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<div class="title">C++ BLAST Options Cookbook </div> </div>
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<div class="contents">
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<div class="textblock"><p>The purpose of the C++ BLAST options APIs is to provide convenient access to the various algorithm options for a variety of users of BLAST as well as a means to validating the options, while isolating them from the details of the CORE BLAST implementation.</p>
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<p>Please note that these objects are instantiated with the default options set and these defaults can be queried via the corresponding accessor method(s).</p>
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<h1><a class="anchor" id="_basic_opts_usage"></a>
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Basic usage</h1>
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<p>For users who only want to perform a single BLAST searches using default options for a specific task (EProgram) <em>without</em> modifying the options, one can let the BLAST search classes create and validate the appropriate BLAST options object internally:</p>
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<div class="fragment"><div class="line"><span class="keyword">using</span> <a class="code" href="namespacencbi_1_1blast.html">ncbi::blast</a>;</div>
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<div class="line"><span class="keywordflow">try</span> {</div>
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<div class="line"> <span class="comment">// Task is specified by the eBlastp argument</span></div>
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<div class="line"> <a class="code" href="classCBl2Seq.html">CBl2Seq</a> bl2seq(<a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>, <a class="code" href="struct__dp__demo_8cpp.html#a4bf92df5572aed4b44e651471f3b4f3b">subject</a>, <a class="code" href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05a56ff985a178a2656db827bd84a47a200">eBlastp</a>);</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> = bl2seq.Run();</div>
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<div class="line">} <span class="keywordflow">catch</span> (<span class="keyword">const</span> <a class="code" href="classCBlastException.html">CBlastException</a>& e) { </div>
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<div class="line"> <span class="comment">// Handle exception ... </span></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_ae1c0ad647974cd781398aef388b3cf05a56ff985a178a2656db827bd84a47a200"><div class="ttname"><a href="blast__types_8hpp.html#ae1c0ad647974cd781398aef388b3cf05a56ff985a178a2656db827bd84a47a200">eBlastp</a></div><div class="ttdeci">@ eBlastp</div><div class="ttdoc">Protein-Protein.</div><div class="ttdef"><b>Definition:</b> <a href="blast__types_8hpp_source.html#l00059">blast_types.hpp:59</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="aclassCBlastException_html"><div class="ttname"><a href="classCBlastException.html">CBlastException</a></div><div class="ttdoc">Defines BLAST error codes (user errors included)</div><div class="ttdef"><b>Definition:</b> <a href="blast__exception_8hpp_source.html#l00070">blast_exception.hpp:71</a></div></div>
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<div class="ttc" id="anamespacencbi_1_1blast_html"><div class="ttname"><a href="namespacencbi_1_1blast.html">ncbi::blast</a></div><div class="ttdef"><b>Definition:</b> <a href="algo_2blast_2unit__tests_2api_2blast__test__util_8hpp_source.html#l00069">blast_test_util.hpp:69</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 --><p>Using the approach above guarantees that the BLAST options will be valid.</p>
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<p>An alternative to this approach is to use the <a class="el" href="classCBlastOptionsFactory.html" title="Creates BlastOptionsHandle objects with default values for the programs/tasks requested.">CBlastOptionsFactory</a> to create a <a class="el" href="classCBlastOptionsHandle.html" title="Handle to the options to the BLAST algorithm.">CBlastOptionsHandle</a> object, which allows the caller to set options which are applicable to all variants of BLAST (e.g.: E-value threshold, effective search space, window size). Furthermore, this approach allows the caller to reuse the <a class="el" href="classCBlastOptionsHandle.html" title="Handle to the options to the BLAST algorithm.">CBlastOptionsHandle</a> object with multiple BLAST search objects:</p>
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<div class="fragment"><div class="line"><span class="keyword">using</span> <a class="code" href="namespacencbi_1_1blast.html">ncbi::blast</a>;</div>
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<div class="line"><a class="code" href="classCRef.html">CRef<CBlastOptionsHandle></a> opts_handle(<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">...</div>
