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<li class="navelem"><a class="el" href="dir_b7a5fe10b55060f48179abd50ad1f335.html">rostlab</a></li> </ul>
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<a href="blast-result_8h.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) 2011 Laszlo Kajan, Technical University of Munich, Germany</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"> This file is part of librostlab.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"></span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> librostlab is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> it under the terms of the GNU Lesser General Public License as published by</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> (at your option) any later version.</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"></span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> This program is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> GNU Lesser General Public License for more details.</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"> You should have received a copy of the GNU Lesser General Public License</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment"> along with this program. If not, see <http://www.gnu.org/licenses/>.</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="preprocessor">#ifndef ROSTLAB_BLAST_RESULT_H</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#define ROSTLAB_BLAST_RESULT_H</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <stdint.h></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <sstream></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#include <rostlab/aux_functions.h></span></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> <span class="keyword">namespace </span><a class="code" href="namespacerostlab.html">rostlab</a> {</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">namespace </span>blast {</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div><div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html"> 32</a></span> <span class="keyword">struct </span><a class="code" href="structrostlab_1_1blast_1_1round.html">round</a> {</div><div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#a20014457c83e1b98684a393828b9f283"> 34</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#a20014457c83e1b98684a393828b9f283">oneline_idx</a>;</div><div class="line"><a name="l00036"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#a69a65504fc939e41824291ef829be3a7"> 36</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#a69a65504fc939e41824291ef829be3a7">oneline_cnt</a>;</div><div class="line"><a name="l00038"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#afb2be3e1a562764f98812553b11dee8e"> 38</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#afb2be3e1a562764f98812553b11dee8e">hit_idx</a>;</div><div class="line"><a name="l00040"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#abe78de9ade912edb4a449ce5b366e933"> 40</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#abe78de9ade912edb4a449ce5b366e933">hit_cnt</a>;</div><div class="line"><a name="l00042"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#aa061fbea3c2a1f288e7afaf297b53ce9"> 42</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#aa061fbea3c2a1f288e7afaf297b53ce9">oneline_new_idx</a>;</div><div class="line"><a name="l00044"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#aab2215bcb9285d328a2acb9e9682a107"> 44</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#aab2215bcb9285d328a2acb9e9682a107">oneline_new_cnt</a>;</div><div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#ad23b74c5b8d122c47a0d54be37aa0cda"> 45</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#ad23b74c5b8d122c47a0d54be37aa0cda">noidx</a> = <span class="keyword">static_cast<</span><span class="keywordtype">size_t</span><span class="keyword">></span>(-1);</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#a0d2c4122d5e867afa678f48fe368f009"> 47</a></span>  <a class="code" href="structrostlab_1_1blast_1_1round.html#a0d2c4122d5e867afa678f48fe368f009">round</a>( <span class="keywordtype">size_t</span> __oneline_idx = 0, <span class="keywordtype">size_t</span> __oneline_cnt = 0, <span class="keywordtype">size_t</span> __hit_idx = 0, <span class="keywordtype">size_t</span> __hit_cnt = 0, <span class="keywordtype">size_t</span> __oneline_new_idx = noidx, <span class="keywordtype">size_t</span> __oneline_new_cnt = 0 ) : oneline_idx( __oneline_idx), oneline_cnt(__oneline_cnt), hit_idx( __hit_idx ), hit_cnt(__hit_cnt), oneline_new_idx(__oneline_new_idx), oneline_new_cnt(__oneline_new_cnt){}</div><div class="line"><a name="l00048"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html#a8bebf94173ff4c6ccb1a4f151d651daa"> 48</a></span>  <span class="keyword">virtual</span> <a class="code" href="structrostlab_1_1blast_1_1round.html#a8bebf94173ff4c6ccb1a4f151d651daa">~round</a>(){}</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> </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="structrostlab_1_1blast_1_1hsp.html"> 53</a></span> <span class="keyword">struct </span><a class="code" href="structrostlab_1_1blast_1_1hsp.html">hsp</a> {</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7"> 56</a></span>  <span class="keyword">typedef</span> <span class="keyword">enum</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7">ECompoAdjustModes</a> {</div><div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7a2c12e463539311bc01711c4a109401f3"> 57</a></span>  eNoCompositionBasedStats = 0,</div><div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7adff245e5ac6c80ba48fb8ee5b130f3eb"> 58</a></span>  eCompositionBasedStats = 1,</div><div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7a9487b2a7f0e25c718d8fdad9e35a06fd"> 59</a></span>  eCompositionMatrixAdjust = 2,</div><div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7aed59ef0cae7de111307257cabf1b7ff1"> 60</a></span>  eCompoForceFullMatrixAdjust = 3,</div><div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7abb9bf00308b59a31b1315399488a01db"> 61</a></span>  eNumCompoAdjustModes</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  } <a class="code" href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7">ECompoAdjustModes</a>; <span class="comment">// ncbi-tools6-6.1.20090809/algo/blast/composition_adjustment/composition_constants.h:51 // a copy is made so we do not have to depend on that library only for this</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a418d58f03289123bc97314aa28612bce"> 64</a></span>  <span class="keywordtype">double</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a418d58f03289123bc97314aa28612bce">bit_score</a>;</div><div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#aaf207b4f63e9bcd357b2829affea1e2a"> 65</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#aaf207b4f63e9bcd357b2829affea1e2a">raw_score</a>;</div><div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a283e1f3a5819dc8d5240e74fd8316f1f"> 66</a></span>  <span class="keywordtype">double</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a283e1f3a5819dc8d5240e74fd8316f1f">e_value</a>;</div><div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#ae343db2eb236c2177c94c20d75f41595"> 67</a></span>  ECompoAdjustModes <a class="code" href="structrostlab_1_1blast_1_1hsp.html#ae343db2eb236c2177c94c20d75f41595">method</a>;</div><div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#adf63035ce02240a58d8656c32cf015e9"> 