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<div class="title">BlastSeqSrcGetSeqArg Struct Reference</div> </div>
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<a class="el" href = "https://www.ncbi.nlm.nih.gov/toolkitbookgh/?term=BlastSeqSrcGetSeqArg">Search Toolkit Book for <i>BlastSeqSrcGetSeqArg</i></a>
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</p>
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<p>Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> interface.
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<a href="structBlastSeqSrcGetSeqArg.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="blast__seqsrc_8h_source.html">algo/blast/core/blast_seqsrc.h</a>></code></p>
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<area shape="rect" title="Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature,..." alt="" coords="95,363,253,389"/>
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<area shape="rect" href="structBLAST__SequenceBlk.html" title="Structure to hold a sequence." alt="" coords="5,273,153,300"/>
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<area shape="rect" href="structSSeqRange.html" title="A structure containing two integers, used e.g." alt="" coords="33,5,125,32"/>
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<area shape="rect" href="structBlastSeqLoc.html" title="Used to hold a set of positions, mostly used for filtering." alt="" coords="103,95,199,121"/>
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<area shape="rect" href="structBlastMaskLoc.html" title="Structure for keeping the query masking information." alt="" coords="101,184,207,211"/>
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<area shape="rect" href="structBlastSeqSrcSetRangesArg.html" title="Structure used as the argument to function SetRanges." alt="" coords="177,273,357,300"/>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
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Public Attributes</h2></td></tr>
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<tr class="memitem:a2d5f1f1917e9c9a9b3baa4868bafc2d3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcGetSeqArg.html#a2d5f1f1917e9c9a9b3baa4868bafc2d3">oid</a></td></tr>
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<tr class="memdesc:a2d5f1f1917e9c9a9b3baa4868bafc2d3"><td class="mdescLeft"> </td><td class="mdescRight">Oid in BLAST database, index in an array of sequences, etc [in]. <a href="structBlastSeqSrcGetSeqArg.html#a2d5f1f1917e9c9a9b3baa4868bafc2d3">More...</a><br /></td></tr>
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<tr class="memitem:a831dfb144c3833fe2e1eb1a30a052d79"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__AlgoBlast.html#ga19e9494c95925637d23089a93349a489">EBlastEncoding</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcGetSeqArg.html#a831dfb144c3833fe2e1eb1a30a052d79">encoding</a></td></tr>
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<tr class="memdesc:a831dfb144c3833fe2e1eb1a30a052d79"><td class="mdescLeft"> </td><td class="mdescRight">Encoding of sequence, i.e. <a href="structBlastSeqSrcGetSeqArg.html#a831dfb144c3833fe2e1eb1a30a052d79">More...</a><br /></td></tr>
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<tr class="memitem:a5362c3629d02205cc5bb033e63a10c71"><td class="memItemLeft" align="right" valign="top"><a class="el" href="ncbi__std_8h.html#a9f6121a7aa37a7e5487a28839b1f44a7">Boolean</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcGetSeqArg.html#a5362c3629d02205cc5bb033e63a10c71">reset_ranges</a></td></tr>
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<tr class="memdesc:a5362c3629d02205cc5bb033e63a10c71"><td class="mdescLeft"> </td><td class="mdescRight">This option allows the BLAST engine to communicate with the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> that the offset ranges for a given OID should be reset and the entire sequence data should be fetched. <a href="structBlastSeqSrcGetSeqArg.html#a5362c3629d02205cc5bb033e63a10c71">More...</a><br /></td></tr>
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<tr class="memitem:a8a4bd699cf35a4cc8c09ea6b1e5791e3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="ncbi__std_8h.html#a9f6121a7aa37a7e5487a28839b1f44a7">Boolean</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcGetSeqArg.html#a8a4bd699cf35a4cc8c09ea6b1e5791e3">check_oid_exclusion</a></td></tr>
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<tr class="memdesc:a8a4bd699cf35a4cc8c09ea6b1e5791e3"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structCheck.html">Check</a> whether an OID is excluded due to overlapping filtering. <a href="structBlastSeqSrcGetSeqArg.html#a8a4bd699cf35a4cc8c09ea6b1e5791e3">More...</a><br /></td></tr>
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<tr class="memitem:ab7ff0e796bb9b0f430b61c7281fe6aea"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcGetSeqArg.html#ab7ff0e796bb9b0f430b61c7281fe6aea">seq</a></td></tr>
