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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 "algorithm"</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include "fstream"</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> </div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include "suffix_tree.h"</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include "alignment.h"</span></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> suffix_node::suffix_node(<span class="keywordtype">int</span> b, <span class="keywordtype">int</span> *e, <a class="code" href="classsuffix__node.html">suffix_node</a> *p, <a class="code" href="classsuffix__node.html">suffix_node</a> *l){</div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span>  this->children = <span class="keyword">new</span> <a class="code" href="classsuffix__node.html">suffix_node</a>*[MAX_CHAR];</div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i < MAX_CHAR;i++)</div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  this->children[i] = 0;</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  this->begin = b;</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  this->end = e;</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  this->nchildren = 0;</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  this->parent = p;</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  this->suffix_link =l;</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">bool</span> suffix_node::is_leaf_node(){</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keywordflow">return</span> (nchildren == 0);</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">bool</span> suffix_node::contains_child(<span class="keywordtype">int</span> ext){</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  <span class="keywordflow">return</span> !(this->children[ext] == 0);</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">int</span> suffix_node::get_length(){</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordflow">if</span>(this->end == 0)</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordflow">return</span> 0; <span class="comment">// For root</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keywordflow">return</span> *(this->end) - this->begin + 1;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> }</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="keywordtype">int</span> suffix_node::get_depth(){</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordtype">int</span> ctr = 0;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <a class="code" href="classsuffix__node.html">suffix_node</a>* n = <span class="keyword">this</span>;</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">while</span>(n->begin!=-1){</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  n = n->parent;</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  ctr++;</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  }</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">return</span> ctr;</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">int</span> get_hamming_distance(std::string s1, std::string s2, <span class="keywordtype">int</span> k){</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">int</span> n = 0;</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i < s1.length(); i++){</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordflow">if</span>(s1[i] != s2[i]){</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  n++;</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">if</span>(n > k)</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  }</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordflow">return</span> 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> std::string suffix_node::get_longest_common_substring(std::string s1, std::string s2){</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  std::string str = s1+<span class="stringliteral">"#"</span>+s2+<span class="stringliteral">"@"</span>;</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  std::string p=<span class="stringliteral">""</span>, tmp, longest_trvsl = <span class="stringliteral">""</span>;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> max = 0, i;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <a class="code" href="classsuffix__node.html">suffix_node</a>* node = <span class="keyword">this</span>;</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordflow">if</span>(node->begin == -1)</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  p = <span class="stringliteral">""</span>;</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordflow">else</span>{</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  tmp = node->get_path(str);</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordflow">if</span>(s1.find(p+tmp) != std::string::npos && s2.find(p+tmp) != std::string::npos)</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  p += tmp;</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>  tmp = <span class="stringliteral">""</span>;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keywordflow">for</span>(i = 0; i < MAX_CHAR;i++){</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">if</span>(node->children[i] == 0)</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  longest_trvsl = node->children[i]->get_longest_common_substring(s1, s2);</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">if</span>(longest_trvsl.length() > max){</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  max = longest_trvsl.length();</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  tmp = longest_trvsl;</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</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>  p += tmp;</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">return</span> p;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> }</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::string suffix_node::get_path(std::string s){</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordflow">if</span>(this->begin == -1)</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordflow">return</span> <span class="stringliteral">"R"</span>;</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordflow">return</span> s.substr(this->begin, *(this->end) - this->begin + 1);</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> }</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <span class="keywordtype">void</span> suffix_node::extend_path(<span class="keywordtype">int</span> *e){</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  this->end = e;</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> </div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <a class="code" href="classsuffix__node.html">suffix_node</a>* suffix_node::add_child(<span class="keywordtype">int</span> ext, <span class="keywordtype">int</span> b, <span class="keywordtype">int</span> *e, <a class="code" href="classsuffix__node.html">suffix_node</a>* l){</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="classsuffix__node.html">suffix_node</a> *n = <span class="keyword">new</span> <a class="code" href="classsuffix__node.html">suffix_node</a>(b, e, <span class="keyword">this</span>, l);</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  