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<div class="title">bl2seq.hpp</div> </div>
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<a href="bl2seq_8hpp.html">Go to the documentation of this file.</a><p><a href="/IEB/ToolBox/CPP_DOC/viewvc.cgi?p=include/algo/blast/api/bl2seq.hpp">Go to the SVN repository for this file.</a></p><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/* $Id: bl2seq.hpp 68872 2015-09-11 14:30:02Z madden $</span></div>
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<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">* ===========================================================================</span></div>
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<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">*</span></div>
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<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">* PUBLIC DOMAIN NOTICE</span></div>
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<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">* National Center for Biotechnology Information</span></div>
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<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">*</span></div>
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<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">* This software/database is a "United States Government Work" under the</span></div>
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<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">* terms of the United States Copyright Act. It was written as part of</span></div>
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<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">* the author's official duties as a United States Government employee and</span></div>
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<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">* thus cannot be copyrighted. This software/database is freely available</span></div>
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<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">* to the public for use. The National Library of Medicine and the U.S.</span></div>
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<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">* Government have not placed any restriction on its use or reproduction.</span></div>
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<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">*</span></div>
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<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">* Although all reasonable efforts have been taken to ensure the accuracy</span></div>
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<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">* and reliability of the software and data, the NLM and the U.S.</span></div>
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<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">* Government do not and cannot warrant the performance or results that</span></div>
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<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">* may be obtained by using this software or data. The NLM and the U.S.</span></div>
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<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">* Government disclaim all warranties, express or implied, including</span></div>
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<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">* warranties of performance, merchantability or fitness for any particular</span></div>
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<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">* purpose.</span></div>
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<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">*</span></div>
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<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">* Please cite the author in any work or product based on this material.</span></div>
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<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">*</span></div>
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<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">* ===========================================================================</span></div>
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<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">*</span></div>
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<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">* Author: Christiam Camacho</span></div>
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<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">*</span></div>
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<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">*/</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment"></span> </div>
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<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">/// @file bl2seq.hpp</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">/// Declares the CBl2Seq (BLAST 2 Sequences) class</span></div>
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<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment"></span> </div>
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<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#ifndef ALGO_BLAST_API___BL2SEQ__HPP</span></div>
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<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#define ALGO_BLAST_API___BL2SEQ__HPP</span></div>
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<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  </div>
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<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#include <<a class="code" href="blast__types_8hpp.html">algo/blast/api/blast_types.hpp</a>></span></div>
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<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor">#include <<a class="code" href="sseqloc_8hpp.html">algo/blast/api/sseqloc.hpp</a>></span></div>
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<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="blast__aux_8hpp.html">algo/blast/api/blast_aux.hpp</a>></span></div>
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<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="blast__options__handle_8hpp.html">algo/blast/api/blast_options_handle.hpp</a>></span></div>
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||
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="blast__results_8hpp.html">algo/blast/api/blast_results.hpp</a>></span></div>
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<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="local__blast_8hpp.html">algo/blast/api/local_blast.hpp</a>></span></div>
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<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment"></span> </div>
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<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment">/** @addtogroup AlgoBlast</span></div>
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<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="comment"> *</span></div>
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||
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="comment"> * @{</span></div>
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<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="comment"> */</span></div>
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<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  </div>
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<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">class </span><a class="code" href="classCBlastFilterTest.html">CBlastFilterTest</a>;</div>
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<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  </div>
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||
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <a class="code" href="group__STL.html#ga55cfdff101a460ea5d0508924d271c39">BEGIN_NCBI_SCOPE</a></div>
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||
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <a class="code" href="group__STL.html#gaa88b271580f823f87ebb467e8d88a0dc">BEGIN_SCOPE</a>(blast)</div>
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<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  </div>
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<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="comment">/// Runs the BLAST algorithm between 2 sequences.</span></div>