68</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#adf63035ce02240a58d8656c32cf015e9">identities</a>;</div><div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a02edceb41106dd8245f8fcb32e0caf03"> 69</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a02edceb41106dd8245f8fcb32e0caf03">positives</a>;</div><div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a8f23027eb2902176f5ecb74574c3f3d9"> 70</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a8f23027eb2902176f5ecb74574c3f3d9">gaps</a>;</div><div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#ae052c615e50b7902cead8934d65d8b54"> 72</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1hsp.html#ae052c615e50b7902cead8934d65d8b54">q_strand</a>;</div><div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a1a478153a91dc88cda04a6be5b5c2e02"> 74</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a1a478153a91dc88cda04a6be5b5c2e02">s_strand</a>;</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div><div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a3b2f013e9803afa48172664d5da386b6"> 77</a></span>  int8_t <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a3b2f013e9803afa48172664d5da386b6">q_frame</a>;</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div><div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#aa4cfa870754ec2243878cd5ae7c885c2"> 80</a></span>  int8_t <a class="code" href="structrostlab_1_1blast_1_1hsp.html#aa4cfa870754ec2243878cd5ae7c885c2">s_frame</a>;</div><div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#ab9636d83143b4e38d8b4f4d162374dd9"> 82</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#ab9636d83143b4e38d8b4f4d162374dd9">q_start</a>;</div><div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a587c9b737149284390266fd7eb3aae90"> 84</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a587c9b737149284390266fd7eb3aae90">q_ali</a>;</div><div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a50994b17ac23cf302100fd2991d2644f"> 86</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a50994b17ac23cf302100fd2991d2644f">q_end</a>;</div><div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a8662fd5b2c93832bbdeb23adea298a8c"> 88</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a8662fd5b2c93832bbdeb23adea298a8c">match_line</a>;</div><div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a6767b36cc92cda9a904b0fc249404bde"> 90</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a6767b36cc92cda9a904b0fc249404bde">s_start</a>;</div><div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#ad2f87e9740abec41b6e52201b0eadda5"> 92</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1hsp.html#ad2f87e9740abec41b6e52201b0eadda5">s_ali</a>;</div><div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a22cea63cd8cf103574a605d8b90f4c50"> 94</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a22cea63cd8cf103574a605d8b90f4c50">s_end</a>;</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#af82dd84c1d093225de32776f35314bd5"> 96</a></span>  <a class="code" href="structrostlab_1_1blast_1_1hsp.html#af82dd84c1d093225de32776f35314bd5">hsp</a>( <span class="keywordtype">double</span> __bit_score = 0, <span class="keywordtype">size_t</span> __raw_score = 0 ) : bit_score(__bit_score), raw_score(__raw_score), e_value(0), method(eNoCompositionBasedStats), identities(0), positives(0), gaps(0), q_frame(32), s_frame(32),</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  q_start(0), q_end(0), s_start(0), s_end(0){}</div><div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#ad648a0d22b886a1f51e0758aaedc1541"> 98</a></span>  <span class="keyword">virtual</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html#ad648a0d22b886a1f51e0758aaedc1541">~hsp</a>(){}</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keyword">inline</span> <span class="keyword">static</span> std::string</div><div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a1c0c3517db82e68550dc76df77723a21"> 108</a></span>  <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a1c0c3517db82e68550dc76df77723a21">methodstr</a>( <span class="keyword">const</span> ECompoAdjustModes __m )</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  {</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordflow">switch</span>( __m )</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>  <span class="keywordflow">case</span> eCompositionBasedStats:</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordflow">return</span> <span class="stringliteral">"Composition-based stats"</span>; <span class="keywordflow">break</span>;</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="keywordflow">case</span> eCompositionMatrixAdjust:</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordflow">return</span> <span class="stringliteral">"Compositional matrix adjust"</span>; <span class="keywordflow">break</span>;</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordflow">default</span>:</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  std::stringstream ss; ss << __m; <span class="keywordflow">return</span> ss.str();</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  }</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  }</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keyword">inline</span> <span class="keyword">static</span> ECompoAdjustModes</div><div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html#a5c05d26bd70c4adcdcf6907b36a39954"> 123</a></span>  <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a5c05d26bd70c4adcdcf6907b36a39954">methfromstr</a>( std::string __m )</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>  <span class="keywordflow">if</span>( __m.size() > 0 && __m[ __m.size()-1 ] == <span class="charliteral">'.'</span> ) __m.resize( __m.size()-1 );</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">// 1</span></div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="comment">// 012345678901</span></div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">// Composition-based stats</span></div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="comment">// Compositional matrix adjust</span></div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordflow">if</span>( __m.size() >= 12 )</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  {</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">if</span>( __m[11] == <span class="charliteral">'-'</span> ) <span class="keywordflow">return</span> eCompositionBasedStats;</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">if</span>( __m[11] == <span class="charliteral">'a'</span> ) <span class="keywordflow">return</span> eCompositionMatrixAdjust;</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>  <span class="keywordflow">return</span> eNoCompositionBasedStats;</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> };</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div><div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html"> 141</a></span> <span class="keyword">struct </span><a class="code" href="structrostlab_1_1blast_1_1hit.html">hit</a> {</div><div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html#af0f70425cc41a304b6bdbe3b0dcdb7a1"> 142</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1hit.html#af0f70425cc41a304b6bdbe3b0dcdb7a1">name</a>;</div><div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html#a65744ca4d3e6bce16e4adae1bbb696bb"> 