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<a href="svsample09_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">Copyright(c) 2002-2019 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"></span> </div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">Licensed under the Apache License, Version 2.0 (the "License");</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">you may not use this file except in compliance with the License.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">You may obtain a copy of the License at</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"></span> </div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> http://www.apache.org/licenses/LICENSE-2.0</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"></span> </div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">Unless required by applicable law or agreed to in writing, software</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">distributed under the License is distributed on an "AS IS" BASIS,</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">See the License for the specific language governing permissions and</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">limitations under the License.</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"></span> </div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">For more information please visit: http://bitmagic.io</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment"></span> </div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">/** \example svsample09.cpp</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment"> Use of sparse vector for compressed DNA strings (2 bits per bp)</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment"> Construction of comparison functions on bit-transposed compressed</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment"> containers, benchmarking.</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment"> </span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment"> \sa bm::sparse_vector</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment"> \sa bm::sparse_vector_find_first_mismatch</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment"></span> </div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment"> \sa bm::bvector<>::find_first_mismatch()</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment"></span> </div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment"></span> </div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">/*! \file svsample09.cpp</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment"> \brief Example: Use of sparse vector mismatch search</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#include <assert.h></span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#include <stdlib.h></span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  </div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <utility></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  </div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include "<a class="code" href="bm_8h.html">bm.h</a>"</span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include "<a class="code" href="bmsparsevec_8h.html">bmsparsevec.h</a>"</span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include "<a class="code" href="bmsparsevec__algo_8h.html">bmsparsevec_algo.h</a>"</span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">using namespace </span>std;</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  </div>
<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="svsample09_8cpp.html#a0d169ec2ee5a4e5265f850f56a3b3452"> 50</a></span> <span class="keyword">typedef</span> <a class="code" href="classbm_1_1sparse__vector.html">bm::sparse_vector<unsigned, bm::bvector<></a> > <a class="code" href="svsample09_8cpp.html#a0d169ec2ee5a4e5265f850f56a3b3452">svector_u32</a>;</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  </div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  </div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="svsample09_8cpp.html#a840291bc02cba5474a4cb46a9b9566fe"> 53</a></span> <span class="keywordtype">int</span> <a class="code" href="svsample09_8cpp.html#a840291bc02cba5474a4cb46a9b9566fe">main</a>(<span class="keywordtype">void</span>)</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> {</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  {</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> pos;</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  cout << <span class="stringliteral">"sparse vectors without NULL:"</span> << endl;</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  {</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv1, sv2;</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  </div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  sv1.<a class="code" href="classbm_1_1sparse__vector.html#a2f8aadebd1cfecd8e70fc771dbbd748d">push_back</a>(1);</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  sv1.<a class="code" href="classbm_1_1sparse__vector.html#a2f8aadebd1cfecd8e70fc771dbbd748d">push_back</a>(2);</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  sv1.<a class="code" href="classbm_1_1sparse__vector.html#a2f8aadebd1cfecd8e70fc771dbbd748d">push_back</a>(2);</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  sv1.<a class="code" href="classbm_1_1sparse__vector.html#a2f8aadebd1cfecd8e70fc771dbbd748d">push_back</a>(3);</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  sv2 = sv1;</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  </div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordtype">bool</span> found = <a class="code" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a>(sv1, sv2, pos);</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  std::cout << <span class="stringliteral">"Mismatch found."</span> << endl; <span class="comment">// this would be an error</span></div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  std::cout << <span class="stringliteral">"Mismatch not found"</span> << endl; <span class="comment">// identical vectors</span></div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  </div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="comment">// modify sv2 to introduce a mismatch</span></div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  sv2[2] = 0;</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  found = <a class="code" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a>(sv1, sv2, pos);</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  {</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  std::cout << <span class="stringliteral">"Mismatch found at: "</span> << pos << endl; <span class="comment">// at 2</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  }</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  }</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="comment">// bm::sparse_vector_find_first_mismatch works with NULL-able vectors</span></div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="comment">// first NULL (unsassigned) between vectors is a mimatch</span></div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  cout << endl << <span class="stringliteral">"sparse vectors with NULL:"</span> << endl;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  {</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv1(<a class="code" href="group__bvector.html#ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79">bm::use_null</a>);</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv2(<a class="code" href="group__bvector.html#ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79">bm::use_null</a>);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  </div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  sv1[1] = 1;</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  sv1[2] = 2;</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  sv1.