"> futures.reserve(8);</div>
<div class="line"> <span class="keywordtype">unsigned</span> range = unsigned(sequence.size() / threads);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> k = 0; k < sequence.size(); k += range)</div>
<div class="line"> {</div>
<div class="line"> futures.emplace_back(std::async(std::launch::async,</div>
<div class="line"> Func(<span class="keyword">this</span>, sequence), k, k + range));</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// wait for all tasks</span></div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keyword">auto</span>& e : futures)</div>
<div class="line"> {</div>
<div class="line"> e.wait();</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> /// Thread sync bit-vector merge</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> MergeVector(<span class="keywordtype">char</span> letter, <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">static</span> std::mutex mtx_A;</div>
<div class="line"> <span class="keyword">static</span> std::mutex mtx_T;</div>
<div class="line"> <span class="keyword">static</span> std::mutex mtx_G;</div>
<div class="line"> <span class="keyword">static</span> std::mutex mtx_C;</div>
<div class="line"> <span class="keyword">static</span> std::mutex mtx_N;</div>
<div class="line"> </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"> {</div>
<div class="line"> std::lock_guard<std::mutex> guard(mtx_A);</div>
<div class="line"> m_FPrintBV[eA].merge(bv);</div>
<div class="line"> }</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"> {</div>
<div class="line"> std::lock_guard<std::mutex> guard(mtx_C);</div>
<div class="line"> m_FPrintBV[eC].merge(bv);</div>
<div class="line"> }</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"> {</div>
<div class="line"> std::lock_guard<std::mutex> guard(mtx_G);</div>
<div class="line"> m_FPrintBV[eG].merge(bv);</div>
<div class="line"> }</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"> {</div>
<div class="line"> std::lock_guard<std::mutex> guard(mtx_T);</div>
<div class="line"> m_FPrintBV[eT].merge(bv);</div>
<div class="line"> }</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"> {</div>
<div class="line"> std::lock_guard<std::mutex> guard(mtx_N);</div>
<div class="line"> m_FPrintBV[eN].merge(bv);</div>
<div class="line"> }</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 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"> </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">};</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Check correctness of indexes constructed using different methods</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="a14"></a><a class="code" href="xsample04a_8cpp.html#a965b42947a68d4c8d7a06095b48327ab">fingerprint_compare</a>(<span class="keyword">const</span> <a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a>& idx1,</div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a>& idx2)</div>
<div class="line">{</div>
<div class="line"> std::vector<char> letters {<span class="charliteral">'A'</span>, <span class="charliteral">'T'</span>, <span class="charliteral">'G'</span>, <span class="charliteral">'C'</span>};</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">char</span> base : letters)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv1 = idx1.<a name="a15"></a><a class="code" href="classDNA__FingerprintScanner.html#a8623c4721c296e6cc065ae6a2ceff980">GetVector</a>(base);</div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>& bv2 = idx2.<a class="code" href="classDNA__FingerprintScanner.html#a8623c4721c296e6cc065ae6a2ceff980">GetVector</a>(base);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">int</span> cmp = bv1.<a name="a16"></a><a class="code" href="classbm_1_1bvector.html#acfb4e0f923e55057db5ed518853fbecf">compare</a>(bv2);</div>
<div class="line"> <span class="keywordflow">if</span> (cmp != 0)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">throw</span> runtime_error(<span class="keywordtype">string</span>(<span class="stringliteral">"Fingerprint mismatch for:"</span>) + <span class="keywordtype">string</span>(1, base));</div>
<div class="line"> }</div>
<div class="line"> } <span class="comment">// for</span></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="a17"></a><a class="code" href="xsample04a_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="xsample04a_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="xsample04a_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> idx1;</div>
<div class="line"> <a class="code" href="classDNA__FingerprintScanner.html">DNA_FingerprintScanner</a> idx2;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (!<a class="code" href="xsample04a_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="xsample04a_8cpp.html#add74621cca7ebe5386556ba01bc35cd2">load_FASTA</a>(<a class="code" href="xsample04a_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="xsample04a_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> idx1.<a name="a18"></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"> <span class="keywordflow">if</span> (<a class="code" href="xsample04a_8cpp.html#aeb19f159bbe1dcac8757cbf6b8c9a334">parallel_jobs</a> > 0)</div>
<div class="line"> {</div>
<div class="line"> std::cout << <span class="stringliteral">"jobs = "</span> << <a class="code" href="xsample04a_8cpp.html#aeb19f159bbe1dcac8757cbf6b8c9a334">parallel_jobs</a> << std::endl;</div>
