139 lines
18 KiB
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139 lines
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<div id="projectname">NCBI C++ ToolKit
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<a href="#pub-types">Public Types</a> |
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<a href="#pub-static-methods">Static Public Member Functions</a> |
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<a href="#pri-methods">Private Member Functions</a> |
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<a href="classCBlastOptionsFactory-members.html">List of all members</a> </div>
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<div class="title">CBlastOptionsFactory Class Reference<div class="ingroups"><a class="el" href="group__ALGO.html">ALGORITHMS</a> » <a class="el" href="group__AlgoBlast.html">BLAST (Basic Local Alignment Search Tool)</a></div></div> </div>
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<a class="el" href = "https://www.ncbi.nlm.nih.gov/toolkitbookgh/?term=CBlastOptionsFactory">Search Toolkit Book for <i>CBlastOptionsFactory</i></a>
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</p>
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<p>Creates BlastOptionsHandle objects with default values for the programs/tasks requested.
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<a href="classCBlastOptionsFactory.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="blast__options__handle_8hpp_source.html">algo/blast/api/blast_options_handle.hpp</a>></code></p>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
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Public Types</h2></td></tr>
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<tr class="memitem:gae6b11daaee72047ca8ae046bcfb22de9"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="group__AlgoBlast.html#gae6b11daaee72047ca8ae046bcfb22de9">ETaskSets</a> { <a class="el" href="group__AlgoBlast.html#ggae6b11daaee72047ca8ae046bcfb22de9a4bf80476720a58b277d639a9d824af9f">eNuclNucl</a>
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, <a class="el" href="group__AlgoBlast.html#ggae6b11daaee72047ca8ae046bcfb22de9a2f7c3123d75828eaa4789c9778edfb74">eProtProt</a>
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, <a class="el" href="group__AlgoBlast.html#ggae6b11daaee72047ca8ae046bcfb22de9ae51fc197129d3bc1a633ee9162cdba37">eMapping</a>
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, <a class="el" href="group__AlgoBlast.html#ggae6b11daaee72047ca8ae046bcfb22de9a57999a919ff78bed193d677f4fce9267">eAll</a>
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}</td></tr>
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<tr class="memdesc:gae6b11daaee72047ca8ae046bcfb22de9"><td class="mdescLeft"> </td><td class="mdescRight">Sets of tasks for the command line BLAST binaries. <a href="group__AlgoBlast.html#gae6b11daaee72047ca8ae046bcfb22de9">More...</a><br /></td></tr>
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<tr class="separator:gae6b11daaee72047ca8ae046bcfb22de9"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga01c6e960031853b799cc25d53b6c114e"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCBlastOptions.html#a92083ed20564d2c4e2f589744ea1c8ab">CBlastOptions::EAPILocality</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__AlgoBlast.html#ga01c6e960031853b799cc25d53b6c114e">EAPILocality</a></td></tr>
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<tr class="memdesc:ga01c6e960031853b799cc25d53b6c114e"><td class="mdescLeft"> </td><td class="mdescRight">Convenience define. <a href="group__AlgoBlast.html#ga01c6e960031853b799cc25d53b6c114e">More...</a><br /></td></tr>
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<tr class="separator:ga01c6e960031853b799cc25d53b6c114e"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
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Static Public Member Functions</h2></td></tr>
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<tr class="memitem:ga59eed1e74b8c89243ae191195f87a90b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__AlgoBlast.html#ga59eed1e74b8c89243ae191195f87a90b">Create</a> (<a class="el" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05">EProgram</a> program, <a class="el" href="classCBlastOptions.html#a92083ed20564d2c4e2f589744ea1c8ab">EAPILocality</a> locality=<a class="el" href="classCBlastOptions.html#a92083ed20564d2c4e2f589744ea1c8aba1fe87d323d4d1756e83255e6ba75c098">CBlastOptions::eLocal</a>)</td></tr>
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<tr class="memdesc:ga59eed1e74b8c89243ae191195f87a90b"><td class="mdescLeft"> </td><td class="mdescRight">Creates an options handle object configured with default options for the requested program, throws an exception if an unsupported program is requested. <a href="group__AlgoBlast.html#ga59eed1e74b8c89243ae191195f87a90b">More...</a><br /></td></tr>
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<tr class="separator:ga59eed1e74b8c89243ae191195f87a90b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:gaf7d75356c79bc5b7b6584582a4e27d3f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__AlgoBlast.html#gaf7d75356c79bc5b7b6584582a4e27d3f">CreateTask</a> (<a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> task, <a class="el" href="classCBlastOptions.html#a92083ed20564d2c4e2f589744ea1c8ab">EAPILocality</a> locality=<a class="el" href="classCBlastOptions.html#a92083ed20564d2c4e2f589744ea1c8aba1fe87d323d4d1756e83255e6ba75c098">CBlastOptions::eLocal</a>)</td></tr>