this->children[ext] = n;</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  this->nchildren++;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordflow">return</span> n;</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> }</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> <span class="keywordtype">void</span> suffix_node::add_child(<a class="code" href="classsuffix__node.html">suffix_node</a>* c, <span class="keywordtype">int</span> ext){</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  this->children[ext] = c;</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  c->parent = <span class="keyword">this</span>;</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  this->nchildren++;</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> }</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <a class="code" href="classsuffix__node.html">suffix_node</a>* suffix_node::get_child(<span class="keywordtype">int</span> ext){</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordflow">return</span> this->children[ext];</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> }</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="keywordtype">bool</span> suffix_node::contains_depth(<span class="keywordtype">int</span> depth){</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordflow">return</span> this->get_depth() <= depth && depth <= (this->get_length() + this->get_depth());</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</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> <span class="keywordtype">void</span> suffix_node::print(std::string s){</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i < this->get_depth(); i++){</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  std::cout << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  }</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  std::string t = (this->begin == -1) ? <span class="stringliteral">"R"</span> : <span class="stringliteral">" "</span>+s.substr(this->begin, *(this->end) - this->begin + 1);</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  std::cout << t;</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordflow">if</span>(this->suffix_link != 0)</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  std::cout << <span class="stringliteral">" --- ( "</span> << this->suffix_link->parent->get_path(s) << <span class="stringliteral">" "</span> << this->suffix_link->get_path(s) << <span class="stringliteral">")"</span>;</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordflow">if</span>(this->begin!=-1)</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  std::cout << <span class="stringliteral">" - "</span> << this->parent->get_path(s);</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  std::cout << std::endl;</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i<alphabet.length();i++){</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordflow">if</span>(this->children[i]!=0)</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  this->children[i]->print(s);</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> }</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> <span class="keywordtype">bool</span> suffix_node::walk_next(<span class="keywordtype">int</span> &beg, <span class="keywordtype">int</span> &suffix_length){</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <a class="code" href="classsuffix__node.html">suffix_node</a> *node = <span class="keyword">this</span>;</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">if</span>(suffix_length >= node->get_length()){</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  beg += node->get_length();</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  suffix_length -= node->get_length();</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  }</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> }</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <a class="code" href="classsuffix__node.html">suffix_node</a>* build_suffix_tree(std::string s){</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <a class="code" href="classsuffix__node.html">suffix_node</a> *root = <span class="keyword">new</span> <a class="code" href="classsuffix__node.html">suffix_node</a>(-1,0,0,0);</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  root->suffix_link = root;</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  root->parent = root;</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <a class="code" href="classsuffix__node.html">suffix_node</a> *cur_node = root, *new_node = 0, *new_cur_node = 0;</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordtype">int</span> str_ind[MAX_SIZE], suffix_length = 0, *leaf_end= <span class="keyword">new</span> int, suffix_count = 0, beg = -1, *end;</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0, n_str_ind = 0;</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">for</span>(i = 0; i < s.length();i++){</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  str_ind[i] = alphabet.find(s[i]);</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  n_str_ind++;</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  }</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  *leaf_end = 0;</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">// root->add_child(str_ind[0], 0, leaf_end, root);</span></div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordflow">for</span>(i = 0; i < n_str_ind;i++){</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  *leaf_end = i; <span class="comment">// Handle Extension Rule 1</span></div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  suffix_count++;</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  new_node = 0;</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keywordflow">while</span>(suffix_count > 0){</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">if</span>(suffix_length == 0)</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  beg = i;</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">if</span>(cur_node->children[str_ind[beg]] == 0){ <span class="comment">// Rule 2</span></div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  cur_node->add_child(str_ind[beg], beg, leaf_end, 0); <span class="comment">// Trick 3</span></div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keywordflow">if</span>(new_node != 0){</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  new_node->suffix_link = cur_node;</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  new_node = 0; <span class="comment">// No internal node created in Rule 2 here.</span></div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  }</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  new_cur_node = cur_node->children[str_ind[beg]];</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordflow">if</span>(new_cur_node->walk_next(beg, suffix_length)){</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  cur_node = new_cur_node;</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  }</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordflow">if</span>(str_ind[new_cur_node->begin + suffix_length] == str_ind[i]){ <span class="comment">// Rule 3</span></div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">if</span>(new_node != 0 && cur_node->end != 0){</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  new_node->suffix_link = cur_node;</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  new_node = 0; <span class="comment">// No internal node created in Rule 2 here.