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<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="comment"></span><span class="comment">/// @note this is a single-BLAST search run object (i.e.: it caches the results</span></div>
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||
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="comment"></span><span class="comment">/// after a BLAST search is done). If multiple BLAST searches with different</span></div>
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<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="comment"></span><span class="comment">/// queries, subjects, or options are required, please create a separate object</span></div>
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<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classCBl2Seq.html"> 57</a></span> <span class="comment"></span>class <a class="code" href="blast__export_8h.html#a13d1ecab7cfce31c8cd6954986d9d09c">NCBI_XBLAST_EXPORT</a> <a class="code" href="classCBl2Seq.html">CBl2Seq</a> : public <a class="code" href="classCObject.html">CObject</a></div>
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||
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> {</div>
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||
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">public</span>:</div>
|
||
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="comment"></span> </div>
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||
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="comment"> /// Constructor to compare 2 sequences with default options</span></div>
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||
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="comment"></span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>, <span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a>, <a class="code" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05">EProgram</a> p);</div>
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||
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="comment"></span> </div>
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<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="comment"> /// Constructor to compare query against all subject sequences with </span></div>
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<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="comment"> /// default options</span></div>
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||
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="comment"> /// @param dbscan_mode Database search mode (as opposed to pairwise)</span></div>
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||
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="comment"></span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>, <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& subjects, <a class="code" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05">EProgram</a> p,</div>
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||
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordtype">bool</span> dbscan_mode=<span class="keyword">false</span>);</div>
|
||
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="comment"></span> </div>
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||
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="comment"> /// Constructor to allow query concatenation with default options</span></div>
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||
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="comment"> /// @param dbscan_mode Database search mode (as opposed to pairwise)</span></div>
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||
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="comment"></span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>(<span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& queries, <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& subjects, </div>
|
||
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05">EProgram</a> p, <span class="keywordtype">bool</span> dbscan_mode=<span class="keyword">false</span>);</div>
|
||
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="comment"> /// Constructor to compare 2 sequences with specified options</span></div>
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||
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="comment"></span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>, <span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a>, </div>
|
||
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>& opts);</div>
|
||
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="comment"> /// Constructor to compare query against all subject sequences with</span></div>
|
||
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="comment"> /// specified options</span></div>
|
||
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="comment"> /// @param dbscan_mode Database search mode (as opposed to pairwise)</span></div>
|
||
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="comment"></span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>, <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& subjects, </div>
|
||
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>& opts, <span class="keywordtype">bool</span> dbscan_mode=<span class="keyword">false</span>);</div>
|
||
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="comment"> /// Constructor to allow query concatenation with specified options</span></div>
|
||
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="comment"> /// @param dbscan_mode Database search mode (as opposed to pairwise)</span></div>
|
||
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="comment"></span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>(<span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& queries, <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& subjects, </div>
|
||
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>& opts, <span class="keywordtype">bool</span> dbscan_mode=<span class="keyword">false</span>);</div>
|
||
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> <span class="comment"></span> </div>
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<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="comment"> /// Destructor</span></div>
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||
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> <span class="comment"></span> <span class="keyword">virtual</span> ~<a class="code" href="classCBl2Seq.html">CBl2Seq</a>();</div>
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||
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="comment"></span></div>
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||
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="comment"> /// Set the query.</span></div>
|
||
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="comment"></span> <span class="keywordtype">void</span> SetQuery(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>);</div>
|
||
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="comment"></span> </div>
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<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> <span class="comment"> /// Retrieve the query sequence.</span></div>
|
||
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="comment"></span> <span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& GetQuery() <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> <span class="comment"> /// Set a vector of query sequences for a concatenated search.</span></div>
|
||
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <span class="comment"></span> <span class="keywordtype">void</span> SetQueries(<span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& queries);</div>
|
||
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="comment"> /// Retrieve a vector of query sequences.</span></div>
|
||
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="comment"></span> <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& GetQueries() <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="comment"> /// Set the subject sequence.</span></div>
|
||
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="comment"></span> <span class="keywordtype">void</span> SetSubject(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a>);</div>
|
||
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> <span class="comment"> /// Retrieve the subject sequence.</span></div>
|
||
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="comment"></span> <span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& GetSubject() <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> <span class="comment"> /// Set a vector of subject sequences.</span></div>