<div class="line"> <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"3. Build DNA index (bulk, parallel)"</span>, 1, &<a class="code" href="xsample04a_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> idx2.<a name="a19"></a><a class="code" href="classDNA__FingerprintScanner.html#a06afb87398746ccffae177848db1566e">BuildParallel</a>(seq_vect, <a class="code" href="xsample04a_8cpp.html#aeb19f159bbe1dcac8757cbf6b8c9a334">parallel_jobs</a>);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// compare results (correctness check)</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <a class="code" href="xsample04a_8cpp.html#a965b42947a68d4c8d7a06095b48327ab">fingerprint_compare</a>(idx1, idx2);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (<a class="code" href="xsample04a_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="a20"></a><a class="code" href="classbm_1_1chrono__taker.html#a30b45453d952d14afe56c29087970899">bm::chrono_taker::print_duration_map</a>(<a class="code" href="xsample04a_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>, <a name="a21"></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="axsample04a_8cpp_html_aeb19f159bbe1dcac8757cbf6b8c9a334"><div class="ttname"><a href="xsample04a_8cpp.html#aeb19f159bbe1dcac8757cbf6b8c9a334">parallel_jobs</a></div><div class="ttdeci">unsigned parallel_jobs</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00068">xsample04a.cpp:68</a></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="aclassbm_1_1bvector_1_1insert__iterator_html"><div class="ttname"><a href="classbm_1_1bvector_1_1insert__iterator.html">bm::bvector::insert_iterator</a></div><div class="ttdoc">Output iterator iterator designed to set "ON" bits based on input sequence of integers (bit indeces).</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00377">bm.h:377</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a06afb87398746ccffae177848db1566e"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a06afb87398746ccffae177848db1566e">DNA_FingerprintScanner::BuildParallel</a></div><div class="ttdeci">void BuildParallel(const vector< char > &sequence, unsigned threads)</div><div class="ttdoc">Build fingerprint bit-vectors using bulk insert iterator and parallel processing.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00234">xsample04a.cpp:234</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_1bvector_html_acfb4e0f923e55057db5ed518853fbecf"><div class="ttname"><a href="classbm_1_1bvector.html#acfb4e0f923e55057db5ed518853fbecf">bm::bvector::compare</a></div><div class="ttdeci">int compare(const bvector< Alloc > &bvect) const BMNOEXCEPT</div><div class="ttdoc">Lexicographical comparison with a bitvector.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l03159">bm.h:3159</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="axsample04a_8cpp_html_a9988650f5c236d5a70e710498d62904c"><div class="ttname"><a href="xsample04a_8cpp.html#a9988650f5c236d5a70e710498d62904c">ifa_name</a></div><div class="ttdeci">std::string ifa_name</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00066">xsample04a.cpp:66</a></div></div>
<div class="ttc" id="axsample04a_8cpp_html_a0ddf1224851353fc92bfbff6f499fa97"><div class="ttname"><a href="xsample04a_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a></div><div class="ttdeci">int main(int argc, char *argv[])</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00417">xsample04a.cpp:417</a></div></div>
<div class="ttc" id="aclassDNA__FingerprintScanner_html_a745f01367c2d7ba05c7595c187b42b61"><div class="ttname"><a href="classDNA__FingerprintScanner.html#a745f01367c2d7ba05c7595c187b42b61">DNA_FingerprintScanner::MergeVector</a></div><div class="ttdeci">void MergeVector(char letter, bm::bvector<> &bv)</div><div class="ttdoc">Thread sync bit-vector merge.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00324">xsample04a.cpp:324</a></div></div>
<div class="ttc" id="axsample04a_8cpp_html_aece8e90d91aaea144d41103f7d2825ee"><div class="ttname"><a href="xsample04a_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a></div><div class="ttdeci">bool is_timing</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00067">xsample04a.cpp:67</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="axsample04a_8cpp_html_a6cb51d150528a5d2d87acb3e88f450bc"><div class="ttname"><a href="xsample04a_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="xsample04a_8cpp_source.html#l00119">xsample04a.cpp:119</a></div></div>
<div class="ttc" id="axsample04a_8cpp_html_a81962ff36a3740bd2a6a458b74e57e26"><div class="ttname"><a href="xsample04a_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a></div><div class="ttdeci">static void show_help()</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00051">xsample04a.cpp:51</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="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="axsample04a_8cpp_html_a965b42947a68d4c8d7a06095b48327ab"><div class="ttname"><a href="xsample04a_8cpp.html#a965b42947a68d4c8d7a06095b48327ab">fingerprint_compare</a></div><div class="ttdeci">static void fingerprint_compare(const DNA_FingerprintScanner &idx1, const DNA_FingerprintScanner &idx2)</div><div class="ttdoc">Check correctness of indexes constructed using different methods.</div><div class="ttdef"><b>Definition:</b> <a href="xsample04a_8cpp_source.html#l00398">xsample04a.cpp:398</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="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="axsample04a_8cpp_html_add74621cca7ebe5386556ba01bc35cd2"><div class="ttname"><a href="xsample04a_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="xsample04a_8cpp_source.html#l00123">xsample04a.cpp:123</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="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="axsample04a_8cpp_html_a1c6cda197a32141227af69a440929ac6"><div class="ttname"><a href="xsample04a_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="xsample04a_8cpp_source.html#l00071">xsample04a.cpp:71</a></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>
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