</span></div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  }</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  suffix_length++;</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  }</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// Rule 2 - New internal node created</span></div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <a class="code" href="classsuffix__node.html">suffix_node</a> *new_int_node;</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  end = <span class="keyword">new</span> int;</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  *end = new_cur_node->begin + suffix_length - 1;</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="comment">//New internal node</span></div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  new_int_node = cur_node->add_child(str_ind[beg], new_cur_node->begin, end, 0);</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  new_int_node->add_child(str_ind[i], i, leaf_end, 0);</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  new_cur_node->begin += suffix_length;</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  new_int_node->add_child(new_cur_node, str_ind[new_cur_node->begin]);</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">if</span>(new_node != 0)</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  new_node->suffix_link = new_int_node;</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  new_node = new_int_node;</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  }</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  suffix_count--;</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordflow">if</span>(cur_node->end==0 && suffix_length > 0){</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  suffix_length--;</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  beg = i - suffix_count + 1;</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(cur_node->end!=0){</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="keywordflow">if</span>(cur_node->suffix_link != 0){</div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  cur_node = cur_node->suffix_link;</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  cur_node = cur_node->parent->suffix_link;</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  }</div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(cur_node->get_length() == 1){</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  cur_node = root;</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  }</div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  }</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  }</div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordflow">return</span> root;</div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span> }</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span> </div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span> std::string get_reverse_complement(std::string rev_read){</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <span class="keywordtype">char</span> t;</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0;i< rev_read.length();i++){</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordflow">switch</span>(rev_read[i]){</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="keywordflow">case</span> <span class="charliteral">'A'</span>:</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  t = <span class="charliteral">'T'</span>;</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordflow">case</span> <span class="charliteral">'G'</span>:</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  t=<span class="charliteral">'C'</span>;</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="keywordflow">case</span> <span class="charliteral">'C'</span>:</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  t=<span class="charliteral">'G'</span>;</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  t=<span class="charliteral">'A'</span>;</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  }</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  rev_read[i] = t;</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  }</div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  std::reverse(rev_read.begin(), rev_read.end());</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="keywordflow">return</span> rev_read;</div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span> }</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span> </div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> std::vector<std::string> read_adapters_from_fasta(std::string p){</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  std::vector<std::string> adp;</div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  std::ifstream fin(p);</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  std::string line;</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordflow">while</span> (std::getline(fin, line)){</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordflow">if</span>(line[0] == <span class="charliteral">'>'</span>)</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  adp.push_back(line);</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  }</div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordflow">return</span> adp;</div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span> }</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span> </div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span> std::string extend_till_mismatches(std::string cmn, std::string l, std::string adp){</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="keywordflow">if</span>(cmn.length() < MIN_LENGTH){</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordflow">return</span> cmn;</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  }</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordtype">int</span> pos = adp.find(cmn);</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="keywordtype">int</span> r_pos = l.find(cmn);</div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="keywordflow">if</span>(pos == 0) <span class="comment">// Beginning of adapter match</span></div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">return</span> cmn;</div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="keywordtype">int</span> k = 0;</div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  pos--;</div><div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  r_pos--;</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">while</span>(r_pos >= 0 && pos >= 0 && k <= MAX_MISMATCHES){</div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  cmn = l[r_pos] + cmn;</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordflow">if</span>(l[r_pos]!