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<div class="line">opts_handle.SetEvalueThreshold(1e-20);</div>
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<div class="line"><a class="code" href="classCBl2Seq.html">CBl2Seq</a> bl2seq(<a class="code" href="struct__dp__demo_8cpp.html#a8bb76a03a06523f30463f825fc0d8bfe">query</a>, subjects, opts_handle);</div>
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<div class="line">...</div>
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<div class="line">opts_handle.SetEvalueThreshold(1e-10);</div>
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<div class="line"><a class="code" href="classCLocalBlast.html">CLocalBlast</a> blast(query_factory, opts_handle, seq_src);</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="aclassCLocalBlast_html"><div class="ttname"><a href="classCLocalBlast.html">CLocalBlast</a></div><div class="ttdoc">Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...</div><div class="ttdef"><b>Definition:</b> <a href="local__blast_8hpp_source.html#l00061">local_blast.hpp:62</a></div></div>
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<div class="ttc" id="aclassCRef_html"><div class="ttname"><a href="classCRef.html">CRef< CBlastOptionsHandle ></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><!-- fragment --><h1><a class="anchor" id="_validating_opts"></a>
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Options validation</h1>
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<p>The <a class="el" href="classCBlastOptionsHandle.html" title="Handle to the options to the BLAST algorithm.">CBlastOptionsHandle</a> classes offers a <code>Validate</code> method in its interface which is called by the BLAST search classes prior to performing the actual search, but users of the C++ BLAST options APIs might also want to invoke this method so that any exceptions thrown by the BLAST search classes can be guaranteed not originate from an incorrect setting of BLAST options. Please note that the <code>Validate</code> method throws a <a class="el" href="classCBlastException.html" title="Defines BLAST error codes (user errors included)">CBlastException</a> in case of failure.</p>
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<h1><a class="anchor" id="_intermediate_opts_usage"></a>
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Intermediate options usage</h1>
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<p>For users who want to obtain default options, yet modify the most popular options, one should create instances of derived classes of the <a class="el" href="classCBlastOptionsHandle.html" title="Handle to the options to the BLAST algorithm.">CBlastOptionsHandle</a>, because these should expose an interface that is relevant to the task at hand (although not an exhaustive interface, for that see <a class="el" href="blast_opts_cookbook.html#_advanced_opts_usage">Advanced options usage</a>):</p>
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<div class="fragment"><div class="line"><span class="keyword">using</span> <a class="code" href="namespacencbi_1_1blast.html">ncbi::blast</a>;</div>
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<div class="line"><a class="code" href="classCBlastNucleotideOptionsHandle.html">CBlastNucleotideOptionsHandle</a> opts_handle;</div>
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<div class="line">opts_handle.<a class="code" href="group__AlgoBlast.html#ga6b3c0e438d4c6cbc4006443b7a83873d">SetTraditionalBlastnDefaults</a>();</div>
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<div class="line">opts_handle.<a class="code" href="group__AlgoBlast.html#gaf8b6653245a785b49df50c5dae5100a2">SetStrandOption</a>(<a class="code" href="group__dataspec__NCBI__Seqloc.html#gga2d4d48fde1d3f62563eac193a3b5afaea04873ff8b0944320dd441268a19b0bae">objects::eNa_strand_plus</a>);</div>
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<div class="line"><a class="code" href="classCBl2Seq.html">CBl2Seq</a> bl2seq(<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_handle);</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> = bl2seq.Run();</div>
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<div class="ttc" id="aclassCBlastNucleotideOptionsHandle_html"><div class="ttname"><a href="classCBlastNucleotideOptionsHandle.html">CBlastNucleotideOptionsHandle</a></div><div class="ttdoc">Handle to the nucleotide-nucleotide options to the BLAST algorithm.</div><div class="ttdef"><b>Definition:</b> <a href="blast__nucl__options_8hpp_source.html#l00058">blast_nucl_options.hpp:60</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_ga6b3c0e438d4c6cbc4006443b7a83873d"><div class="ttname"><a href="group__AlgoBlast.html#ga6b3c0e438d4c6cbc4006443b7a83873d">CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults</a></div><div class="ttdeci">void SetTraditionalBlastnDefaults()</div><div class="ttdoc">Sets TraditionalBlastnDefaults.</div><div class="ttdef"><b>Definition:</b> <a href="blast__nucl__options_8cpp_source.html#l00070">blast_nucl_options.cpp:70</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_gaf8b6653245a785b49df50c5dae5100a2"><div class="ttname"><a href="group__AlgoBlast.html#gaf8b6653245a785b49df50c5dae5100a2">CBlastNucleotideOptionsHandle::SetStrandOption</a></div><div class="ttdeci">void SetStrandOption(objects::ENa_strand strand)</div><div class="ttdoc">Sets StrandOption.</div><div class="ttdef"><b>Definition:</b> <a href="blast__nucl__options_8hpp_source.html#l00098">blast_nucl_options.hpp:98</a></div></div>