|
||
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="comment"></span> <span class="keywordtype">void</span> SetSubjects(<span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& subjects);</div>
|
||
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> <span class="comment"> /// Retrieve a vector of subject sequences.</span></div>
|
||
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="comment"></span> <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& GetSubjects() <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="comment"> /// Set the options handle.</span></div>
|
||
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="comment"></span> <a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>& SetOptionsHandle();</div>
|
||
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="comment"> /// Retrieve the options handle.</span></div>
|
||
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="comment"></span> <span class="keyword">const</span> <a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>& GetOptionsHandle() <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="comment"> /// Perform BLAST search</span></div>
|
||
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="comment"> /// Assuming N queries and M subjects, the structure of the returned </span></div>
|
||
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="comment"> /// vector is as follows, with types indicated in parenthesis:</span></div>
|
||
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="comment"> /// TSeqAlignVector = </span></div>
|
||
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="comment"> /// [ {Results for query 1 and subject 1 (Seq-align-set)},</span></div>
|
||
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="comment"> /// {Results for query 1 and subject 2 (Seq-align-set)}, ...</span></div>
|
||
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="comment"> /// {Results for query 1 and subject M (Seq-align-set)},</span></div>
|
||
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="comment"> /// {Results for query 2 and subject 1 (Seq-align-set)},</span></div>
|
||
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="comment"> /// {Results for query 2 and subject 2 (Seq-align-set)}, ...</span></div>
|
||
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="comment"> /// {Results for query 2 and subject M (Seq-align-set)},</span></div>
|
||
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="comment"> /// {Results for query 3 and subject 1 (Seq-align-set)}, ...</span></div>
|
||
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="comment"> /// {Results for query N and subject M (Seq-align-set)} ]</span></div>
|
||
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> <span class="comment"></span> <span class="keyword">virtual</span> <a class="code" href="blast__types_8hpp.html#a1e3e43ad38b78139db1afdfe5c72e991">TSeqAlignVector</a> <a class="code" href="group__ThreadedServer.html#ga70dd74cc9782fb43f761cd4b581bc622">Run</a>();</div>
|
||
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> <span class="comment"> /// Performs the same functionality as Run(), but it returns a different</span></div>
|
||
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> <span class="comment"> /// data type</span></div>
|
||
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> <span class="comment"> /// @note the number of CSearchResultSet::value_type objects in this</span></div>
|
||
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="comment"> /// function's return value will be (number of queries * number of</span></div>
|
||
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> <span class="comment"> /// subjects)</span></div>
|
||
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="comment"></span> <a class="code" href="classCRef.html">CRef<CSearchResultSet></a> RunEx();</div>
|
||
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> <span class="comment"> /// Retrieves regions filtered on the query/queries</span></div>
|
||
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> <span class="comment"></span> <a class="code" href="seqlocinfo_8hpp.html#a7807a2ac27d1103272461fb78b4fbbff">TSeqLocInfoVector</a> GetFilteredQueryRegions() <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="comment"> /// Retrieves regions filtered on the subject sequence(s)</span></div>
|
||
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="comment"> /// @param retval the return value of this method [in|out]</span></div>
|
||
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="comment"></span> <span class="keywordtype">void</span> GetFilteredSubjectRegions(vector<TSeqLocInfoVector>& retval) <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="comment"> /// Retrieves the diagnostics information returned from the engine</span></div>
|
||
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="comment"></span> <a class="code" href="structBlastDiagnostics.html">BlastDiagnostics</a>* GetDiagnostics() <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> <span class="comment"> /// Get the ancillary results for a BLAST search (to be used with the Run()</span></div>
|
||
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span> <span class="comment"> /// method)</span></div>
|
||
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> <span class="comment"> /// @param retval the return value of this method [in|out]</span></div>
|
||
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> <span class="comment"></span> <span class="keywordtype">void</span> GetAncillaryResults(<a class="code" href="group__AlgoBlast.html#gade842c867ed4fb95d3621bf006e35256">CSearchResultSet::TAncillaryVector</a>& retval) <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="comment"> /// Returns error messages/warnings.</span></div>
|
||
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="comment"></span> <span class="keywordtype">void</span> GetMessages(<a class="code" href="classTSearchMessages.html">TSearchMessages</a>& messages) <span class="keyword">const</span>;</div>
|
||
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="comment"> /// Set a function callback to be invoked by the CORE of BLAST to allow</span></div>
|
||
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> <span class="comment"> /// interrupting a BLAST search in progress.</span></div>
|
||
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="comment"> /// @param fnptr pointer to callback function [in]</span></div>
|
||
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> <span class="comment"> /// @param user_data user data to be attached to SBlastProgress structure</span></div>
|
||
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> <span class="comment"> /// [in]</span></div>
|
||
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> <span class="comment"> /// @return the previously set TInterruptFnPtr (NULL if none was</span></div>
|
||
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> <span class="comment"> /// provided before)</span></div>
|
||
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="comment"></span> <a class="code" href="blast__def_8h.html#a3d0d4e6f739bff33d3cd532f63fafb18">TInterruptFnPtr</a> SetInterruptCallback(<a class="code" href="blast__def_8h.html#a3d0d4e6f739bff33d3cd532f63fafb18">TInterruptFnPtr</a> fnptr, </div>
|
||
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordtype">void</span>* user_data = <a class="code" href="group__CToolsBridge.html#ga070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>);</div>
|
||
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> <span class="comment"> /// Converts m_Results data member to a TSeqAlignVector</span></div>
|
||
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> <span class="comment"></span> <span class="keyword">static</span> <a class="code" href="blast__types_8hpp.html#a1e3e43ad38b78139db1afdfe5c72e991">TSeqAlignVector</a></div>
|
||
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  CSearchResultSet2TSeqAlignVector(<a class="code" href="classCRef.html">CRef<CSearchResultSet></a> res);</div>
|
||
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> <span class="keyword">protected</span>:<span class="comment"></span></div>
|
||
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> <span class="comment"> /// Populate the internal m_AncillaryData member</span></div>
|
||
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span> <span class="comment"></span> <span class="keywordtype">void</span> x_BuildAncillaryData();</div>
|
||
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  </div>
|
||
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span> <span class="keyword">private</span>:</div>
|
||
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// Data members received from client code</span></div>