<a class="code" href="classbm_1_1sparse__vector.html#a152b0daf6be6a12d3b814783f4be3017">set_null</a>(3); <span class="comment">// set element 3 to NULL</span></div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  sv1[4] = 0;</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  </div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  sv2 = sv1;</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">bool</span> found = <a class="code" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a>(sv1, sv2, pos);</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  std::cout << <span class="stringliteral">"Mismatch found."</span> << endl; <span class="comment">// this would be an error</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  std::cout << <span class="stringliteral">"Mismatch not found"</span> << endl; <span class="comment">// identical vectors</span></div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  sv2[4] = 10;</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  found = <a class="code" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a>(sv1, sv2, pos);</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  {</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  std::cout << <span class="stringliteral">"Mismatch found at: "</span> << pos << endl; <span class="comment">// at 4</span></div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  }</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  </div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="comment">// set element 3 to 0, now we have a situation when element 3 in both</span></div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="comment">// vectors has value 0, except it is NULL value in vector 1</span></div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">// mismatch search should detect it</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  sv2[3] = 0;</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  found = <a class="code" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a>(sv1, sv2, pos);</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  {</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  std::cout << <span class="stringliteral">"Mismatch found at: "</span> << pos << endl; <span class="comment">// at 3</span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  }</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  }</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  }</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordflow">catch</span>(std::exception& ex)</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  {</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  std::cerr << ex.what() << std::endl;</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  }</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  </div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  </div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> }</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  </div>
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<div class="ttc" id="abmsparsevec__algo_8h_html"><div class="ttname"><a href="bmsparsevec__algo_8h.html">bmsparsevec_algo.h</a></div><div class="ttdoc">Algorithms for bm::sparse_vector.</div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html"><div class="ttname"><a href="classbm_1_1sparse__vector.html">bm::sparse_vector</a></div><div class="ttdoc">sparse vector with runtime compression using bit transposition method</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00081">bmsparsevec.h:81</a></div></div>
<div class="ttc" id="abmsparsevec_8h_html"><div class="ttname"><a href="bmsparsevec_8h.html">bmsparsevec.h</a></div><div class="ttdoc">Sparse constainer sparse_vector<> for integer types using bit-transposition transform.</div></div>
<div class="ttc" id="agroup__bvector_html_ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79"><div class="ttname"><a href="group__bvector.html#ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79">bm::use_null</a></div><div class="ttdeci">@ use_null</div><div class="ttdoc">support "non-assigned" or "NULL" logic</div><div class="ttdef"><b>Definition:</b> <a href="bmconst_8h_source.html#l00215">bmconst.h:215</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a152b0daf6be6a12d3b814783f4be3017"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a152b0daf6be6a12d3b814783f4be3017">bm::sparse_vector::set_null</a></div><div class="ttdeci">void set_null(size_type idx)</div><div class="ttdoc">set specified element to unassigned value (NULL)</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00986">bmsparsevec.h:986</a></div></div>
<div class="ttc" id="agroup__svalgo_html_ga5b8ca92c5fff30f5b741fc95fe2b3199"><div class="ttname"><a href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a></div><div class="ttdeci">bool sparse_vector_find_first_mismatch(const SV &sv1, const SV &sv2, typename SV::size_type &midx, bm::null_support null_proc=bm::use_null)</div><div class="ttdoc">Find first mismatch (element which is different) between two sparse vectors (uses linear scan in bit-...</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__algo_8h_source.html#l00170">bmsparsevec_algo.h:170</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a2f8aadebd1cfecd8e70fc771dbbd748d"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a2f8aadebd1cfecd8e70fc771dbbd748d">bm::sparse_vector::push_back</a></div><div class="ttdeci">void push_back(value_type v)</div><div class="ttdoc">push value back into vector</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01498">bmsparsevec.h:1498</a></div></div>
<div class="ttc" id="asvsample09_8cpp_html_a840291bc02cba5474a4cb46a9b9566fe"><div class="ttname"><a href="svsample09_8cpp.html#a840291bc02cba5474a4cb46a9b9566fe">main</a></div><div class="ttdeci">int main(void)</div><div class="ttdef"><b>Definition:</b> <a href="svsample09_8cpp_source.html#l00053">svsample09.cpp:53</a></div></div>
<div class="ttc" id="asvsample09_8cpp_html_a0d169ec2ee5a4e5265f850f56a3b3452"><div class="ttname"><a href="svsample09_8cpp.html#a0d169ec2ee5a4e5265f850f56a3b3452">svector_u32</a></div><div class="ttdeci">bm::sparse_vector< unsigned, bm::bvector<> > svector_u32</div><div class="ttdef"><b>Definition:</b> <a href="svsample09_8cpp_source.html#l00050">svsample09.cpp:50</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="aclassbm_1_1sparse__vector_html_a0ce76a1e2cec9034664fb7ce4d5c23ae"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">bm::sparse_vector< unsigned, bm::bvector<> >::size_type</a></div><div class="ttdeci">bvector_type::size_type size_type</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00087">bmsparsevec.h:87</a></div></div>
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