librostlab-blast-doc 1.0.1-8 / usr / share / doc / librostlab-blast-doc / html / blast-result_8h_source.html

This file is indexed.

/usr/share/doc/librostlab-blast-doc/html/blast-result_8h_source.html is in librostlab-blast-doc 1.0.1-8.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.13"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>librostlab-blast: rostlab/blast-result.h Source File</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  <td id="projectalign" style="padding-left: 0.5em;">
   <div id="projectname">librostlab-blast
   &#160;<span id="projectnumber">1.0.1</span>
   </div>
  </td>
 </tr>
 </tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.13 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
$(function() {
  initMenu('',true,false,'search.php','Search');
  $(document).ready(function() { init_search(); });
});
</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>

<div id="nav-path" class="navpath">
  <ul>
<li class="navelem"><a class="el" href="dir_b7a5fe10b55060f48179abd50ad1f335.html">rostlab</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">blast-result.h</div>  </div>
</div><!--header-->
<div class="contents">
<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>&#160;<span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<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>&#160;<span class="comment"></span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">    This file is part of librostlab.</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">    (at your option) any later version.</span></div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment"></span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<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>&#160;<span class="comment">    along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">*/</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="preprocessor">#ifndef ROSTLAB_BLAST_RESULT_H</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="preprocessor">#define ROSTLAB_BLAST_RESULT_H</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="preprocessor">#include &lt;stdint.h&gt;</span></div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="preprocessor">#include &lt;sstream&gt;</span></div><div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div><div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div><div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="preprocessor">#include &lt;rostlab/aux_functions.h&gt;</span></div><div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;</div><div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<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>&#160;</div><div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="keyword">namespace </span>blast {</div><div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;</div><div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1round.html">   32</a></span>&#160;<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>&#160;    <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>&#160;    <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>&#160;    <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>&#160;    <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>&#160;    <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>&#160;    <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>&#160;    <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&lt;</span><span class="keywordtype">size_t</span><span class="keyword">&gt;</span>(-1);</div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;  <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>&#160;                  <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>&#160;    <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>&#160;};</div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;</div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;</div><div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hsp.html">   53</a></span>&#160;<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>&#160;</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>&#160;    <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>&#160;        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>&#160;        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>&#160;        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>&#160;        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>&#160;        eNumCompoAdjustModes</div><div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    } <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>&#160;  <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>&#160;    <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>&#160;    <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>&#160;    <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>&#160;    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>&#160;    <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>&#160;    <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>&#160;    <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>&#160;    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>&#160;    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>&#160;</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>&#160;    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>&#160;</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>&#160;    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>&#160;    <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>&#160;    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>&#160;    <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>&#160;    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>&#160;    <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>&#160;    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>&#160;    <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>&#160;  <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>&#160;                  <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>&#160;                    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>&#160;    <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>&#160;</div><div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div><div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;    <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>&#160;                    <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>&#160;    {</div><div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        <span class="keywordflow">switch</span>( __m )</div><div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        {</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;            <span class="keywordflow">case</span> eCompositionBasedStats:</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;                <span class="keywordflow">return</span> <span class="stringliteral">&quot;Composition-based stats&quot;</span>; <span class="keywordflow">break</span>;</div><div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;            <span class="keywordflow">case</span> eCompositionMatrixAdjust:</div><div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;                <span class="keywordflow">return</span> <span class="stringliteral">&quot;Compositional matrix adjust&quot;</span>; <span class="keywordflow">break</span>;</div><div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;            <span class="keywordflow">default</span>:</div><div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;                std::stringstream ss; ss &lt;&lt; __m; <span class="keywordflow">return</span> ss.str();</div><div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        }</div><div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;    }</div><div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div><div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;    <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>&#160;                    <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>&#160;    {</div><div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;        <span class="keywordflow">if</span>( __m.size() &gt; 0 &amp;&amp; __m[ __m.size()-1 ] == <span class="charliteral">&#39;.&#39;</span> ) __m.resize( __m.size()-1 );</div><div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;        <span class="comment">//           1</span></div><div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;        <span class="comment">// 012345678901</span></div><div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;        <span class="comment">// Composition-based stats</span></div><div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;        <span class="comment">// Compositional matrix adjust</span></div><div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        <span class="keywordflow">if</span>( __m.size() &gt;= 12 )</div><div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;        {</div><div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;            <span class="keywordflow">if</span>( __m[11] == <span class="charliteral">&#39;-&#39;</span> ) <span class="keywordflow">return</span> eCompositionBasedStats;</div><div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;            <span class="keywordflow">if</span>( __m[11] == <span class="charliteral">&#39;a&#39;</span> ) <span class="keywordflow">return</span> eCompositionMatrixAdjust;</div><div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;        }</div><div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;        <span class="keywordflow">return</span> eNoCompositionBasedStats;</div><div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;    }</div><div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;};</div><div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;</div><div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;</div><div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1hit.html">  141</a></span>&#160;<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>&#160;    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>&#160;    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>&#160;    <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>&#160;    std::vector&lt;hsp&gt;    <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>&#160;  <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>&#160;                  <a class="code" href="structrostlab_1_1blast_1_1hit.html#a7847e0f5d63534eb5f8908a5d9e043cb">hit</a>( <span class="keyword">const</span> std::string&amp; __name = <span class="stringliteral">&quot;&quot;</span>, <span class="keyword">const</span> std::string&amp; __desc = <span class="stringliteral">&quot;&quot;</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>&#160;    <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>&#160;};</div><div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;</div><div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1oneline.html">  153</a></span>&#160;<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>&#160;    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>&#160;    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>&#160;    <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>&#160;    <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>&#160;                    <a class="code" href="structrostlab_1_1blast_1_1oneline.html#ad96e0307e8e645dfe3aba5d7aadd5e7e">oneline</a>( <span class="keyword">const</span> std::string&amp; __name = <span class="stringliteral">&quot;&quot;</span>, <span class="keyword">const</span> std::string&amp; __desc = <span class="stringliteral">&quot;&quot;</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>&#160;                    <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>&amp; __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>&#160;    <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>&#160;};</div><div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;</div><div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="structrostlab_1_1blast_1_1result.html">  165</a></span>&#160;<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>&#160;    <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>&#160;    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>&#160;    std::vector&lt;std::string&gt;</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>&#160;                    <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>&#160;    std::vector&lt;rostlab::blast::round&gt;</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>&#160;                    <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>&#160;    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>&#160;    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>&#160;    <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>&#160;    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>&#160;    <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>&#160;    <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>&#160;    std::vector&lt;rostlab::blast::oneline&gt;</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>&#160;                    <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>&#160;    <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>&#160;    std::vector&lt;rostlab::blast::hit&gt;</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>&#160;                    <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>&#160;    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>&#160;  <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>&#160;                    <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>&#160;    <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>&#160;</div><div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;</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>&#160;    <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>&#160;};</div><div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;</div><div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;} <span class="comment">// namespace blast</span></div><div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;</div><div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;<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>&#160;std::ostream&amp;     <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator&lt;&lt;</a>( std::ostream&amp; __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1round.html">rostlab::blast::round</a>&amp; __r )</div><div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;{</div><div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;  __os &lt;&lt; <span class="stringliteral">&quot;ol_idx = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#a20014457c83e1b98684a393828b9f283">oneline_idx</a> &lt;&lt; <span class="stringliteral">&quot;, ol_cnt = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#a69a65504fc939e41824291ef829be3a7">oneline_cnt</a> &lt;&lt; <span class="stringliteral">&quot;, hit_idx = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#afb2be3e1a562764f98812553b11dee8e">hit_idx</a> &lt;&lt; <span class="stringliteral">&quot;, hit_cnt = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#abe78de9ade912edb4a449ce5b366e933">hit_cnt</a> &lt;&lt; <span class="stringliteral">&quot;, ol_new_idx = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1round.html#aa061fbea3c2a1f288e7afaf297b53ce9">oneline_new_idx</a> &lt;&lt; <span class="stringliteral">&quot;, ol_new_cnt = &quot;</span> &lt;&lt; __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>&#160;  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;}</div><div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;</div><div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;<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>&#160;std::ostream&amp;     <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator&lt;&lt;</a>( std::ostream&amp; __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1oneline.html">rostlab::blast::oneline</a>&amp; __r )</div><div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;{</div><div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;  __os &lt;&lt; <span class="stringliteral">&quot;n = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#a3fbcd78ceac1b92d2d16bcb73ed09a7f">name</a> &lt;&lt; <span class="stringliteral">&quot; d = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#afaf02fa6e84bfaad7fc5d8bf26cc314f">desc</a> &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#a3cfca57c6ded9a2daa9ce77e0f004040">bit_score</a> &lt;&lt; <span class="stringliteral">&quot; bits, &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1oneline.html#a12cf72720d730b7bdfa93521b4d3b933">e_value</a> &lt;&lt; <span class="stringliteral">&quot; E&quot;</span>;</div><div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;}</div><div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</div><div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;<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>&#160;std::ostream&amp;     <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator&lt;&lt;</a>( std::ostream&amp; __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1hsp.html">rostlab::blast::hsp</a>&amp; __r )</div><div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;{</div><div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;  __os &lt;&lt; <span class="stringliteral">&quot;bits = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a418d58f03289123bc97314aa28612bce">bit_score</a> &lt;&lt; <span class="stringliteral">&quot;, raw = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#aaf207b4f63e9bcd357b2829affea1e2a">raw_score</a> &lt;&lt; <span class="stringliteral">&quot;, E = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a283e1f3a5819dc8d5240e74fd8316f1f">e_value</a> &lt;&lt; <span class="stringliteral">&quot;, method = &quot;</span> &lt;&lt; <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>) &lt;&lt; <span class="stringliteral">&quot;, ident = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#adf63035ce02240a58d8656c32cf015e9">identities</a> &lt;&lt;</div><div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;    <span class="stringliteral">&quot;, pos = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a02edceb41106dd8245f8fcb32e0caf03">positives</a> &lt;&lt; <span class="stringliteral">&quot;, gaps = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a8f23027eb2902176f5ecb74574c3f3d9">gaps</a> &lt;&lt; <span class="stringliteral">&quot;, q_strand = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#ae052c615e50b7902cead8934d65d8b54">q_strand</a> &lt;&lt; <span class="stringliteral">&quot;, s_strand = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a1a478153a91dc88cda04a6be5b5c2e02">s_strand</a> &lt;&lt; <span class="stringliteral">&quot;, q_frame = &quot;</span> &lt;&lt; (int)__r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a3b2f013e9803afa48172664d5da386b6">q_frame</a> &lt;&lt;</div><div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;    <span class="stringliteral">&quot;, s_frame = &quot;</span> &lt;&lt; (<span class="keywordtype">int</span>)__r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#aa4cfa870754ec2243878cd5ae7c885c2">s_frame</a> &lt;&lt; <span class="stringliteral">&quot;, q_start = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#ab9636d83143b4e38d8b4f4d162374dd9">q_start</a> &lt;&lt; <span class="stringliteral">&quot;, q_ali = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a587c9b737149284390266fd7eb3aae90">q_ali</a> &lt;&lt; <span