|
||
<div class="line"><a name="l00181"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12"> 181</a></span>  <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a> <a class="code" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">m_tQueries</a>; <span class="comment">///< query sequence(s)</span></div>
|
||
<div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f"> 182</a></span>  <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a> <a class="code" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">m_tSubjects</a>; <span class="comment">///< sequence(s) to BLAST against</span></div>
|
||
<div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga1698700fa4e5f4118ce1968948a56f14"> 183</a></span>  <a class="code" href="classCRef.html">CRef<CBlastOptionsHandle></a> <a class="code" href="group__AlgoBlast.html#ga1698700fa4e5f4118ce1968948a56f14">m_OptsHandle</a>; <span class="comment">///< Blast options</span></div>
|
||
<div class="line"><a name="l00184"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gaf04643a702cde29eb95b097d0b67292c"> 184</a></span>  <a class="code" href="classCRef.html">CRef<CLocalBlast></a> <a class="code" href="group__AlgoBlast.html#gaf04643a702cde29eb95b097d0b67292c">m_Blast</a>; <span class="comment">///< The actual BLAST instance</span></div>
|
||
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga2a8fe715887977edf81c06dc56805012"> 185</a></span>  <span class="keywordtype">bool</span> <a class="code" href="group__AlgoBlast.html#ga2a8fe715887977edf81c06dc56805012">m_DbScanMode</a>; <span class="comment">///< Scan like a databsase (as opposed to pairwise)</span></div>
|
||
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> <span class="comment"> /// Common initialization code for all c-tors</span></div>
|
||
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> <span class="comment"></span> <span class="keywordtype">void</span> x_Init(<span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& queries, <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& subjs);<span class="comment"></span></div>
|
||
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> <span class="comment"> /// Common initialization of the CLocalBlast object</span></div>
|
||
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span> <span class="comment"></span> <span class="keywordtype">void</span> x_InitCLocalBlast();</div>
|
||
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span> <span class="comment"> /// Prohibit copy constructor</span></div>
|
||
<div class="line"><a name="l00193"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gadbeb75f2dc9f909fc3941606dc9f170f"> 193</a></span> <span class="comment"></span> <a class="code" href="group__AlgoBlast.html#gadbeb75f2dc9f909fc3941606dc9f170f">CBl2Seq</a>(<span class="keyword">const</span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>& rhs);<span class="comment"></span></div>
|
||
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span> <span class="comment"> /// Prohibit assignment operator</span></div>
|
||
<div class="line"><a name="l00195"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gaddd3d184f490d01a160ccab3b36255f6"> 195</a></span> <span class="comment"></span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>& <a class="code" href="group__AlgoBlast.html#gaddd3d184f490d01a160ccab3b36255f6">operator=</a>(<span class="keyword">const</span> <a class="code" href="classCBl2Seq.html">CBl2Seq</a>& rhs);</div>
|
||
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> <span class="comment"> /// Stores any warnings emitted during query setup</span></div>
|
||
<div class="line"><a name="l00198"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga0da7f774793232de1af3e86e4aa2402d"> 198</a></span> <span class="comment"></span> <a class="code" href="classTSearchMessages.html">TSearchMessages</a> <a class="code" href="group__AlgoBlast.html#ga0da7f774793232de1af3e86e4aa2402d">m_Messages</a>;</div>
|
||
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  </div>
|
||
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="comment"> /************ Internal data structures (m_i = internal members)***********/</span><span class="comment"></span></div>
|
||
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="comment"> /// Return search statistics data</span></div>
|
||
<div class="line"><a name="l00202"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga2754e5dc7c52dccd1a8aec58d8646448"> 202</a></span> <span class="comment"></span> <a class="code" href="structBlastDiagnostics.html">BlastDiagnostics</a>* <a class="code" href="group__AlgoBlast.html#ga2754e5dc7c52dccd1a8aec58d8646448">mi_pDiagnostics</a>;</div>
|
||
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> <span class="comment"> /// Ancillary BLAST data</span></div>
|
||
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga448282ab2d877ce013872ba3261daaf8"> 205</a></span> <span class="comment"></span> <a class="code" href="group__AlgoBlast.html#gade842c867ed4fb95d3621bf006e35256">CSearchResultSet::TAncillaryVector</a> <a class="code" href="group__AlgoBlast.html#ga448282ab2d877ce013872ba3261daaf8">m_AncillaryData</a>;</div>
|
||
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="comment"></span></div>
|
||
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="comment"> /// CLocalBlast results</span></div>
|
||
<div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga8ec5c7d96d52baf95a43b36a65f41986"> 208</a></span> <span class="comment"></span> <a class="code" href="classCRef.html">CRef<CSearchResultSet></a> <a class="code" href="group__AlgoBlast.html#ga8ec5c7d96d52baf95a43b36a65f41986">m_Results</a>;</div>
|
||
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> <span class="comment"> /// Interrupt callback</span></div>
|
||
<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga0ec18a121b14f1046c92effcacb58a06"> 211</a></span> <span class="comment"></span> <a class="code" href="blast__def_8h.html#a3d0d4e6f739bff33d3cd532f63fafb18">TInterruptFnPtr</a> <a class="code" href="group__AlgoBlast.html#ga0ec18a121b14f1046c92effcacb58a06">m_InterruptFnx</a>;<span class="comment"></span></div>
|
||
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="comment"> /// Interrupt user datacallback</span></div>
|
||
<div class="line"><a name="l00213"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga3b85f3ac0c50046e6e8c319ad2f95d37"> 213</a></span> <span class="comment"></span> <span class="keywordtype">void</span>* <a class="code" href="group__AlgoBlast.html#ga3b85f3ac0c50046e6e8c319ad2f95d37">m_InterruptUserData</a>;</div>
|
||
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="comment"></span> </div>
|
||
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="comment"> /// Clean up structures and results from any previous search</span></div>
|
||
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span> <span class="comment"></span> <span class="keywordtype">void</span> x_ResetInternalDs();</div>
|
||
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  </div>
|
||
<div class="line"><a name="l00218"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga5685cac1c5e8e1fac4570809b5b14d6f"> 218</a></span>  <span class="keyword">friend</span> class ::CBlastFilterTest;</div>
|
||
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span> };</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> <span class="keyword">inline</span> <span class="keywordtype">void</span></div>
|
||
<div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gae03c57169279c557877192a914230776"> 222</a></span> <a class="code" href="group__AlgoBlast.html#gae03c57169279c557877192a914230776">CBl2Seq::SetQuery</a>(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>)</div>
|
||
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> {</div>
|
||
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <a class="code" href="group__AlgoBlast.html#ga10219c03473b1fff6a846c0dec9cf6ca">x_ResetInternalDs</a>();</div>
|
||
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <a class="code" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">m_tQueries</a>.clear();</div>
|
||
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <a class="code" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">m_tQueries</a>.push_back(<a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>);</div>
|
||
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> }</div>
|
||
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  </div>
|
||
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> <span class="keyword">inline</span> <span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>&</div>
|
||