143</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1hit.html#a65744ca4d3e6bce16e4adae1bbb696bb">desc</a>;</div><div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html#aa8228dc11dcf6b5c8bbf988a5a3c9a9e"> 145</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1hit.html#aa8228dc11dcf6b5c8bbf988a5a3c9a9e">length</a>;</div><div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html#ac8f7bd3ac9148992a66c067578fb3d58"> 146</a></span>  std::vector<hsp> <a class="code" href="structrostlab_1_1blast_1_1hit.html#ac8f7bd3ac9148992a66c067578fb3d58">hsps</a>;</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html#a7847e0f5d63534eb5f8908a5d9e043cb"> 148</a></span>  <a class="code" href="structrostlab_1_1blast_1_1hit.html#a7847e0f5d63534eb5f8908a5d9e043cb">hit</a>( <span class="keyword">const</span> std::string& __name = <span class="stringliteral">""</span>, <span class="keyword">const</span> std::string& __desc = <span class="stringliteral">""</span>, <span class="keywordtype">size_t</span> __length = 0 ) : name(__name), desc(__desc), length(__length) {}</div><div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html#a64797840c95a52f0180d1aece620377e"> 149</a></span>  <span class="keyword">virtual</span> <a class="code" href="structrostlab_1_1blast_1_1hit.html#a64797840c95a52f0180d1aece620377e">~hit</a>(){}</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> </div><div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html"> 153</a></span> <span class="keyword">struct </span><a class="code" href="structrostlab_1_1blast_1_1oneline.html">oneline</a> {</div><div class="line"><a name="l00154"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html#a3fbcd78ceac1b92d2d16bcb73ed09a7f"> 154</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1oneline.html#a3fbcd78ceac1b92d2d16bcb73ed09a7f">name</a>;</div><div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html#afaf02fa6e84bfaad7fc5d8bf26cc314f"> 155</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1oneline.html#afaf02fa6e84bfaad7fc5d8bf26cc314f">desc</a>;</div><div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html#a3cfca57c6ded9a2daa9ce77e0f004040"> 157</a></span>  <span class="keywordtype">double</span> <a class="code" href="structrostlab_1_1blast_1_1oneline.html#a3cfca57c6ded9a2daa9ce77e0f004040">bit_score</a>;</div><div class="line"><a name="l00158"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html#a12cf72720d730b7bdfa93521b4d3b933"> 158</a></span>  <span class="keywordtype">double</span> <a class="code" href="structrostlab_1_1blast_1_1oneline.html#a12cf72720d730b7bdfa93521b4d3b933">e_value</a>;</div><div class="line"><a name="l00159"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html#ad96e0307e8e645dfe3aba5d7aadd5e7e"> 159</a></span>  <a class="code" href="structrostlab_1_1blast_1_1oneline.html#ad96e0307e8e645dfe3aba5d7aadd5e7e">oneline</a>( <span class="keyword">const</span> std::string& __name = <span class="stringliteral">""</span>, <span class="keyword">const</span> std::string& __desc = <span class="stringliteral">""</span>, <span class="keywordtype">double</span> __bit_score = 0, <span class="keywordtype">double</span> __e_value = 0 ) : name(__name), desc(__desc), bit_score(__bit_score), e_value(__e_value){}</div><div class="line"><a name="l00160"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html#a5dacf3503b1c90cc3a381356e6b4d5e7"> 160</a></span>  <a class="code" href="structrostlab_1_1blast_1_1oneline.html#a5dacf3503b1c90cc3a381356e6b4d5e7">oneline</a>( <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1hit.html">hit</a>& __h ) : name(__h.name), desc(__h.desc), bit_score(__h.hsps.at(0).bit_score), e_value(__h.hsps.at(0).e_value){}</div><div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html#ab98dfee5b8690fe1257c47164b182f93"> 161</a></span>  <span class="keyword">virtual</span> <a class="code" href="structrostlab_1_1blast_1_1oneline.html#ab98dfee5b8690fe1257c47164b182f93">~oneline</a>(){}</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> };</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div><div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html"> 165</a></span> <span class="keyword">struct </span><a class="code" href="structrostlab_1_1blast_1_1result.html">result</a> {</div><div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a436ceffc106e8706c4a8a47eb04dff17"> 166</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structrostlab_1_1blast_1_1result.html#a436ceffc106e8706c4a8a47eb04dff17">empty</a>;</div><div class="line"><a name="l00167"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a8d1d7dde8b87ea8230948bf355cb6b6c"> 167</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1result.html#a8d1d7dde8b87ea8230948bf355cb6b6c">blast_version</a>;</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  std::vector<std::string></div><div class="line"><a name="l00169"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a8525a2fea583e9167f7bfd51589faf43"> 169</a></span>  <a class="code" href="structrostlab_1_1blast_1_1result.html#a8525a2fea583e9167f7bfd51589faf43">references</a>;</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  std::vector<rostlab::blast::round></div><div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#abab428d7a9f9e6f78a20e29321ee459c"> 172</a></span>  <a class="code" href="structrostlab_1_1blast_1_1result.html#abab428d7a9f9e6f78a20e29321ee459c">rounds</a>;</div><div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a316fbedbe5f98cfbe844e78679dbebb7"> 174</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1result.html#a316fbedbe5f98cfbe844e78679dbebb7">q_name</a>;</div><div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#aa9578da85b347db66328e7c4e15728f8"> 176</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1result.html#aa9578da85b347db66328e7c4e15728f8">q_desc</a>;</div><div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#af526ca95288ae2b023e9c71fd09ac7fe"> 178</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1result.html#af526ca95288ae2b023e9c71fd09ac7fe">q_length</a>;</div><div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#ad6c47a5c5964b571f395511523b07306"> 180</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1result.html#ad6c47a5c5964b571f395511523b07306">db_name</a>;</div><div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a788ab03e62122890f53fea49d0429a0a"> 182</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1result.html#a788ab03e62122890f53fea49d0429a0a">db_nseq</a>;</div><div class="line"><a name="l00184"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a8a85eacaee52d5a5d916cc28be8e92bf"> 184</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structrostlab_1_1blast_1_1result.html#a8a85eacaee52d5a5d916cc28be8e92bf">db_nletter</a>;</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  std::vector<rostlab::blast::oneline></div><div class="line"><a name="l00187"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a329c8c96f8a616d37a3ba48e4f1739b7"> 187</a></span>  <a class="code" href="structrostlab_1_1blast_1_1result.html#a329c8c96f8a616d37a3ba48e4f1739b7">onelines</a>;</div><div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a35a136ba09a81bdfddec789fad657164"> 189</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structrostlab_1_1blast_1_1result.html#a35a136ba09a81bdfddec789fad657164">converged</a>;</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  std::vector<rostlab::blast::hit></div><div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a660159704e5334ec0bd606e270abe27d"> 