class="stringliteral">&quot;, q_end = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a50994b17ac23cf302100fd2991d2644f">q_end</a> &lt;&lt; <span class="stringliteral">&quot;, match_line = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a8662fd5b2c93832bbdeb23adea298a8c">match_line</a> &lt;&lt;</div><div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;    <span class="stringliteral">&quot;, s_start = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#a6767b36cc92cda9a904b0fc249404bde">s_start</a> &lt;&lt; <span class="stringliteral">&quot;, s_ali = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hsp.html#ad2f87e9740abec41b6e52201b0eadda5">s_ali</a> &lt;&lt; <span class="stringliteral">&quot;, s_end = &quot;</span> &lt;&lt; __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>&#160;  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;}</div><div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;</div><div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;<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>&#160;std::ostream&amp;     <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator&lt;&lt;</a>( std::ostream&amp; __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1hit.html">rostlab::blast::hit</a>&amp; __r )</div><div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;{</div><div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;  __os &lt;&lt; <span class="stringliteral">&quot;n = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hit.html#af0f70425cc41a304b6bdbe3b0dcdb7a1">name</a> &lt;&lt; <span class="stringliteral">&quot; d = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hit.html#a65744ca4d3e6bce16e4adae1bbb696bb">desc</a> &lt;&lt; <span class="stringliteral">&quot; Length = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1hit.html#aa8228dc11dcf6b5c8bbf988a5a3c9a9e">length</a> &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; __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>&#160;  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;}</div><div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;</div><div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;<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>&#160;std::ostream&amp;     <a class="code" href="namespacerostlab_1_1blast.html#a56e758d5677ea69317d889fbd2966aad">operator&lt;&lt;</a>( std::ostream&amp; __os, <span class="keyword">const</span> <a class="code" href="structrostlab_1_1blast_1_1result.html">rostlab::blast::result</a>&amp; __r )</div><div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;{</div><div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;  __os &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a8d1d7dde8b87ea8230948bf355cb6b6c">blast_version</a> &lt;&lt; <span class="stringliteral">&quot;\n\nreferences: &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a8525a2fea583e9167f7bfd51589faf43">references</a> &lt;&lt; <span class="stringliteral">&quot;\n\nrounds: &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#abab428d7a9f9e6f78a20e29321ee459c">rounds</a> &lt;&lt; <span class="stringliteral">&quot;\n\nn = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a316fbedbe5f98cfbe844e78679dbebb7">q_name</a> &lt;&lt; <span class="stringliteral">&quot; d = &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#aa9578da85b347db66328e7c4e15728f8">q_desc</a> &lt;&lt; <span class="stringliteral">&quot; (&quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#af526ca95288ae2b023e9c71fd09ac7fe">q_length</a> &lt;&lt;</div><div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;    <span class="stringliteral">&quot; letters)\n\nDatabase: &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#ad6c47a5c5964b571f395511523b07306">db_name</a> &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a788ab03e62122890f53fea49d0429a0a">db_nseq</a> &lt;&lt; <span class="stringliteral">&quot; sequences; &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a8a85eacaee52d5a5d916cc28be8e92bf">db_nletter</a> &lt;&lt; <span class="stringliteral">&quot; total letters\n\none-line desc: &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a329c8c96f8a616d37a3ba48e4f1739b7">onelines</a> &lt;&lt; <span class="stringliteral">&quot;\n\n&quot;</span> &lt;&lt;</div><div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;    ( __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a35a136ba09a81bdfddec789fad657164">converged</a> ? <span class="stringliteral">&quot;CONVERGED!\n\n&quot;</span> : <span class="stringliteral">&quot;&quot;</span> ) &lt;&lt; <span class="stringliteral">&quot;hits: &quot;</span> &lt;&lt; __r.<a class="code" href="structrostlab_1_1blast_1_1result.html#a660159704e5334ec0bd606e270abe27d">hits</a> &lt;&lt; <span class="stringliteral">&quot;\n\n&quot;</span> &lt;&lt; __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>&#160;  <span class="keywordflow">return</span> __os;</div><div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;}</div><div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;</div><div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;} <span class="comment">// namespace rostlab</span></div><div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div><div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;<span class="preprocessor">#endif // ROSTLAB_BLAST_RESULT_H</span></div><div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;<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&lt; hsp &gt; 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&lt; std::string &gt; 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&lt;&lt;</a></div><div class="ttdeci">std::basic_ostream&lt; YYChar &gt; &amp; operator&lt;&lt;(std::basic_ostream&lt; YYChar &gt; &amp;ostr, const location &amp;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 &amp;__name=&quot;&quot;, const std::string &amp;__desc=&quot;&quot;, 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 &amp;__name=&quot;&quot;, const std::string &amp;__desc=&quot;&quot;, 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&lt; rostlab::blast::round &gt; 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 &amp;__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&lt; rostlab::blast::hit &gt; 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&lt; rostlab::blast::oneline &gt; 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>
</div><!-- fragment --></div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.13
</small></address>
</body>
</html>

APT Browse - Built by Thomas Orozco.