<div class="line"><a name="l00230"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga3fd98744d17e01091e3be8c60f8bd9a1"> 230</a></span> <a class="code" href="group__AlgoBlast.html#ga3fd98744d17e01091e3be8c60f8bd9a1">CBl2Seq::GetQuery</a>()<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">return</span> <a class="code" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">m_tQueries</a>.front();</div>
|
||
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> }</div>
|
||
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  </div>
|
||
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> <span class="keyword">inline</span> <span class="keywordtype">void</span></div>
|
||
<div class="line"><a name="l00236"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga58ec2878f0a3b8aa8ed4d4889a9f9540"> 236</a></span> <a class="code" href="group__AlgoBlast.html#ga58ec2878f0a3b8aa8ed4d4889a9f9540">CBl2Seq::SetQueries</a>(<span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& queries)</div>
|
||
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> {</div>
|
||
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <a class="code" href="group__AlgoBlast.html#ga10219c03473b1fff6a846c0dec9cf6ca">x_ResetInternalDs</a>();</div>
|
||
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <a class="code" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">m_tQueries</a>.clear();</div>
|
||
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <a class="code" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">m_tQueries</a> = queries;</div>
|
||
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span> }</div>
|
||
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  </div>
|
||
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span> <span class="keyword">inline</span> <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>&</div>
|
||
<div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gaad5b96cc914eb2dcd33ad03229b97ef9"> 244</a></span> <a class="code" href="group__AlgoBlast.html#gaad5b96cc914eb2dcd33ad03229b97ef9">CBl2Seq::GetQueries</a>()<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keywordflow">return</span> <a class="code" href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">m_tQueries</a>;</div>
|
||
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> }</div>
|
||
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  </div>
|
||
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span> <span class="keyword">inline</span> <span class="keywordtype">void</span></div>
|
||
<div class="line"><a name="l00250"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga1df0b4ba84f06dc021f33457890a334b"> 250</a></span> <a class="code" href="group__AlgoBlast.html#ga1df0b4ba84f06dc021f33457890a334b">CBl2Seq::SetSubject</a>(<span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>& <a class="code" href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a>)</div>
|
||
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> {</div>
|
||
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <a class="code" href="group__AlgoBlast.html#ga10219c03473b1fff6a846c0dec9cf6ca">x_ResetInternalDs</a>();</div>
|
||
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <a class="code" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">m_tSubjects</a>.clear();</div>
|
||
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <a class="code" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">m_tSubjects</a>.push_back(<a class="code" href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a>);</div>
|
||
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span> }</div>
|
||
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  </div>
|
||
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> <span class="keyword">inline</span> <span class="keyword">const</span> <a class="code" href="structSSeqLoc.html">SSeqLoc</a>&</div>
|
||
<div class="line"><a name="l00258"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga1adaeeeb475b274fa9e079517bc93f52"> 258</a></span> <a class="code" href="group__AlgoBlast.html#ga1adaeeeb475b274fa9e079517bc93f52">CBl2Seq::GetSubject</a>()<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="keywordflow">return</span> <a class="code" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">m_tSubjects</a>.front();</div>
|
||
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> }</div>
|
||
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  </div>
|
||
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> <span class="keyword">inline</span> <span class="keywordtype">void</span></div>
|
||
<div class="line"><a name="l00264"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga36993e6e5ca762b7addf6e5f9c871744"> 264</a></span> <a class="code" href="group__AlgoBlast.html#ga36993e6e5ca762b7addf6e5f9c871744">CBl2Seq::SetSubjects</a>(<span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>& subjects)</div>
|
||
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span> {</div>
|
||
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <a class="code" href="group__AlgoBlast.html#ga10219c03473b1fff6a846c0dec9cf6ca">x_ResetInternalDs</a>();</div>
|
||
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="code" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">m_tSubjects</a>.clear();</div>
|
||
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <a class="code" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">m_tSubjects</a> = subjects;</div>
|
||
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span> }</div>
|
||
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  </div>
|
||
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span> <span class="keyword">inline</span> <span class="keyword">const</span> <a class="code" href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a>&</div>
|
||
<div class="line"><a name="l00272"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gaf300276c8caf693019e95910940a985d"> 272</a></span> <a class="code" href="group__AlgoBlast.html#gaf300276c8caf693019e95910940a985d">CBl2Seq::GetSubjects</a>()<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <span class="keywordflow">return</span> <a class="code" href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">m_tSubjects</a>;</div>
|
||
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> }</div>
|
||
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  </div>
|
||
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> <span class="keyword">inline</span> <a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>&</div>
|
||
<div class="line"><a name="l00278"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gaae48fd02aa22287f8d8535a1231c20c0"> 278</a></span> <a class="code" href="group__AlgoBlast.html#gaae48fd02aa22287f8d8535a1231c20c0">CBl2Seq::SetOptionsHandle</a>()</div>
|
||
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> {</div>
|
||
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <a class="code" href="group__AlgoBlast.html#ga10219c03473b1fff6a846c0dec9cf6ca">x_ResetInternalDs</a>();</div>
|
||
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordflow">return</span> *<a class="code" href="group__AlgoBlast.html#ga1698700fa4e5f4118ce1968948a56f14">m_OptsHandle</a>;</div>
|
||
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span> }</div>
|
||
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  </div>
|
||
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span> <span class="keyword">inline</span> <span class="keyword">const</span> <a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>&</div>
|
||
<div class="line"><a name="l00285"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga1d5c4eb42522d89199e26b82320891fe"> 285</a></span> <a class="code" href="group__AlgoBlast.html#ga1d5c4eb42522d89199e26b82320891fe">CBl2Seq::GetOptionsHandle</a>()<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keywordflow">return</span> *<a class="code" href="group__AlgoBlast.html#ga1698700fa4e5f4118ce1968948a56f14">m_OptsHandle</a>;</div>
|
||
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span> }</div>
|
||
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  </div>
|
||
<div class="line"><a name="l00290"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#gafd4c46281edb3a609daf85dd5a18ba00"> 290</a></span> <span class="keyword">inline</span> <a class="code" href="structBlastDiagnostics.html">BlastDiagnostics</a>* <a class="code" href="group__AlgoBlast.html#gafd4c46281edb3a609daf85dd5a18ba00">CBl2Seq::GetDiagnostics</a>()<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="keywordflow">return</span> <a class="code" href="group__AlgoBlast.html#ga2754e5dc7c52dccd1a8aec58d8646448">mi_pDiagnostics</a>;</div>
|
||
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span> }</div>
|
||
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  </div>
|
||
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span> <span class="keyword">inline</span> <span class="keywordtype">void</span></div>