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<div class="ttc" id="agroup__dataspec__NCBI__Seqloc_html_gga2d4d48fde1d3f62563eac193a3b5afaea04873ff8b0944320dd441268a19b0bae"><div class="ttname"><a href="group__dataspec__NCBI__Seqloc.html#gga2d4d48fde1d3f62563eac193a3b5afaea04873ff8b0944320dd441268a19b0bae">eNa_strand_plus</a></div><div class="ttdeci">@ eNa_strand_plus</div><div class="ttdef"><b>Definition:</b> <a href="Na__strand___8hpp_source.html#l00066">Na_strand_.hpp:66</a></div></div>
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</div><!-- fragment --><p>By using this interface, the likelihood of setting invalid options is reduced, but the validity of the options cannot be fully guaranteed. </p><dl class="section note"><dt>Note</dt><dd>BLAST help desk and developers reserve the right to determine which options are popular.</dd></dl>
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<h1><a class="anchor" id="_advanced_opts_usage"></a>
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Advanced options usage</h1>
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<p>For users who want to have full control over setting the algorithm's options, or whose options of interest are not available in any of the classes in the <a class="el" href="classCBlastOptionsHandle.html" title="Handle to the options to the BLAST algorithm.">CBlastOptionsHandle</a> hierarchy, the <code>GetOptions</code> and <code>SetOptions</code> methods of the <a class="el" href="classCBlastOptionsHandle.html" title="Handle to the options to the BLAST algorithm.">CBlastOptionsHandle</a> hierarchy allow access to the <a class="el" href="classCBlastOptions.html" title="Encapsulates ALL the BLAST algorithm's options.">CBlastOptions</a> class, the lowest level class in the C++ BLAST options API which contains all options available to all variants of the BLAST algorithm. No guarantees about the validity of the options are made if this interface is used, therefore invoking <code>Validate</code> is <em>strongly</em> recommended.</p>
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<div class="fragment"><div class="line"><span class="keyword">using</span> <a class="code" href="namespacencbi_1_1blast.html">ncbi::blast</a>;</div>
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<div class="line"><span class="keywordflow">try</span> {</div>
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<div class="line"> <a class="code" href="classCBlastProteinOptionsHandle.html">CBlastProteinOptionsHandle</a> opts_handle;</div>
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<div class="line"> opts_handle.<a class="code" href="group__AlgoBlast.html#ga9639398804465f1601a5e14fb6abfbea">SetMatrixName</a>(<span class="stringliteral">"PAM30"</span>);</div>
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<div class="line"> opts_handle.<a class="code" href="group__AlgoBlast.html#ga53c7675067994ff54d5378d44e8b7cd3">SetGapOpeningCost</a>(9);</div>
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<div class="line"> opts_handle.<a class="code" href="group__AlgoBlast.html#ga07ebf101b4166cc0fbfbd2ce563152ce">SetGapExtensionCost</a>(1);</div>
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<div class="line"> opts_handle.<a class="code" href="group__AlgoBlast.html#ga5b6928ce3ef8ef99b60cd372264854cc">SetOptions</a>().<a class="code" href="group__AlgoBlast.html#ga094648b2dddbae728de84b18ae627ec3">SetCompositionBasedStats</a>(<a class="code" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbda5bdbfb18db42593b530a19e2ef77edff">eCompositionBasedStats</a>);</div>
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<div class="line"> opts_handle.<a class="code" href="group__AlgoBlast.html#gaa9b361bf1d476216378da8fecbab960f">Validate</a>();</div>
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<div class="line"> </div>
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<div class="line"> <a class="code" href="classCBl2Seq.html">CBl2Seq</a> bl2seq(<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_handle);</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> = bl2seq.Run();</div>
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<div class="line">} <span class="keywordflow">catch</span> (<span class="keyword">const</span> <a class="code" href="classCBlastException.html">CBlastException</a>& e) {</div>
