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<div class="title">get_common_consensus.cpp</div> </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include<iostream></span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#include<iterator></span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include<sstream></span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include<vector></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include<fstream></span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> </div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="keyword">const</span> uint32_t MAX_SIZE = 100000;</div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> </div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="keywordtype">bool</span> check_if_equal(<span class="keywordtype">char</span>** n, <span class="keywordtype">int</span> n_size, std::ifstream *f){</div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span>  <span class="keywordflow">if</span>(*n[0] == <span class="charliteral">'\n'</span> || *n[0] == <span class="charliteral">'\0'</span> || *n[0]==EOF || f[0].eof())</div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 1; i < n_size;i++){</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  <span class="keywordflow">if</span>(*n[i] != *n[0] || *n[i] == <span class="charliteral">'\0'</span> || *n[i] == <span class="charliteral">'\n'</span> || *n[0]==EOF || f[i].eof())</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  }</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> }</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keywordtype">int</span> compare_consensus(<span class="keywordtype">char</span>** f, <span class="keywordtype">int</span> n_string, std::string out){</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  std::ifstream *cns = <span class="keyword">new</span> std::ifstream[n_string];</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  std::ofstream o(out+<span class="stringliteral">".fa"</span>);</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  o << <span class="stringliteral">">Common_Consensus"</span> << std::endl;</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordtype">int</span> i, j;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  <span class="keywordtype">char</span>** l = <span class="keyword">new</span> <span class="keywordtype">char</span>*[n_string];</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  <span class="keywordflow">for</span>(i = 0; i < n_string;i++){</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  std::cout << f[i+1] << std::endl;</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  l[i] = <span class="keyword">new</span> char;</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  cns[i].open(f[i + 1]);</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  cns[i].read(l[i], 1);</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordflow">if</span>(*l[i]!=<span class="charliteral">'>'</span>){</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  std::cout << <span class="stringliteral">"Error "</span> << f[i] << <span class="stringliteral">" is not a fasta file."</span> << std::endl;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  }</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordflow">while</span>(*l[i] !=<span class="charliteral">'\n'</span>){</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  cns[i].read(l[i], 1);</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  }</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  cns[i].read(l[i], 1); <span class="comment">// Read next character after \n</span></div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  }</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="comment">// Get to beginning of matching substring</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordflow">while</span>(!check_if_equal(l, n_string, cns)){</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">for</span>(j = 0; j<n_string;j++){</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  cns[j].read(l[j], 1);</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  }</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  }</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordflow">for</span>(j = 0; j < n_string; j++)</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordflow">if</span>(*l[j] == EOF){</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  std::cout << <span class="stringliteral">"Warning: No common regions between consensus sequences"</span> << std::endl;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  }</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordflow">while</span>(check_if_equal(l, n_string, cns)){</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  o << *l[0];</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordflow">for</span>(j = 0; j<n_string;j++){</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  cns[j].read(l[j], 1);</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>  }</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">for</span>(i = 0; i < n_string; i++){</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  cns[i].close();</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>  o.close();</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">delete</span>[] cns;</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">delete</span>[] l;</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> }</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keywordtype">int</span> <a class="code" href="ivar_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a>(<span class="keywordtype">int</span> argv, <span class="keywordtype">char</span>** argc){</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  compare_consensus(argc, argv - 1, <span class="stringliteral">"test"</span>);</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> }</div><div class="ttc" id="ivar_8cpp_html_a0ddf1224851353fc92bfbff6f499fa97"><div class="ttname"><a href="ivar_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a></div><div class="ttdeci">int main(int argc, char *argv[])</div><div class="ttdef"><b>Definition:</b> <a href="ivar_8cpp_source.html#l00144">ivar.cpp:144</a></div></div>
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