|
||
<div class="line"><a name="l00296"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga28d9e208175d4cea38d6d66e0e59712a"> 296</a></span> <a class="code" href="group__AlgoBlast.html#ga28d9e208175d4cea38d6d66e0e59712a">CBl2Seq::GetMessages</a>(<a class="code" href="classTSearchMessages.html">TSearchMessages</a>& messages)<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  messages = <a class="code" href="group__AlgoBlast.html#ga0da7f774793232de1af3e86e4aa2402d">m_Messages</a>;</div>
|
||
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> }</div>
|
||
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  </div>
|
||
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span> <span class="keyword">inline</span> <a class="code" href="blast__def_8h.html#a3d0d4e6f739bff33d3cd532f63fafb18">TInterruptFnPtr</a></div>
|
||
<div class="line"><a name="l00302"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga546378f725a880807ac685715a46c1b5"> 302</a></span> <a class="code" href="group__AlgoBlast.html#ga546378f725a880807ac685715a46c1b5">CBl2Seq::SetInterruptCallback</a>(<a class="code" href="blast__def_8h.html#a3d0d4e6f739bff33d3cd532f63fafb18">TInterruptFnPtr</a> fnptr, <span class="keywordtype">void</span>* user_data)</div>
|
||
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span> {</div>
|
||
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <a class="code" href="blast__def_8h.html#a3d0d4e6f739bff33d3cd532f63fafb18">TInterruptFnPtr</a> <a class="code" href="ftds100_2freetds_2odbc_2unittests_2utf8_8c.html#a8f569d3d23819e94978fdb714242636e">tmp</a> = <a class="code" href="group__AlgoBlast.html#ga0ec18a121b14f1046c92effcacb58a06">m_InterruptFnx</a>;</div>
|
||
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <a class="code" href="group__AlgoBlast.html#ga0ec18a121b14f1046c92effcacb58a06">m_InterruptFnx</a> = fnptr;</div>
|
||
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <a class="code" href="group__AlgoBlast.html#ga3b85f3ac0c50046e6e8c319ad2f95d37">m_InterruptUserData</a> = user_data;</div>
|
||
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="keywordflow">return</span> <a class="code" href="ftds100_2freetds_2odbc_2unittests_2utf8_8c.html#a8f569d3d23819e94978fdb714242636e">tmp</a>;</div>
|
||
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span> }</div>
|
||
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  </div>
|
||
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span> <span class="keyword">inline</span> <span class="keywordtype">void</span> </div>
|
||
<div class="line"><a name="l00311"></a><span class="lineno"><a class="line" href="group__AlgoBlast.html#ga96e1c8b0d77c995287e3a9aad756072b"> 311</a></span> <a class="code" href="group__AlgoBlast.html#ga96e1c8b0d77c995287e3a9aad756072b">CBl2Seq::GetAncillaryResults</a>(<a class="code" href="group__AlgoBlast.html#gade842c867ed4fb95d3621bf006e35256">CSearchResultSet::TAncillaryVector</a>& retval)<span class="keyword"> const</span></div>
|
||
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span> <span class="keyword"></span>{</div>
|
||
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  retval = <a class="code" href="group__AlgoBlast.html#ga448282ab2d877ce013872ba3261daaf8">m_AncillaryData</a>;</div>
|
||
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span> }</div>
|
||
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  </div>
|
||
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span> <a class="code" href="group__STL.html#ga3f265382caed3a6f25c5078530410011">END_SCOPE</a>(blast)</div>
|
||
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span> <a class="code" href="group__STL.html#ga1dfff9dfa1ad3d389a63581ffffc97e3">END_NCBI_SCOPE</a></div>
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<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  </div>
|
||
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> <span class="comment">/* @} */</span></div>
|
||
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  </div>
|
||
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span> <span class="preprocessor">#endif </span><span class="comment">/* ALGO_BLAST_API___BL2SEQ__HPP */</span><span class="preprocessor"></span></div>
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||
<div class="ttc" id="ablast__aux_8hpp_html"><div class="ttname"><a href="blast__aux_8hpp.html">blast_aux.hpp</a></div><div class="ttdoc">Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...</div></div>
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||
<div class="ttc" id="ablast__def_8h_html_a3d0d4e6f739bff33d3cd532f63fafb18"><div class="ttname"><a href="blast__def_8h.html#a3d0d4e6f739bff33d3cd532f63fafb18">TInterruptFnPtr</a></div><div class="ttdeci">Boolean(* TInterruptFnPtr)(SBlastProgress *progress_info)</div><div class="ttdoc">Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted...</div><div class="ttdef"><b>Definition:</b> <a href="blast__def_8h_source.html#l00354">blast_def.h:354</a></div></div>
|
||
<div class="ttc" id="ablast__export_8h_html_a13d1ecab7cfce31c8cd6954986d9d09c"><div class="ttname"><a href="blast__export_8h.html#a13d1ecab7cfce31c8cd6954986d9d09c">NCBI_XBLAST_EXPORT</a></div><div class="ttdeci">#define NCBI_XBLAST_EXPORT</div><div class="ttdoc">NULL operations for other cases.</div><div class="ttdef"><b>Definition:</b> <a href="blast__export_8h_source.html#l00065">blast_export.h:65</a></div></div>
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||
<div class="ttc" id="ablast__options__handle_8hpp_html"><div class="ttname"><a href="blast__options__handle_8hpp.html">blast_options_handle.hpp</a></div><div class="ttdoc">Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.</div></div>
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||
<div class="ttc" id="ablast__results_8hpp_html"><div class="ttname"><a href="blast__results_8hpp.html">blast_results.hpp</a></div><div class="ttdoc">Definition of classes which constitute the results of running a BLAST search.</div></div>
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||
<div class="ttc" id="ablast__types_8hpp_html"><div class="ttname"><a href="blast__types_8hpp.html">blast_types.hpp</a></div><div class="ttdoc">Definitions of special type used in BLAST.</div></div>
|
||
<div class="ttc" id="ablast__types_8hpp_html_a1e3e43ad38b78139db1afdfe5c72e991"><div class="ttname"><a href="blast__types_8hpp.html#a1e3e43ad38b78139db1afdfe5c72e991">TSeqAlignVector</a></div><div class="ttdeci">vector< CRef< objects::CSeq_align_set > > TSeqAlignVector</div><div class="ttdoc">Vector of Seq-align-sets.</div><div class="ttdef"><b>Definition:</b> <a href="blast__types_8hpp_source.html#l00274">blast_types.hpp:274</a></div></div>
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||
<div class="ttc" id="ablast__types_8hpp_html_ae1c0ad647974cd781398aef388b3cf05"><div class="ttname"><a href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05">EProgram</a></div><div class="ttdeci">EProgram</div><div class="ttdoc">This enumeration is to evolve into a task/program specific list that specifies sets of default parame...</div><div class="ttdef"><b>Definition:</b> <a href="blast__types_8hpp_source.html#l00056">blast_types.hpp:56</a></div></div>
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||
<div class="ttc" id="aclassCBl2Seq_html"><div class="ttname"><a href="classCBl2Seq.html">CBl2Seq</a></div><div class="ttdoc">Runs the BLAST algorithm between 2 sequences.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00057">bl2seq.hpp:58</a></div></div>
|
||
<div class="ttc" id="aclassCBlastFilterTest_html"><div class="ttname"><a href="classCBlastFilterTest.html">CBlastFilterTest</a></div><div class="ttdef"><b>Definition:</b> <a href="blastfilter__unit__test_8cpp_source.html#l00165">blastfilter_unit_test.cpp:165</a></div></div>
|
||
<div class="ttc" id="aclassCBlastOptionsHandle_html"><div class="ttname"><a href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a></div><div class="ttdoc">Handle to the options to the BLAST algorithm.</div><div class="ttdef"><b>Definition:</b> <a href="blast__options__handle_8hpp_source.html#l00141">blast_options_handle.hpp:142</a></div></div>
|
||
<div class="ttc" id="aclassCObject_html"><div class="ttname"><a href="classCObject.html">CObject</a></div><div class="ttdoc">CObject –.</div><div class="ttdef"><b>Definition:</b> <a href="ncbiobj_8hpp_source.html#l00179">ncbiobj.hpp:180</a></div></div>
|
||
<div class="ttc" id="aclassCRef_html"><div class="ttname"><a href="classCRef.html">CRef< CSearchResultSet ></a></div></div>
|
||
<div class="ttc" id="aclassTSearchMessages_html"><div class="ttname"><a href="classTSearchMessages.html">TSearchMessages</a></div><div class="ttdoc">typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...</div><div class="ttdef"><b>Definition:</b> <a href="blast__types_8hpp_source.html#l00234">blast_types.hpp:235</a></div></div>