=adp[pos])</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  k++;</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  r_pos--;</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  pos--;</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  }</div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keywordflow">return</span> cmn;</div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span> }</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span> </div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span> <span class="keywordtype">int</span> trim_adapter(std::string f1, std::string f2, std::string adp_path, std::string p){</div><div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  std::string l1, l2, l1_rc, l2_rc, s, cmn, trmd_read;</div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordtype">int</span> *t = <span class="keyword">new</span> <span class="keywordtype">int</span>[2], beg;</div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> pos;</div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  std::ifstream ff1(f1), ff2, pf(p);</div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  std::ofstream out(p+<span class="stringliteral">".trimmed.fastq"</span>);</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  std::vector<std::string>::iterator it;</div><div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <a class="code" href="classsuffix__node.html">suffix_node</a> *root = (<a class="code" href="classsuffix__node.html">suffix_node</a>*) malloc(<span class="keyword">sizeof</span>(<a class="code" href="classsuffix__node.html">suffix_node</a>));</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  std::vector<std::string> adp = read_adapters_from_fasta(adp_path);</div><div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <span class="keywordtype">int</span> i = -1, n = 0, adp_pos;</div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">if</span>(!f2.empty()){</div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  ff2.open(f2);</div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <span class="keywordflow">while</span> (std::getline(ff1, l1) && std::getline(ff2, l2)){</div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  i++;</div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordflow">if</span>((i - 1)%4 != 0)</div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  }</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keywordflow">while</span> (std::getline(ff1, l1)){</div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  i++;</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keywordflow">if</span>((i - 1)%4 != 0){</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  out << l1 << std::endl;</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  }</div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  beg = 0;</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  pos = l1.length();</div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  trmd_read = l1;</div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="keywordflow">for</span>(it = adp.begin(); it != adp.end(); ++it) {</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  s = l1 + <span class="stringliteral">"#"</span> + *it + <span class="stringliteral">"@"</span>;</div><div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  root = build_suffix_tree(s);</div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  cmn = root->get_longest_common_substring(l1, *it);</div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  cmn = extend_till_mismatches(cmn, l1, *it);</div><div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="keywordflow">if</span>(cmn.empty()){</div><div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  l1_rc = get_reverse_complement(l1);</div><div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  s = l1_rc + <span class="stringliteral">"#"</span> + *it + <span class="stringliteral">"@"</span>;</div><div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  root = build_suffix_tree(s);</div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  cmn = root->get_longest_common_substring(l1_rc, *it);</div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  cmn = extend_till_mismatches(cmn, l1_rc, *it);</div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  pos = l1_rc.find(cmn);</div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  beg = l1_rc.length() - pos;</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  adp_pos = (*it).find(cmn);</div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  beg = 0;</div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  pos = l1.find(cmn);</div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  adp_pos = (*it).find(cmn);</div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  }</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="keywordflow">if</span>(cmn.length() >= MIN_LENGTH && adp_pos != 0){</div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  beg = 0;</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  pos = l1.length();</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  t = align_seqs(l1, *it);</div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <span class="keywordflow">if</span>(*t != -1){</div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  beg = 0;</div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  pos = *(t+1);</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  std::cout << <span class="stringliteral">"Reverse!"</span> << std::endl;</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  l1_rc = get_reverse_complement(l1);</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  t = align_seqs(l1_rc, *it);</div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">if</span>(*t != -1){</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  pos = l1.length() - *(t+1);</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  beg = *(t+1);</div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  }</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  }</div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  }</div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  std::cout << beg << <span class="stringliteral">" "</span> << pos << std::endl;</div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordflow">if</span>(beg != 0 || pos != l1.length()){</div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  trmd_read = l1.substr(beg, pos);</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  n++;</div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  }</div><div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  }</div><div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  out << trmd_read << std::endl;</div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  }</div><div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  }</div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  std::cout << <span class="stringliteral">"Number of Adapter Trimmed: :"</span> << n << std::endl;</div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keyword">delete</span> root;</div><div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="keyword">delete</span>[] t;</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  ff1.close();</div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  ff2.close();</div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  pf.close();</div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span> }</div><div class="ttc" id="classsuffix__node_html"><div class="ttname"><a href="classsuffix__node.html">suffix_node</a></div><div class="ttdef"><b>Definition:</b> <a href="suffix__tree_8h_source.html#l00014">suffix_tree.h:14</a></div></div>
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