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<tr class="memdesc:ab7ff0e796bb9b0f430b61c7281fe6aea"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="classSequence.html">Sequence</a> to return, if NULL, it should allocated by GetSeqBlkFnPtr (using BlastSeqBlkNew or BlastSetUp_SeqBlkNew), else its contents are freed (using BlastSequenceBlkClean) and the structure is reused [out]. <a href="structBlastSeqSrcGetSeqArg.html#ab7ff0e796bb9b0f430b61c7281fe6aea">More...</a><br /></td></tr>
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<tr class="memitem:ab2e2c9b548b8ae1b13196bad8c475625"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcGetSeqArg.html#ab2e2c9b548b8ae1b13196bad8c475625">ranges</a></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> interface. </p>
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<p>Index-based implementations include BLAST databases or an array/vector of sequences. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00257">257</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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</div><h2 class="groupheader">Member Data Documentation</h2>
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<a id="a8a4bd699cf35a4cc8c09ea6b1e5791e3"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a8a4bd699cf35a4cc8c09ea6b1e5791e3">◆ </a></span>check_oid_exclusion</h2>
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<td class="memname"><a class="el" href="ncbi__std_8h.html#a9f6121a7aa37a7e5487a28839b1f44a7">Boolean</a> BlastSeqSrcGetSeqArg::check_oid_exclusion</td>
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<p><a class="el" href="structCheck.html">Check</a> whether an OID is excluded due to overlapping filtering. </p>
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<p>The disease is rare, and the test for it is somewhat expensive, so it is deferred to the traceback stage. TRUE to enable this test. [in] </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00279">279</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01436">BLAST_ComputeTraceback_MT()</a>, <a class="el" href="blast__hits_8c_source.html#l02607">Blast_HSPListReevaluateUngapped()</a>, <a class="el" href="traceback__unit__test_8cpp_source.html#l01147">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__kappa_8c_source.html#l01357">s_MatchingSequenceInitialize()</a>, and <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00287">s_SeqDbGetSequence()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a831dfb144c3833fe2e1eb1a30a052d79">◆ </a></span>encoding</h2>
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<td class="memname"><a class="el" href="group__AlgoBlast.html#ga19e9494c95925637d23089a93349a489">EBlastEncoding</a> BlastSeqSrcGetSeqArg::encoding</td>
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<p>Encoding of sequence, i.e. </p>
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<p>: eBlastEncodingProtein, eBlastEncodingNucleotide, etc [in] </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00263">263</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01436">BLAST_ComputeTraceback_MT()</a>, <a class="el" href="blast__hits_8c_source.html#l02607">Blast_HSPListReevaluateUngapped()</a>, <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00159">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01725">NaHashLookupThreadDataNew()</a>, <a class="el" href="seedtop_8cpp_source.html#l00102">CSeedTop::Run()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>, <a class="el" href="blast__kappa_8c_source.html#l01357">s_MatchingSequenceInitialize()</a>, <a class="el" href="seqsrc__multiseq_8cpp_source.html#l00334">s_MultiSeqGetSequence()</a>, <a class="el" href="seqsrc__query__factory_8cpp_source.html#l00314">s_QueryFactoryGetSequence()</a>, <a class="el" href="blast__traceback_8c_source.html#l01046">s_RPSComputeTraceback()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>, <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00287">s_SeqDbGetSequence()</a>, <a class="el" href="seqsrc__vdb_8c_source.html#l00137">s_VDBSRC_GetSequence()</a>, and <a class="el" href="seqsrc__mock_8cpp_source.html#l00143">CRandomlyFailMockBlastSeqSrc::x_PopulateBLAST_SequenceBlk()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2d5f1f1917e9c9a9b3baa4868bafc2d3">◆ </a></span>oid</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcGetSeqArg::oid</td>