|
||
<div class="ttc" id="aftds100_2freetds_2odbc_2unittests_2utf8_8c_html_a8f569d3d23819e94978fdb714242636e"><div class="ttname"><a href="ftds100_2freetds_2odbc_2unittests_2utf8_8c.html#a8f569d3d23819e94978fdb714242636e">tmp</a></div><div class="ttdeci">static char tmp[3200]</div><div class="ttdef"><b>Definition:</b> <a href="ftds100_2freetds_2odbc_2unittests_2utf8_8c_source.html#l00042">utf8.c:42</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga0da7f774793232de1af3e86e4aa2402d"><div class="ttname"><a href="group__AlgoBlast.html#ga0da7f774793232de1af3e86e4aa2402d">CBl2Seq::m_Messages</a></div><div class="ttdeci">TSearchMessages m_Messages</div><div class="ttdoc">Stores any warnings emitted during query setup.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00198">bl2seq.hpp:198</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga0ec18a121b14f1046c92effcacb58a06"><div class="ttname"><a href="group__AlgoBlast.html#ga0ec18a121b14f1046c92effcacb58a06">CBl2Seq::m_InterruptFnx</a></div><div class="ttdeci">TInterruptFnPtr m_InterruptFnx</div><div class="ttdoc">Interrupt callback.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00211">bl2seq.hpp:211</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga10219c03473b1fff6a846c0dec9cf6ca"><div class="ttname"><a href="group__AlgoBlast.html#ga10219c03473b1fff6a846c0dec9cf6ca">CBl2Seq::x_ResetInternalDs</a></div><div class="ttdeci">void x_ResetInternalDs()</div><div class="ttdoc">Clean up structures and results from any previous search.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8cpp_source.html#l00141">bl2seq.cpp:141</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga1698700fa4e5f4118ce1968948a56f14"><div class="ttname"><a href="group__AlgoBlast.html#ga1698700fa4e5f4118ce1968948a56f14">CBl2Seq::m_OptsHandle</a></div><div class="ttdeci">CRef< CBlastOptionsHandle > m_OptsHandle</div><div class="ttdoc">Blast options.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00183">bl2seq.hpp:183</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga1adaeeeb475b274fa9e079517bc93f52"><div class="ttname"><a href="group__AlgoBlast.html#ga1adaeeeb475b274fa9e079517bc93f52">CBl2Seq::GetSubject</a></div><div class="ttdeci">const SSeqLoc & GetSubject() const</div><div class="ttdoc">Retrieve the subject sequence.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00258">bl2seq.hpp:258</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga1d5c4eb42522d89199e26b82320891fe"><div class="ttname"><a href="group__AlgoBlast.html#ga1d5c4eb42522d89199e26b82320891fe">CBl2Seq::GetOptionsHandle</a></div><div class="ttdeci">const CBlastOptionsHandle & GetOptionsHandle() const</div><div class="ttdoc">Retrieve the options handle.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00285">bl2seq.hpp:285</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga1df0b4ba84f06dc021f33457890a334b"><div class="ttname"><a href="group__AlgoBlast.html#ga1df0b4ba84f06dc021f33457890a334b">CBl2Seq::SetSubject</a></div><div class="ttdeci">void SetSubject(const SSeqLoc &subject)</div><div class="ttdoc">Set the subject sequence.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00250">bl2seq.hpp:250</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga2754e5dc7c52dccd1a8aec58d8646448"><div class="ttname"><a href="group__AlgoBlast.html#ga2754e5dc7c52dccd1a8aec58d8646448">CBl2Seq::mi_pDiagnostics</a></div><div class="ttdeci">BlastDiagnostics * mi_pDiagnostics</div><div class="ttdoc">Return search statistics data.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00202">bl2seq.hpp:202</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga28d9e208175d4cea38d6d66e0e59712a"><div class="ttname"><a href="group__AlgoBlast.html#ga28d9e208175d4cea38d6d66e0e59712a">CBl2Seq::GetMessages</a></div><div class="ttdeci">void GetMessages(TSearchMessages &messages) const</div><div class="ttdoc">Returns error messages/warnings.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00296">bl2seq.hpp:296</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga2a8fe715887977edf81c06dc56805012"><div class="ttname"><a href="group__AlgoBlast.html#ga2a8fe715887977edf81c06dc56805012">CBl2Seq::m_DbScanMode</a></div><div class="ttdeci">bool m_DbScanMode</div><div class="ttdoc">Scan like a databsase (as opposed to pairwise)</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00185">bl2seq.hpp:185</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga36993e6e5ca762b7addf6e5f9c871744"><div class="ttname"><a href="group__AlgoBlast.html#ga36993e6e5ca762b7addf6e5f9c871744">CBl2Seq::SetSubjects</a></div><div class="ttdeci">void SetSubjects(const TSeqLocVector &subjects)</div><div class="ttdoc">Set a vector of subject sequences.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00264">bl2seq.hpp:264</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga3b85f3ac0c50046e6e8c319ad2f95d37"><div class="ttname"><a href="group__AlgoBlast.html#ga3b85f3ac0c50046e6e8c319ad2f95d37">CBl2Seq::m_InterruptUserData</a></div><div class="ttdeci">void * m_InterruptUserData</div><div class="ttdoc">Interrupt user datacallback.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00213">bl2seq.hpp:213</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga3fd98744d17e01091e3be8c60f8bd9a1"><div class="ttname"><a href="group__AlgoBlast.html#ga3fd98744d17e01091e3be8c60f8bd9a1">CBl2Seq::GetQuery</a></div><div class="ttdeci">const SSeqLoc & GetQuery() const</div><div class="ttdoc">Retrieve the query sequence.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00230">bl2seq.hpp:230</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga448282ab2d877ce013872ba3261daaf8"><div class="ttname"><a href="group__AlgoBlast.html#ga448282ab2d877ce013872ba3261daaf8">CBl2Seq::m_AncillaryData</a></div><div class="ttdeci">CSearchResultSet::TAncillaryVector m_AncillaryData</div><div class="ttdoc">Ancillary BLAST data.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00205">bl2seq.hpp:205</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga546378f725a880807ac685715a46c1b5"><div class="ttname"><a href="group__AlgoBlast.html#ga546378f725a880807ac685715a46c1b5">CBl2Seq::SetInterruptCallback</a></div><div class="ttdeci">TInterruptFnPtr SetInterruptCallback(TInterruptFnPtr fnptr, void *user_data=NULL)</div><div class="ttdoc">Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in pr...</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00302">bl2seq.hpp:302</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga58ec2878f0a3b8aa8ed4d4889a9f9540"><div class="ttname"><a href="group__AlgoBlast.html#ga58ec2878f0a3b8aa8ed4d4889a9f9540">CBl2Seq::SetQueries</a></div><div class="ttdeci">void SetQueries(const TSeqLocVector &queries)</div><div class="ttdoc">Set a vector of query sequences for a concatenated search.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00236">bl2seq.hpp:236</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga8ec5c7d96d52baf95a43b36a65f41986"><div class="ttname"><a href="group__AlgoBlast.html#ga8ec5c7d96d52baf95a43b36a65f41986">CBl2Seq::m_Results</a></div><div class="ttdeci">CRef< CSearchResultSet > m_Results</div><div class="ttdoc">CLocalBlast results.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00208">bl2seq.hpp:208</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_ga96e1c8b0d77c995287e3a9aad756072b"><div class="ttname"><a href="group__AlgoBlast.html#ga96e1c8b0d77c995287e3a9aad756072b">CBl2Seq::GetAncillaryResults</a></div><div class="ttdeci">void GetAncillaryResults(CSearchResultSet::TAncillaryVector &retval) const</div><div class="ttdoc">Get the ancillary results for a BLAST search (to be used with the Run() method)</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00311">bl2seq.hpp:311</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gaa6eceae7375583819b4105c0ec214b12"><div class="ttname"><a href="group__AlgoBlast.html#gaa6eceae7375583819b4105c0ec214b12">CBl2Seq::m_tQueries</a></div><div class="ttdeci">TSeqLocVector m_tQueries</div><div class="ttdoc">query sequence(s)</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00181">bl2seq.hpp:181</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gaad5b96cc914eb2dcd33ad03229b97ef9"><div class="ttname"><a href="group__AlgoBlast.html#gaad5b96cc914eb2dcd33ad03229b97ef9">CBl2Seq::GetQueries</a></div><div class="ttdeci">const TSeqLocVector & GetQueries() const</div><div class="ttdoc">Retrieve a vector of query sequences.