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<div class="line"> <span class="comment">// Handle exception ...</span></div>
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<div class="line">}</div>
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<div class="ttc" id="aclassCBlastProteinOptionsHandle_html"><div class="ttname"><a href="classCBlastProteinOptionsHandle.html">CBlastProteinOptionsHandle</a></div><div class="ttdoc">Handle to the protein-protein options to the BLAST algorithm.</div><div class="ttdef"><b>Definition:</b> <a href="blast__prot__options_8hpp_source.html#l00053">blast_prot_options.hpp:55</a></div></div>
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<div class="ttc" id="acomposition__constants_8h_html_a13a00fe8dcff838754d4d76347612fbda5bdbfb18db42593b530a19e2ef77edff"><div class="ttname"><a href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbda5bdbfb18db42593b530a19e2ef77edff">eCompositionBasedStats</a></div><div class="ttdeci">@ eCompositionBasedStats</div><div class="ttdoc">Composition-based statistics as in NAR 29:2994-3005, 2001.</div><div class="ttdef"><b>Definition:</b> <a href="composition__constants_8h_source.html#l00063">composition_constants.h:63</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_ga07ebf101b4166cc0fbfbd2ce563152ce"><div class="ttname"><a href="group__AlgoBlast.html#ga07ebf101b4166cc0fbfbd2ce563152ce">CBlastProteinOptionsHandle::SetGapExtensionCost</a></div><div class="ttdeci">void SetGapExtensionCost(int e)</div><div class="ttdoc">Sets GapExtensionCost.</div><div class="ttdef"><b>Definition:</b> <a href="blast__prot__options_8hpp_source.html#l00127">blast_prot_options.hpp:127</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_ga094648b2dddbae728de84b18ae627ec3"><div class="ttname"><a href="group__AlgoBlast.html#ga094648b2dddbae728de84b18ae627ec3">CBlastOptions::SetCompositionBasedStats</a></div><div class="ttdeci">void SetCompositionBasedStats(ECompoAdjustModes mode)</div><div class="ttdef"><b>Definition:</b> <a href="blast__options__cxx_8cpp_source.html#l01654">blast_options_cxx.cpp:1654</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_ga53c7675067994ff54d5378d44e8b7cd3"><div class="ttname"><a href="group__AlgoBlast.html#ga53c7675067994ff54d5378d44e8b7cd3">CBlastProteinOptionsHandle::SetGapOpeningCost</a></div><div class="ttdeci">void SetGapOpeningCost(int g)</div><div class="ttdoc">Sets GapOpeningCost.</div><div class="ttdef"><b>Definition:</b> <a href="blast__prot__options_8hpp_source.html#l00121">blast_prot_options.hpp:121</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_ga5b6928ce3ef8ef99b60cd372264854cc"><div class="ttname"><a href="group__AlgoBlast.html#ga5b6928ce3ef8ef99b60cd372264854cc">CBlastOptionsHandle::SetOptions</a></div><div class="ttdeci">CBlastOptions & SetOptions()</div><div class="ttdoc">Returns a reference to the internal options class which this object is a handle for.</div><div class="ttdef"><b>Definition:</b> <a href="blast__options__handle_8hpp_source.html#l00169">blast_options_handle.hpp:169</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_ga9639398804465f1601a5e14fb6abfbea"><div class="ttname"><a href="group__AlgoBlast.html#ga9639398804465f1601a5e14fb6abfbea">CBlastProteinOptionsHandle::SetMatrixName</a></div><div class="ttdeci">void SetMatrixName(const char *matrix)</div><div class="ttdoc">Sets MatrixName.</div><div class="ttdef"><b>Definition:</b> <a href="blast__prot__options_8hpp_source.html#l00115">blast_prot_options.hpp:115</a></div></div>
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<div class="ttc" id="agroup__AlgoBlast_html_gaa9b361bf1d476216378da8fecbab960f"><div class="ttname"><a href="group__AlgoBlast.html#gaa9b361bf1d476216378da8fecbab960f">CBlastOptionsHandle::Validate</a></div><div class="ttdeci">bool Validate() const</div><div class="ttdoc">Validate the options contained in this object.</div><div class="ttdef"><b>Definition:</b> <a href="blast__options__handle_8cpp_source.html#l00092">blast_options_handle.cpp:92</a></div></div>
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</div><!-- fragment --><dl class="section see"><dt>See also</dt><dd><a class="el" href="blast_opts_cpp_design.html">C++ BLAST Options Design</a>.</dd></dl>
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<dl class="section author"><dt>Author</dt><dd>Christiam Camacho <a href="#" onclick="location.href='mai'+'lto:'+'cam'+'ac'+'ho@'+'nc'+'bi.'+'nl'+'m.n'+'ih'+'.go'+'v'; return false;">camac<span style="display: none;">.nosp@m.</span>ho@n<span style="display: none;">.nosp@m.</span>cbi.n<span style="display: none;">.nosp@m.</span>lm.n<span style="display: none;">.nosp@m.</span>ih.go<span style="display: none;">.nosp@m.</span>v</a> </dd></dl>
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<address style="align: right;"><small>Modified on Fri Sep 20 14:56:58 2024 by modify_doxy.py rev. 669887</small></address>
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