192</a></span>  <a class="code" href="structrostlab_1_1blast_1_1result.html#a660159704e5334ec0bd606e270abe27d">hits</a>;</div><div class="line"><a name="l00194"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a58bd767de4077f1ca154d103fa523900"> 194</a></span>  std::string <a class="code" href="structrostlab_1_1blast_1_1result.html#a58bd767de4077f1ca154d103fa523900">tail</a>;</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#ab9c59fe3193479880e965e44d0f379da"> 196</a></span>  <a class="code" href="structrostlab_1_1blast_1_1result.html#ab9c59fe3193479880e965e44d0f379da">result</a>() : empty(true), q_length(0), db_nseq(0), db_nletter(0), converged(false) {}</div><div class="line"><a name="l00197"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a8c4194988077ad1ef2f1fde6a2ab8d18"> 197</a></span>  <span class="keyword">virtual</span> <a class="code" href="structrostlab_1_1blast_1_1result.html#a8c4194988077ad1ef2f1fde6a2ab8d18">~result</a>(){}</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> </div><div class="line"><a name="l00201"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html#a9dc7a630ec438e487f4223b4560a7086"> 201</a></span>  <span class="keyword">operator</span> bool()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> !empty; }</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> </div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span> } <span class="comment">// namespace blast</span></div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span> </div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="keyword">inline</span></div><div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="namespacerostlab.html#a3659849ade911f89ce6aaf216ac25ce6"> 208</a></span> std::ostream& <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator<<</a>( std::ostream& __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1round.html">rostlab::blast::round</a>& __r )</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>  __os << <span class="stringliteral">"ol_idx = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#a20014457c83e1b98684a393828b9f283">oneline_idx</a> << <span class="stringliteral">", ol_cnt = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#a69a65504fc939e41824291ef829be3a7">oneline_cnt</a> << <span class="stringliteral">", hit_idx = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#afb2be3e1a562764f98812553b11dee8e">hit_idx</a> << <span class="stringliteral">", hit_cnt = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#abe78de9ade912edb4a449ce5b366e933">hit_cnt</a> << <span class="stringliteral">", ol_new_idx = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#aa061fbea3c2a1f288e7afaf297b53ce9">oneline_new_idx</a> << <span class="stringliteral">", ol_new_cnt = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#aab2215bcb9285d328a2acb9e9682a107">oneline_new_cnt</a>;</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span> }</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span> </div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="keyword">inline</span></div><div class="line"><a name="l00216"></a><span class="lineno"><a class="line" href="namespacerostlab.html#aeb29d130128ec9a0f13041d424b270ab"> 216</a></span> std::ostream& <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator<<</a>( std::ostream& __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1oneline.html">rostlab::blast::oneline</a>& __r )</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span> {</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  __os << <span class="stringliteral">"n = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#a3fbcd78ceac1b92d2d16bcb73ed09a7f">name</a> << <span class="stringliteral">" d = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#afaf02fa6e84bfaad7fc5d8bf26cc314f">desc</a> << <span class="stringliteral">": "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#a3cfca57c6ded9a2daa9ce77e0f004040">bit_score</a> << <span class="stringliteral">" bits, "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#a12cf72720d730b7bdfa93521b4d3b933">e_value</a> << <span class="stringliteral">" E"</span>;</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span> }</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span> <span class="keyword">inline</span></div><div class="line"><a name="l00224"></a><span class="lineno"><a class="line" href="namespacerostlab.html#a73042b1cf36aff9c6f2bce88da759ebe"> 224</a></span> std::ostream& <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator<<</a>( std::ostream& __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html">rostlab::blast::hsp</a>& __r )</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> {</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  __os << <span class="stringliteral">"bits = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a418d58f03289123bc97314aa28612bce">bit_score</a> << <span class="stringliteral">", raw = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#aaf207b4f63e9bcd357b2829affea1e2a">raw_score</a> << <span class="stringliteral">", E = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a283e1f3a5819dc8d5240e74fd8316f1f">e_value</a> << <span class="stringliteral">", method = "</span> << <a class="code" href="structrostlab_1_1blast_1_1hsp.html#a1c0c3517db82e68550dc76df77723a21">blast::hsp::methodstr</a>(__r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#ae343db2eb236c2177c94c20d75f41595">method</a>) << <span class="stringliteral">", ident = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#adf63035ce02240a58d8656c32cf015e9">identities</a> <<</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="stringliteral">", pos = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a02edceb41106dd8245f8fcb32e0caf03">positives</a> << <span class="stringliteral">", gaps = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a8f23027eb2902176f5ecb74574c3f3d9">gaps</a> << <span class="stringliteral">", q_strand = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#ae052c615e50b7902cead8934d65d8b54">q_strand</a> << <span class="stringliteral">", s_strand = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a1a478153a91dc88cda04a6be5b5c2e02">s_strand</a> << <span class="stringliteral">", q_frame = "</span> << (int)__r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a3b2f013e9803afa48172664d5da386b6">q_frame</a> <<</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="stringliteral">", s_frame = "</span> << (<span class="keywordtype">int</span>)__r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#aa4cfa870754ec2243878cd5ae7c885c2">s_frame</a> << <span class="stringliteral">", q_start = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#ab9636d83143b4e38d8b4f4d162374dd9">q_start</a> << <span class="stringliteral">", q_ali = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a587c9b737149284390266fd7eb3aae90">q_ali</a> << <span class="stringliteral">", q_end = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a50994b17ac23cf302100fd2991d2644f">q_end</a> << <span class="stringliteral">", match_line = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a8662fd5b2c93832bbdeb23adea298a8c">match_line</a> <<</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="stringliteral">", s_start = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a6767b36cc92cda9a904b0fc249404bde">s_start</a> << <span class="stringliteral">", s_ali = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#ad2f87e9740abec41b6e52201b0eadda5">s_ali</a> << <span class="stringliteral">", s_end = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a22cea63cd8cf103574a605d8b90f4c50">s_end</a>;</div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span> }</div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span> </div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> <span class="keyword">inline</span></div><div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="namespacerostlab.html#a8e0b3e6a8bfa4eee9b617279bda11e00"> 235</a></span> std::ostream& <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator<<</a>( std::ostream& __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1hit.html">rostlab::blast::hit</a>& __r )</div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span> {</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  __os << <span class="stringliteral">"n = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hit.html#af0f70425cc41a304b6bdbe3b0dcdb7a1">name</a> << <span class="stringliteral">" d = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hit.html#a65744ca4d3e6bce16e4adae1bbb696bb">desc</a> << <span class="stringliteral">" Length = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hit.html#aa8228dc11dcf6b5c8bbf988a5a3c9a9e">length</a> << <span class="stringliteral">" "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1hit.html#ac8f7bd3ac9148992a66c067578fb3d58">hsps</a>;</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span> }</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span> </div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span> <span class="keyword">inline</span></div><div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="namespacerostlab.html#a2e770bc9680b32ea928844d45623a837"> 243</a></span> std::ostream& <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator<<</a>( std::ostream& __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1result.html">rostlab::blast::result</a>& __r )</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>  __os << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a8d1d7dde8b87ea8230948bf355cb6b6c">blast_version</a> << <span class="stringliteral">"\n\nreferences: "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a8525a2fea583e9167f7bfd51589faf43">references</a> << <span class="stringliteral">"\n\nrounds: "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#abab428d7a9f9e6f78a20e29321ee459c">rounds</a> << <span class="stringliteral">"\n\nn = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a316fbedbe5f98cfbe844e78679dbebb7">q_name</a> << <span class="stringliteral">" d = "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#aa9578da85b347db66328e7c4e15728f8">q_desc</a> << <span class="stringliteral">" ("</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#af526ca95288ae2b023e9c71fd09ac7fe">q_length</a> <<</div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="stringliteral">" letters)\n\nDatabase: "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#ad6c47a5c5964b571f395511523b07306">db_name</a> << <span class="stringliteral">" "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a788ab03e62122890f53fea49d0429a0a">db_nseq</a> << <span class="stringliteral">" sequences; "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a8a85eacaee52d5a5d916cc28be8e92bf">db_nletter</a> << <span class="stringliteral">" total letters\n\none-line desc: "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a329c8c96f8a616d37a3ba48e4f1739b7">onelines</a> << <span class="stringliteral">"\n\n"</span> <<</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  ( __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a35a136ba09a81bdfddec789fad657164">converged</a> ? <span class="stringliteral">"CONVERGED!\n\n"</span> : <span class="stringliteral">""</span> ) << <span class="stringliteral">"hits: "</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a660159704e5334ec0bd606e270abe27d">hits</a> << <span class="stringliteral">"\n\n"</span> << __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a58bd767de4077f1ca154d103fa523900">tail</a>;</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordflow">return</span> __os;</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> </div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span> } <span class="comment">// namespace rostlab</span></div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span> </div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span> <span class="preprocessor">#endif // ROSTLAB_BLAST_RESULT_H</span></div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span> <span class="comment">// vim:et:ts=4:ai:</span></div><div class="ttc" id="structrostlab_1_1blast_1_1oneline_html_afaf02fa6e84bfaad7fc5d8bf26cc314f"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html#afaf02fa6e84bfaad7fc5d8bf26cc314f">rostlab::blast::oneline::desc</a></div><div class="ttdeci">std::string desc</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00155">blast-result.h:155</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a3b2f013e9803afa48172664d5da386b6"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a3b2f013e9803afa48172664d5da386b6">rostlab::blast::hsp::q_frame</a></div><div class="ttdeci">int8_t q_frame</div><div class="ttdoc">Query frame. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00077">blast-result.h:77</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a35a136ba09a81bdfddec789fad657164"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a35a136ba09a81bdfddec789fad657164">rostlab::blast::result::converged</a></div><div class="ttdeci">bool converged</div><div class="ttdoc">Indicates that the search has converged. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00189">blast-result.h:189</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_aaf207b4f63e9bcd357b2829affea1e2a"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#aaf207b4f63e9bcd357b2829affea1e2a">rostlab::blast::hsp::raw_score</a></div><div class="ttdeci">size_t raw_score</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00065">blast-result.h:65</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a5c05d26bd70c4adcdcf6907b36a39954"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a5c05d26bd70c4adcdcf6907b36a39954">rostlab::blast::hsp::methfromstr</a></div><div class="ttdeci">static ECompoAdjustModes methfromstr(std::string __m)</div><div class="ttdoc">Translate method description to mode code. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00123">blast-result.h:123</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1oneline_html_a12cf72720d730b7bdfa93521b4d3b933"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html#a12cf72720d730b7bdfa93521b4d3b933">rostlab::blast::oneline::e_value</a></div><div class="ttdeci">double e_value</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00158">blast-result.h:158</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hit_html"><div class="ttname"><a href="structrostlab_1_1blast_1_1hit.html">rostlab::blast::hit</a></div><div class="ttdoc">Blast hit. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00141">blast-result.h:141</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hit_html_ac8f7bd3ac9148992a66c067578fb3d58"><div class="ttname"><a href="structrostlab_1_1blast_1_1hit.html#ac8f7bd3ac9148992a66c067578fb3d58">rostlab::blast::hit::hsps</a></div><div class="ttdeci">std::vector< hsp > hsps</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00146">blast-result.h:146</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a283e1f3a5819dc8d5240e74fd8316f1f"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a283e1f3a5819dc8d5240e74fd8316f1f">rostlab::blast::hsp::e_value</a></div><div class="ttdeci">double e_value</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00066">blast-result.h:66</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a418d58f03289123bc97314aa28612bce"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a418d58f03289123bc97314aa28612bce">rostlab::blast::hsp::bit_score</a></div><div class="ttdeci">double bit_score</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00064">blast-result.h:64</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_ab9c59fe3193479880e965e44d0f379da"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#ab9c59fe3193479880e965e44d0f379da">rostlab::blast::result::result</a></div><div class="ttdeci">result()</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00196">blast-result.h:196</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1oneline_html"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html">rostlab::blast::oneline</a></div><div class="ttdoc">One-line description. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00153">blast-result.h:153</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_a20014457c83e1b98684a393828b9f283"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#a20014457c83e1b98684a393828b9f283">rostlab::blast::round::oneline_idx</a></div><div class="ttdeci">size_t oneline_idx</div><div class="ttdoc">Index of first one-line description of this round in vector of all one-line descriptions. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00034">blast-result.h:34</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1oneline_html_ab98dfee5b8690fe1257c47164b182f93"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html#ab98dfee5b8690fe1257c47164b182f93">rostlab::blast::oneline::~oneline</a></div><div class="ttdeci">virtual ~oneline()</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00161">blast-result.h:161</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_a8bebf94173ff4c6ccb1a4f151d651daa"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#a8bebf94173ff4c6ccb1a4f151d651daa">rostlab::blast::round::~round</a></div><div class="ttdeci">virtual ~round()</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00048">blast-result.h:48</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hit_html_af0f70425cc41a304b6bdbe3b0dcdb7a1"><div class="ttname"><a href="structrostlab_1_1blast_1_1hit.html#af0f70425cc41a304b6bdbe3b0dcdb7a1">rostlab::blast::hit::name</a></div><div class="ttdeci">std::string name</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00142">blast-result.h:142</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a8a85eacaee52d5a5d916cc28be8e92bf"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a8a85eacaee52d5a5d916cc28be8e92bf">rostlab::blast::result::db_nletter</a></div><div class="ttdeci">size_t db_nletter</div><div class="ttdoc">Number of letters in database. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00184">blast-result.h:184</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_ae052c615e50b7902cead8934d65d8b54"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#ae052c615e50b7902cead8934d65d8b54">rostlab::blast::hsp::q_strand</a></div><div class="ttdeci">std::string q_strand</div><div class="ttdoc">Query strand [Plus|Minus]. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00072">blast-result.h:72</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_aab2215bcb9285d328a2acb9e9682a107"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#aab2215bcb9285d328a2acb9e9682a107">rostlab::blast::round::oneline_new_cnt</a></div><div class="ttdeci">size_t oneline_new_cnt</div><div class="ttdoc">Count of one-line descriptions for sequences not found previously. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00044">blast-result.h:44</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_af526ca95288ae2b023e9c71fd09ac7fe"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#af526ca95288ae2b023e9c71fd09ac7fe">rostlab::blast::result::q_length</a></div><div class="ttdeci">size_t q_length</div><div class="ttdoc">Query length. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00178">blast-result.h:178</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1oneline_html_a3cfca57c6ded9a2daa9ce77e0f004040"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html#a3cfca57c6ded9a2daa9ce77e0f004040">rostlab::blast::oneline::bit_score</a></div><div class="ttdeci">double bit_score</div><div class="ttdoc">Bit score. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00157">blast-result.h:157</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_aa9578da85b347db66328e7c4e15728f8"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#aa9578da85b347db66328e7c4e15728f8">rostlab::blast::result::q_desc</a></div><div class="ttdeci">std::string q_desc</div><div class="ttdoc">Query description. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00176">blast-result.h:176</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_ad648a0d22b886a1f51e0758aaedc1541"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#ad648a0d22b886a1f51e0758aaedc1541">rostlab::blast::hsp::~hsp</a></div><div class="ttdeci">virtual ~hsp()</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00098">blast-result.h:98</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a788ab03e62122890f53fea49d0429a0a"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a788ab03e62122890f53fea49d0429a0a">rostlab::blast::result::db_nseq</a></div><div class="ttdeci">size_t db_nseq</div><div class="ttdoc">Number of sequences in database. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00182">blast-result.h:182</a></div></div>
<div class="ttc" id="namespacerostlab_html"><div class="ttname"><a href="namespacerostlab.html">rostlab</a></div><div class="ttdef"><b>Definition:</b> <a href="blast-parser-driver_8h_source.html#l00045">blast-parser-driver.h:45</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a8662fd5b2c93832bbdeb23adea298a8c"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a8662fd5b2c93832bbdeb23adea298a8c">rostlab::blast::hsp::match_line</a></div><div class="ttdeci">std::string match_line</div><div class="ttdoc">Match line. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00088">blast-result.h:88</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_a0d2c4122d5e867afa678f48fe368f009"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#a0d2c4122d5e867afa678f48fe368f009">rostlab::blast::round::round</a></div><div class="ttdeci">round(size_t __oneline_idx=0, size_t __oneline_cnt=0, size_t __hit_idx=0, size_t __hit_cnt=0, size_t __oneline_new_idx=noidx, size_t __oneline_new_cnt=0)</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00047">blast-result.h:47</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a8525a2fea583e9167f7bfd51589faf43"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a8525a2fea583e9167f7bfd51589faf43">rostlab::blast::result::references</a></div><div class="ttdeci">std::vector< std::string > references</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00169">blast-result.h:169</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html">rostlab::blast::result</a></div><div class="ttdoc">Blast result for one query. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00165">blast-result.h:165</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_ad23b74c5b8d122c47a0d54be37aa0cda"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#ad23b74c5b8d122c47a0d54be37aa0cda">rostlab::blast::round::noidx</a></div><div class="ttdeci">static const size_t noidx</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00045">blast-result.h:45</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_abe78de9ade912edb4a449ce5b366e933"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#abe78de9ade912edb4a449ce5b366e933">rostlab::blast::round::hit_cnt</a></div><div class="ttdeci">size_t hit_cnt</div><div class="ttdoc">Count of hits in round. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00040">blast-result.h:40</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_aa4cfa870754ec2243878cd5ae7c885c2"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#aa4cfa870754ec2243878cd5ae7c885c2">rostlab::blast::hsp::s_frame</a></div><div class="ttdeci">int8_t s_frame</div><div class="ttdoc">Subject frame. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00080">blast-result.h:80</a></div></div>
<div class="ttc" id="namespacerostlab_1_1blast_html_a56e758d5677ea69317d889fbd2966aad"><div class="ttname"><a href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">rostlab::blast::operator<<</a></div><div class="ttdeci">std::basic_ostream< YYChar > & operator<<(std::basic_ostream< YYChar > &ostr, const location &loc)</div><div class="ttdoc">Intercept output stream redirection. </div><div class="ttdef"><b>Definition:</b> <a href="blast-parser-location_8h_source.html#l00174">blast-parser-location.h:174</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hit_html_a65744ca4d3e6bce16e4adae1bbb696bb"><div class="ttname"><a href="structrostlab_1_1blast_1_1hit.html#a65744ca4d3e6bce16e4adae1bbb696bb">rostlab::blast::hit::desc</a></div><div class="ttdeci">std::string desc</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00143">blast-result.h:143</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a587c9b737149284390266fd7eb3aae90"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a587c9b737149284390266fd7eb3aae90">rostlab::blast::hsp::q_ali</a></div><div class="ttdeci">std::string q_ali</div><div class="ttdoc">Query alignment string. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00084">blast-result.h:84</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a8c4194988077ad1ef2f1fde6a2ab8d18"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a8c4194988077ad1ef2f1fde6a2ab8d18">rostlab::blast::result::~result</a></div><div class="ttdeci">virtual ~result()</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00197">blast-result.h:197</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hit_html_a7847e0f5d63534eb5f8908a5d9e043cb"><div class="ttname"><a href="structrostlab_1_1blast_1_1hit.html#a7847e0f5d63534eb5f8908a5d9e043cb">rostlab::blast::hit::hit</a></div><div class="ttdeci">hit(const std::string &__name="", const std::string &__desc="", size_t __length=0)</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00148">blast-result.h:148</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1oneline_html_ad96e0307e8e645dfe3aba5d7aadd5e7e"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html#ad96e0307e8e645dfe3aba5d7aadd5e7e">rostlab::blast::oneline::oneline</a></div><div class="ttdeci">oneline(const std::string &__name="", const std::string &__desc="", double __bit_score=0, double __e_value=0)</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00159">blast-result.h:159</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a22cea63cd8cf103574a605d8b90f4c50"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a22cea63cd8cf103574a605d8b90f4c50">rostlab::blast::hsp::s_end</a></div><div class="ttdeci">size_t s_end</div><div class="ttdoc">Subject end (1-based). </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00094">blast-result.h:94</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a1a478153a91dc88cda04a6be5b5c2e02"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a1a478153a91dc88cda04a6be5b5c2e02">rostlab::blast::hsp::s_strand</a></div><div class="ttdeci">std::string s_strand</div><div class="ttdoc">Subject strand [Plus|Minus]. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00074">blast-result.h:74</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_abab428d7a9f9e6f78a20e29321ee459c"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#abab428d7a9f9e6f78a20e29321ee459c">rostlab::blast::result::rounds</a></div><div class="ttdeci">std::vector< rostlab::blast::round > rounds</div><div class="ttdoc">Vector of iterated blast round information. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00172">blast-result.h:172</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a6767b36cc92cda9a904b0fc249404bde"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a6767b36cc92cda9a904b0fc249404bde">rostlab::blast::hsp::s_start</a></div><div class="ttdeci">size_t s_start</div><div class="ttdoc">Subject start (1-based). </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00090">blast-result.h:90</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a436ceffc106e8706c4a8a47eb04dff17"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a436ceffc106e8706c4a8a47eb04dff17">rostlab::blast::result::empty</a></div><div class="ttdeci">bool empty</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00166">blast-result.h:166</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a8f23027eb2902176f5ecb74574c3f3d9"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a8f23027eb2902176f5ecb74574c3f3d9">rostlab::blast::hsp::gaps</a></div><div class="ttdeci">size_t gaps</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00070">blast-result.h:70</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_ab9636d83143b4e38d8b4f4d162374dd9"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#ab9636d83143b4e38d8b4f4d162374dd9">rostlab::blast::hsp::q_start</a></div><div class="ttdeci">size_t q_start</div><div class="ttdoc">Query start (1-based). </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00082">blast-result.h:82</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_af82dd84c1d093225de32776f35314bd5"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#af82dd84c1d093225de32776f35314bd5">rostlab::blast::hsp::hsp</a></div><div class="ttdeci">hsp(double __bit_score=0, size_t __raw_score=0)</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00096">blast-result.h:96</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a50994b17ac23cf302100fd2991d2644f"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a50994b17ac23cf302100fd2991d2644f">rostlab::blast::hsp::q_end</a></div><div class="ttdeci">size_t q_end</div><div class="ttdoc">Query end (1-based). </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00086">blast-result.h:86</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_afb2be3e1a562764f98812553b11dee8e"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#afb2be3e1a562764f98812553b11dee8e">rostlab::blast::round::hit_idx</a></div><div class="ttdeci">size_t hit_idx</div><div class="ttdoc">Index of first hit of this round in vector of all hits. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00038">blast-result.h:38</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a02edceb41106dd8245f8fcb32e0caf03"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a02edceb41106dd8245f8fcb32e0caf03">rostlab::blast::hsp::positives</a></div><div class="ttdeci">size_t positives</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00069">blast-result.h:69</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hit_html_aa8228dc11dcf6b5c8bbf988a5a3c9a9e"><div class="ttname"><a href="structrostlab_1_1blast_1_1hit.html#aa8228dc11dcf6b5c8bbf988a5a3c9a9e">rostlab::blast::hit::length</a></div><div class="ttdeci">size_t length</div><div class="ttdoc">Full length of subject sequence. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00145">blast-result.h:145</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_adf63035ce02240a58d8656c32cf015e9"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#adf63035ce02240a58d8656c32cf015e9">rostlab::blast::hsp::identities</a></div><div class="ttdeci">size_t identities</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00068">blast-result.h:68</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_acf0abaa669acd23fc4a0038e194041d7"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#acf0abaa669acd23fc4a0038e194041d7">rostlab::blast::hsp::ECompoAdjustModes</a></div><div class="ttdeci">ECompoAdjustModes</div><div class="ttdoc">An collection of constants that specify all permissible modes of composition adjustment. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00056">blast-result.h:56</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html">rostlab::blast::hsp</a></div><div class="ttdoc">High-scoring segment pair. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00053">blast-result.h:53</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hit_html_a64797840c95a52f0180d1aece620377e"><div class="ttname"><a href="structrostlab_1_1blast_1_1hit.html#a64797840c95a52f0180d1aece620377e">rostlab::blast::hit::~hit</a></div><div class="ttdeci">virtual ~hit()</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00149">blast-result.h:149</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1oneline_html_a3fbcd78ceac1b92d2d16bcb73ed09a7f"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html#a3fbcd78ceac1b92d2d16bcb73ed09a7f">rostlab::blast::oneline::name</a></div><div class="ttdeci">std::string name</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00154">blast-result.h:154</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a58bd767de4077f1ca154d103fa523900"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a58bd767de4077f1ca154d103fa523900">rostlab::blast::result::tail</a></div><div class="ttdeci">std::string tail</div><div class="ttdoc">Tail part of blast result as a long string. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00194">blast-result.h:194</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_aa061fbea3c2a1f288e7afaf297b53ce9"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#aa061fbea3c2a1f288e7afaf297b53ce9">rostlab::blast::round::oneline_new_idx</a></div><div class="ttdeci">size_t oneline_new_idx</div><div class="ttdoc">Index of first one-line description of sequences not found previously in this round. noidx if there is no such, i.e. in case there are no new sequences in this round. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00042">blast-result.h:42</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_ad6c47a5c5964b571f395511523b07306"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#ad6c47a5c5964b571f395511523b07306">rostlab::blast::result::db_name</a></div><div class="ttdeci">std::string db_name</div><div class="ttdoc">Database name. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00180">blast-result.h:180</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_a1c0c3517db82e68550dc76df77723a21"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#a1c0c3517db82e68550dc76df77723a21">rostlab::blast::hsp::methodstr</a></div><div class="ttdeci">static std::string methodstr(const ECompoAdjustModes __m)</div><div class="ttdoc">Translate method code to string. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00108">blast-result.h:108</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html">rostlab::blast::round</a></div><div class="ttdoc">Data specific to an iterated blast round. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00032">blast-result.h:32</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1oneline_html_a5dacf3503b1c90cc3a381356e6b4d5e7"><div class="ttname"><a href="structrostlab_1_1blast_1_1oneline.html#a5dacf3503b1c90cc3a381356e6b4d5e7">rostlab::blast::oneline::oneline</a></div><div class="ttdeci">oneline(const hit &__h)</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00160">blast-result.h:160</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_ae343db2eb236c2177c94c20d75f41595"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#ae343db2eb236c2177c94c20d75f41595">rostlab::blast::hsp::method</a></div><div class="ttdeci">ECompoAdjustModes method</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00067">blast-result.h:67</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1hsp_html_ad2f87e9740abec41b6e52201b0eadda5"><div class="ttname"><a href="structrostlab_1_1blast_1_1hsp.html#ad2f87e9740abec41b6e52201b0eadda5">rostlab::blast::hsp::s_ali</a></div><div class="ttdeci">std::string s_ali</div><div class="ttdoc">Subject alignment string. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00092">blast-result.h:92</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a660159704e5334ec0bd606e270abe27d"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a660159704e5334ec0bd606e270abe27d">rostlab::blast::result::hits</a></div><div class="ttdeci">std::vector< rostlab::blast::hit > hits</div><div class="ttdoc">Vector of all hits. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00192">blast-result.h:192</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a316fbedbe5f98cfbe844e78679dbebb7"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a316fbedbe5f98cfbe844e78679dbebb7">rostlab::blast::result::q_name</a></div><div class="ttdeci">std::string q_name</div><div class="ttdoc">Query name. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00174">blast-result.h:174</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a329c8c96f8a616d37a3ba48e4f1739b7"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a329c8c96f8a616d37a3ba48e4f1739b7">rostlab::blast::result::onelines</a></div><div class="ttdeci">std::vector< rostlab::blast::oneline > onelines</div><div class="ttdoc">Vector of all one-line descriptions. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00187">blast-result.h:187</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1result_html_a8d1d7dde8b87ea8230948bf355cb6b6c"><div class="ttname"><a href="structrostlab_1_1blast_1_1result.html#a8d1d7dde8b87ea8230948bf355cb6b6c">rostlab::blast::result::blast_version</a></div><div class="ttdeci">std::string blast_version</div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00167">blast-result.h:167</a></div></div>
<div class="ttc" id="structrostlab_1_1blast_1_1round_html_a69a65504fc939e41824291ef829be3a7"><div class="ttname"><a href="structrostlab_1_1blast_1_1round.html#a69a65504fc939e41824291ef829be3a7">rostlab::blast::round::oneline_cnt</a></div><div class="ttdeci">size_t oneline_cnt</div><div class="ttdoc">Count of one-line descriptions in round. </div><div class="ttdef"><b>Definition:</b> <a href="blast-result_8h_source.html#l00036">blast-result.h:36</a></div></div>
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