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00244">bl2seq.hpp:244</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gaadd305360c638c5305d1357974efb85f"><div class="ttname"><a href="group__AlgoBlast.html#gaadd305360c638c5305d1357974efb85f">CBl2Seq::m_tSubjects</a></div><div class="ttdeci">TSeqLocVector m_tSubjects</div><div class="ttdoc">sequence(s) to BLAST against</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00182">bl2seq.hpp:182</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gaae48fd02aa22287f8d8535a1231c20c0"><div class="ttname"><a href="group__AlgoBlast.html#gaae48fd02aa22287f8d8535a1231c20c0">CBl2Seq::SetOptionsHandle</a></div><div class="ttdeci">CBlastOptionsHandle & SetOptionsHandle()</div><div class="ttdoc">Set the options handle.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00278">bl2seq.hpp:278</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gadbeb75f2dc9f909fc3941606dc9f170f"><div class="ttname"><a href="group__AlgoBlast.html#gadbeb75f2dc9f909fc3941606dc9f170f">CBl2Seq::CBl2Seq</a></div><div class="ttdeci">CBl2Seq(const CBl2Seq &rhs)</div><div class="ttdoc">Prohibit copy constructor.</div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gaddd3d184f490d01a160ccab3b36255f6"><div class="ttname"><a href="group__AlgoBlast.html#gaddd3d184f490d01a160ccab3b36255f6">CBl2Seq::operator=</a></div><div class="ttdeci">CBl2Seq & operator=(const CBl2Seq &rhs)</div><div class="ttdoc">Prohibit assignment operator.</div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gade842c867ed4fb95d3621bf006e35256"><div class="ttname"><a href="group__AlgoBlast.html#gade842c867ed4fb95d3621bf006e35256">CSearchResultSet::TAncillaryVector</a></div><div class="ttdeci">vector< CRef< CBlastAncillaryData > > TAncillaryVector</div><div class="ttdoc">typedef for a vector of CRef<CBlastAncillaryData></div><div class="ttdef"><b>Definition:</b> <a href="blast__results_8hpp_source.html#l00319">blast_results.hpp:319</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gae03c57169279c557877192a914230776"><div class="ttname"><a href="group__AlgoBlast.html#gae03c57169279c557877192a914230776">CBl2Seq::SetQuery</a></div><div class="ttdeci">void SetQuery(const SSeqLoc &query)</div><div class="ttdoc">Set the query.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00222">bl2seq.hpp:222</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gaf04643a702cde29eb95b097d0b67292c"><div class="ttname"><a href="group__AlgoBlast.html#gaf04643a702cde29eb95b097d0b67292c">CBl2Seq::m_Blast</a></div><div class="ttdeci">CRef< CLocalBlast > m_Blast</div><div class="ttdoc">The actual BLAST instance.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00184">bl2seq.hpp:184</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gaf300276c8caf693019e95910940a985d"><div class="ttname"><a href="group__AlgoBlast.html#gaf300276c8caf693019e95910940a985d">CBl2Seq::GetSubjects</a></div><div class="ttdeci">const TSeqLocVector & GetSubjects() const</div><div class="ttdoc">Retrieve a vector of subject sequences.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00272">bl2seq.hpp:272</a></div></div>
|
||
<div class="ttc" id="agroup__AlgoBlast_html_gafd4c46281edb3a609daf85dd5a18ba00"><div class="ttname"><a href="group__AlgoBlast.html#gafd4c46281edb3a609daf85dd5a18ba00">CBl2Seq::GetDiagnostics</a></div><div class="ttdeci">BlastDiagnostics * GetDiagnostics() const</div><div class="ttdoc">Retrieves the diagnostics information returned from the engine.</div><div class="ttdef"><b>Definition:</b> <a href="bl2seq_8hpp_source.html#l00290">bl2seq.hpp:290</a></div></div>
|
||
<div class="ttc" id="agroup__CToolsBridge_html_ga070d2ce7b6bb7e5c05602aa8c308d0c4"><div class="ttname"><a href="group__CToolsBridge.html#ga070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a></div><div class="ttdeci">#define NULL</div><div class="ttdef"><b>Definition:</b> <a href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">ncbistd.hpp:225</a></div></div>
|
||
<div class="ttc" id="agroup__STL_html_ga1dfff9dfa1ad3d389a63581ffffc97e3"><div class="ttname"><a href="group__STL.html#ga1dfff9dfa1ad3d389a63581ffffc97e3">END_NCBI_SCOPE</a></div><div class="ttdeci">#define END_NCBI_SCOPE</div><div class="ttdoc">End previously defined NCBI scope.</div><div class="ttdef"><b>Definition:</b> <a href="ncbistl_8hpp_source.html#l00103">ncbistl.hpp:103</a></div></div>
|
||
<div class="ttc" id="agroup__STL_html_ga3f265382caed3a6f25c5078530410011"><div class="ttname"><a href="group__STL.html#ga3f265382caed3a6f25c5078530410011">END_SCOPE</a></div><div class="ttdeci">#define END_SCOPE(ns)</div><div class="ttdoc">End the previously defined scope.</div><div class="ttdef"><b>Definition:</b> <a href="ncbistl_8hpp_source.html#l00075">ncbistl.hpp:75</a></div></div>
|
||
<div class="ttc" id="agroup__STL_html_ga55cfdff101a460ea5d0508924d271c39"><div class="ttname"><a href="group__STL.html#ga55cfdff101a460ea5d0508924d271c39">BEGIN_NCBI_SCOPE</a></div><div class="ttdeci">#define BEGIN_NCBI_SCOPE</div><div class="ttdoc">Define ncbi namespace.</div><div class="ttdef"><b>Definition:</b> <a href="ncbistl_8hpp_source.html#l00100">ncbistl.hpp:100</a></div></div>
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<div class="ttc" id="agroup__STL_html_gaa88b271580f823f87ebb467e8d88a0dc"><div class="ttname"><a href="group__STL.html#gaa88b271580f823f87ebb467e8d88a0dc">BEGIN_SCOPE</a></div><div class="ttdeci">#define BEGIN_SCOPE(ns)</div><div class="ttdoc">Define a new scope.</div><div class="ttdef"><b>Definition:</b> <a href="ncbistl_8hpp_source.html#l00072">ncbistl.hpp:72</a></div></div>
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<div class="ttc" id="agroup__ThreadedServer_html_ga70dd74cc9782fb43f761cd4b581bc622"><div class="ttname"><a href="group__ThreadedServer.html#ga70dd74cc9782fb43f761cd4b581bc622">Run</a></div><div class="ttdeci">void Run(void)</div><div class="ttdoc">Enter the main loop.</div></div>
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<div class="ttc" id="alocal__blast_8hpp_html"><div class="ttname"><a href="local__blast_8hpp.html">local_blast.hpp</a></div><div class="ttdoc">Main class to perform a BLAST search on the local machine.</div></div>
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<div class="ttc" id="aseqlocinfo_8hpp_html_a7807a2ac27d1103272461fb78b4fbbff"><div class="ttname"><a href="seqlocinfo_8hpp.html#a7807a2ac27d1103272461fb78b4fbbff">TSeqLocInfoVector</a></div><div class="ttdeci">vector< TMaskedQueryRegions > TSeqLocInfoVector</div><div class="ttdoc">Collection of masked regions for all queries in a BLAST search.</div><div class="ttdef"><b>Definition:</b> <a href="seqlocinfo_8hpp_source.html#l00139">seqlocinfo.hpp:139</a></div></div>
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<div class="ttc" id="asseqloc_8hpp_html"><div class="ttname"><a href="sseqloc_8hpp.html">sseqloc.hpp</a></div><div class="ttdoc">Definition of SSeqLoc structure.</div></div>
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<div class="ttc" id="asseqloc_8hpp_html_a973dc27f83b37dc1df879bd86570e800"><div class="ttname"><a href="sseqloc_8hpp.html#a973dc27f83b37dc1df879bd86570e800">TSeqLocVector</a></div><div class="ttdeci">vector< SSeqLoc > TSeqLocVector</div><div class="ttdoc">Vector of sequence locations.</div><div class="ttdef"><b>Definition:</b> <a href="sseqloc_8hpp_source.html#l00129">sseqloc.hpp:129</a></div></div>
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<div class="ttc" id="astructBlastDiagnostics_html"><div class="ttname"><a href="structBlastDiagnostics.html">BlastDiagnostics</a></div><div class="ttdoc">Return statistics from the BLAST search.</div><div class="ttdef"><b>Definition:</b> <a href="blast__diagnostics_8h_source.html#l00082">blast_diagnostics.h:82</a></div></div>
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<div class="ttc" id="astructSSeqLoc_html"><div class="ttname"><a href="structSSeqLoc.html">SSeqLoc</a></div><div class="ttdoc">Structure to represent a single sequence to be fed to BLAST.</div><div class="ttdef"><b>Definition:</b> <a href="sseqloc_8hpp_source.html#l00047">sseqloc.hpp:47</a></div></div>
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<div class="ttc" id="astruct__dp__demo_8cpp_html_a4bf92df5572aed4b44e651471f3b4f3b"><div class="ttname"><a href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a></div><div class="ttdeci">static string subject</div><div class="ttdef"><b>Definition:</b> <a href="struct__dp__demo_8cpp_source.html#l00088">struct_dp_demo.cpp:88</a></div></div>
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<div class="ttc" id="astruct__dp__demo_8cpp_html_a8bb76a03a06523f30463f825fc0d8bfe"><div class="ttname"><a href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a></div><div class="ttdeci">static string query</div><div class="ttdef"><b>Definition:</b> <a href="struct__dp__demo_8cpp_source.html#l00088">struct_dp_demo.cpp:88</a></div></div>
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<address style="align: right;"><small>Modified on Fri Sep 20 14:57:48 2024 by modify_doxy.py rev. 669887</small></address>
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