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<div class="title">primer_bed.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 <vector></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 <fstream></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> </div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include "primer_bed.h"</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> </div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> std::string primer::get_name(){</div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span>  <span class="keywordflow">return</span> name;</div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> }</div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> std::string primer::get_region(){</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  <span class="keywordflow">return</span> region;</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</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="keywordtype">int</span> primer::get_score(){</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <span class="keywordflow">return</span> score;</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> </div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> primer::get_start(){</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keywordflow">return</span> start;</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> }</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> primer::get_end(){</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  <span class="keywordflow">return</span> end;</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> }</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="keywordtype">char</span> primer::get_strand(){</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordflow">return</span> strand;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> }</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keywordtype">int</span> primer::get_length(){</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">return</span> end - start + 1;</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> </div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keywordtype">void</span> primer::set_start(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> s){</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  start = s;</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> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">void</span> primer::set_end(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> e){</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  end = e;</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> }</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keywordtype">void</span> primer::set_strand(<span class="keywordtype">char</span> s){</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  strand = s;</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> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keywordtype">void</span> primer::set_region(std::string r){</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  region = r;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> }</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keywordtype">void</span> primer::set_name(std::string n){</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  name = n;</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="keywordtype">void</span> primer::set_score(<span class="keywordtype">int</span> s){</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  score = s;</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> </div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> std::vector<primer> populate_from_file(std::string path){</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  std::ifstream data(path);</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  std::string line;</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  std::vector<primer> primers;</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">while</span>(std::getline(data,line)){ <span class="comment">// Remove extra lineStream</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  std::stringstream lineStream(line);</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  std::string cell;</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">int</span> ctr = 0;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <a class="code" href="classprimer.html">primer</a> p;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keywordflow">while</span>(std::getline(lineStream,cell,<span class="charliteral">'\t'</span>)){</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">switch</span>(ctr){</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordflow">case</span> 0:</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  p.set_region(cell);</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">case</span> 1:</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  p.set_start(std::stoul(cell));</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordflow">case</span> 2:</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  p.set_end(std::stoul(cell)-1); <span class="comment">// Bed format - End is not 0 based</span></div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordflow">case</span> 3:</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  p.set_name(cell);</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordflow">case</span> 4:</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  p.set_score(std::stoi(cell));</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordflow">case</span> 5:</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  p.set_strand(cell[0]);</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  }</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  ctr++;</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>  primers.push_back(p);</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  }</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordflow">return</span> primers;</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> }</div><div class="ttc" id="classprimer_html"><div class="ttname"><a href="classprimer.html">primer</a></div><div class="ttdef"><b>Definition:</b> <a href="primer__bed_8h_source.html#l00007">primer_bed.h:7</a></div></div>
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