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<tr class="memdesc:gaf7d75356c79bc5b7b6584582a4e27d3f"><td class="mdescLeft"> </td><td class="mdescRight">Creates an options handle object configured with default options for the requested task, throws an exception if an unsupported task is requested. <a href="group__AlgoBlast.html#gaf7d75356c79bc5b7b6584582a4e27d3f">More...</a><br /></td></tr>
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<tr class="memitem:ga8e78d9fd3a99c2d95b3b684c7895e49e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classset.html">set</a>< <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__AlgoBlast.html#ga8e78d9fd3a99c2d95b3b684c7895e49e">GetTasks</a> (<a class="el" href="group__AlgoBlast.html#gae6b11daaee72047ca8ae046bcfb22de9">ETaskSets</a> choice=<a class="el" href="group__AlgoBlast.html#ggae6b11daaee72047ca8ae046bcfb22de9a57999a919ff78bed193d677f4fce9267">eAll</a>)</td></tr>
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<tr class="memdesc:ga8e78d9fd3a99c2d95b3b684c7895e49e"><td class="mdescLeft"> </td><td class="mdescRight">Retrieve the set of supported tasks. <a href="group__AlgoBlast.html#ga8e78d9fd3a99c2d95b3b684c7895e49e">More...</a><br /></td></tr>
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<tr class="separator:ga8e78d9fd3a99c2d95b3b684c7895e49e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ga3bde2648ed650656120728ca814dc91e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__AlgoBlast.html#ga3bde2648ed650656120728ca814dc91e">GetDocumentation</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="group__CGIBase.html#ga338951b7e7607b65262fb051e7804d91">string</a> &task_name)</td></tr>
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<tr class="memdesc:ga3bde2648ed650656120728ca814dc91e"><td class="mdescLeft"> </td><td class="mdescRight">Return the documentation for the provided task. <a href="group__AlgoBlast.html#ga3bde2648ed650656120728ca814dc91e">More...</a><br /></td></tr>
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<tr class="separator:ga3bde2648ed650656120728ca814dc91e"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
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Private Member Functions</h2></td></tr>
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<tr class="memitem:gac89fbbe8706775d432f4057899d8a147"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__AlgoBlast.html#gac89fbbe8706775d432f4057899d8a147">CBlastOptionsFactory</a> ()</td></tr>
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<tr class="memdesc:gac89fbbe8706775d432f4057899d8a147"><td class="mdescLeft"> </td><td class="mdescRight">Private c-tor. <a href="group__AlgoBlast.html#gac89fbbe8706775d432f4057899d8a147">More...</a><br /></td></tr>
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</table>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Creates BlastOptionsHandle objects with default values for the programs/tasks requested. </p>
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<p>This factory is provided as a convenience to create CBlastOptionsHandles which are configured with default values for a given program/task and will NOT be modified before passing them to objects which will execute the BLAST algorithm. If you need to set options for the specific task at hand, please instantiate the appropriate <a class="el" href="classCBlastOptionsHandle.html" title="Handle to the options to the BLAST algorithm.">CBlastOptionsHandle</a> subclass.</p>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="blast_opts_cookbook.html">C++ BLAST Options Cookbook</a></dd></dl>
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<p>Example: </p><div class="fragment"><div class="line">...</div>
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<div class="line">CRef<<a class="code" href="classCBlastOptionsHandle.html">CBlastOptionsHandle</a>> opts(<a class="code" href="group__AlgoBlast.html#ga59eed1e74b8c89243ae191195f87a90b">CBlastOptionsFactory::Create</a>(<a class="code" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05a4a7e6dbe2b27d372f3093b45f5b2c75f">eBlastn</a>));</div>
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<div class="line"><a class="code" href="classCBl2Seq.html">CBl2Seq</a> blaster(<a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>, <a class="code" href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a>, *opts);</div>
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<div class="line"><a class="code" href="blast__types_8hpp.html#a1e3e43ad38b78139db1afdfe5c72e991">TSeqAlignVector</a> <a class="code" href="pcre2posix__test_8c.html#ae49d5a6ffb834af8456177024a50fe43">results</a> = blaster.Run();</div>
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<div class="line">...</div>
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<div class="line">opts.Reset(<a class="code" href="group__AlgoBlast.html#ga59eed1e74b8c89243ae191195f87a90b">CBlastOptionsFactory::Create</a>(<a class="code" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05aabbf906edd711e4cca274987eefcf31d">eMegablast</a>));</div>
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<div class="line">blaster.SetOptionsHandle() = *opts;</div>
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<div class="line"><a class="code" href="pcre2posix__test_8c.html#ae49d5a6ffb834af8456177024a50fe43">results</a> = blaster.Run();</div>
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<div class="line">...</div>
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<div class="line">opts.Reset(<a class="code" href="group__AlgoBlast.html#ga59eed1e74b8c89243ae191195f87a90b">CBlastOptionsFactory::Create</a>(<a class="code" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05ad110f788c357eecc460329a401217336">eDiscMegablast</a>));</div>
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<div class="line">blaster.SetOptionsHandle() = *opts;</div>
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<div class="line"><a class="code" href="pcre2posix__test_8c.html#ae49d5a6ffb834af8456177024a50fe43">results</a> = blaster.Run();</div>
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<div class="line">...</div>
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<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_ae1c0ad647974cd781398aef388b3cf05a4a7e6dbe2b27d372f3093b45f5b2c75f"><div class="ttname"><a href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05a4a7e6dbe2b27d372f3093b45f5b2c75f">eBlastn</a></div><div class="ttdeci">@ eBlastn</div><div class="ttdoc">Nucl-Nucl (traditional blastn)</div><div class="ttdef"><b>Definition:</b> <a href="blast__types_8hpp_source.html#l00058">blast_types.hpp:58</a></div></div>
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<div class="ttc" id="ablast__types_8hpp_html_ae1c0ad647974cd781398aef388b3cf05aabbf906edd711e4cca274987eefcf31d"><div class="ttname"><a href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05aabbf906edd711e4cca274987eefcf31d">eMegablast</a></div><div class="ttdeci">@ eMegablast</div><div class="ttdoc">Nucl-Nucl (traditional megablast)</div><div class="ttdef"><b>Definition:</b> <a href="blast__types_8hpp_source.html#l00065">blast_types.hpp:65</a></div></div>
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<div class="ttc" id="ablast__types_8hpp_html_ae1c0ad647974cd781398aef388b3cf05ad110f788c357eecc460329a401217336"><div class="ttname"><a href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05ad110f788c357eecc460329a401217336">eDiscMegablast</a></div><div class="ttdeci">@ eDiscMegablast</div><div class="ttdoc">Nucl-Nucl using discontiguous megablast.</div><div class="ttdef"><b>Definition:</b> <a href="blast__types_8hpp_source.html#l00066">blast_types.hpp:66</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>
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<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>
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<div class="ttc" id="agroup__AlgoBlast_html_ga59eed1e74b8c89243ae191195f87a90b"><div class="ttname"><a href="group__AlgoBlast.html#ga59eed1e74b8c89243ae191195f87a90b">CBlastOptionsFactory::Create</a></div><div class="ttdeci">static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)</div><div class="ttdoc">Creates an options handle object configured with default options for the requested program,...</div><div class="ttdef"><b>Definition:</b> <a href="blast__options__handle_8cpp_source.html#l00110">blast_options_handle.cpp:110</a></div></div>
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<div class="ttc" id="apcre2posix__test_8c_html_ae49d5a6ffb834af8456177024a50fe43"><div class="ttname"><a href="pcre2posix__test_8c.html#ae49d5a6ffb834af8456177024a50fe43">results</a></div><div class="ttdeci">static int * results[]</div><div class="ttdef"><b>Definition:</b> <a href="pcre2posix__test_8c_source.html#l00111">pcre2posix_test.c:111</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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</div><!-- fragment -->
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<p class="definition">Definition at line <a class="el" href="blast__options__handle_8hpp_source.html#l00080">80</a> of file <a class="el" href="blast__options__handle_8hpp_source.html">blast_options_handle.hpp</a>.</p>
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</div><hr/>The documentation for this class was generated from the following files:<ul>
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<li>include/algo/blast/api/<a class="el" href="blast__options__handle_8hpp_source.html">blast_options_handle.hpp</a></li>
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<li>src/algo/blast/api/<a class="el" href="blast__options__handle_8cpp_source.html">blast_options_handle.cpp</a></li>
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</ul>
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</div><!-- contents -->
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Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.0
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<address style="align: right;"><small>Modified on Fri Sep 20 14:58:04 2024 by modify_doxy.py rev. 669887</small></address>
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