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<p>Oid in BLAST database, index in an array of sequences, etc [in]. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00259">259</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01436">BLAST_ComputeTraceback_MT()</a>, <a class="el" href="blast__hits_8c_source.html#l02607">Blast_HSPListReevaluateUngapped()</a>, <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00122">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__vdb__cmd_8cpp_source.html#l00268">CVdbFastaExtractor::DumpAll()</a>, <a class="el" href="seqsrc__mock_8cpp_source.html#l00118">CRandomlyFailMockBlastSeqSrc::GetSequence()</a>, <a class="el" href="seedtop_8cpp_source.html#l00102">CSeedTop::Run()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>, <a class="el" href="blast__kappa_8c_source.html#l01357">s_MatchingSequenceInitialize()</a>, <a class="el" href="seqsrc__multiseq_8cpp_source.html#l00334">s_MultiSeqGetSequence()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01827">s_NaHashLookupScanSubjectForWordCounts()</a>, <a class="el" href="seqsrc__query__factory_8cpp_source.html#l00314">s_QueryFactoryGetSequence()</a>, <a class="el" href="blast__traceback_8c_source.html#l01046">s_RPSComputeTraceback()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>, <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00287">s_SeqDbGetSequence()</a>, <a class="el" href="seqsrc__vdb_8c_source.html#l00137">s_VDBSRC_GetSequence()</a>, and <a class="el" href="seqsrc__vdb_8c_source.html#l00273">s_VDBSRC_ReleaseSequence()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab2e2c9b548b8ae1b13196bad8c475625">◆ </a></span>ranges</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a>* BlastSeqSrcGetSeqArg::ranges</td>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00286">286</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01436">BLAST_ComputeTraceback_MT()</a>, <a class="el" href="traceback__unit__test_8cpp_source.html#l01147">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__kappa_8c_source.html#l00459">s_ComputeNumIdentities()</a>, <a class="el" href="blast__kappa_8c_source.html#l01357">s_MatchingSequenceInitialize()</a>, <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00287">s_SeqDbGetSequence()</a>, and <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00417">s_SeqDbReleaseSequence()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a5362c3629d02205cc5bb033e63a10c71">◆ </a></span>reset_ranges</h2>
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<td class="memname"><a class="el" href="ncbi__std_8h.html#a9f6121a7aa37a7e5487a28839b1f44a7">Boolean</a> BlastSeqSrcGetSeqArg::reset_ranges</td>
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<p>This option allows the BLAST engine to communicate with the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> that the offset ranges for a given OID should be reset and the entire sequence data should be fetched. </p>
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<p>The motivation for this option is to exploit <a class="el" href="classCSeqDB.html" title="CSeqDB.">CSeqDB</a>'s performance feature that allows to retrieve only pre-selected portions of the sequence data for the traceback stage. <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> implementations that do not have this feature can safely ignore this field. By default, this should be set to FALSE. [in] </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00273">273</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01436">BLAST_ComputeTraceback_MT()</a>, <a class="el" href="traceback__unit__test_8cpp_source.html#l01147">BOOST_AUTO_TEST_CASE()</a>, and <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00287">s_SeqDbGetSequence()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab7ff0e796bb9b0f430b61c7281fe6aea">◆ </a></span>seq</h2>
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<td class="memname"><a class="el" href="structBLAST__SequenceBlk.html">BLAST_SequenceBlk</a>* BlastSeqSrcGetSeqArg::seq</td>
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<p><a class="el" href="classSequence.html">Sequence</a> to return, if NULL, it should allocated by GetSeqBlkFnPtr (using BlastSeqBlkNew or BlastSetUp_SeqBlkNew), else its contents are freed (using BlastSequenceBlkClean) and the structure is reused [out]. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00284">284</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01436">BLAST_ComputeTraceback_MT()</a>, <a class="el" href="blast__hits_8c_source.html#l02607">Blast_HSPListReevaluateUngapped()</a>, <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="mockseqsrc2__unit__test_8cpp_source.html#l00115">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="seqsrc__mock_8cpp_source.html#l00136">CRandomlyFailMockBlastSeqSrc::ReleaseSequence()</a>, <a class="el" href="seedtop_8cpp_source.html#l00102">CSeedTop::Run()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>, <a class="el" href="blast__kappa_8c_source.html#l01357">s_MatchingSequenceInitialize()</a>, <a class="el" href="blast__kappa_8c_source.html#l00908">s_MatchingSequenceRelease()</a>, <a class="el" href="seqsrc__multiseq_8cpp_source.html#l00334">s_MultiSeqGetSequence()</a>, <a class="el" href="seqsrc__multiseq_8cpp_source.html#l00375">s_MultiSeqReleaseSequence()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01827">s_NaHashLookupScanSubjectForWordCounts()</a>, <a class="el" href="seqsrc__query__factory_8cpp_source.html#l00314">s_QueryFactoryGetSequence()</a>, <a class="el" href="seqsrc__query__factory_8cpp_source.html#l00355">s_QueryFactoryReleaseSequence()</a>, <a class="el" href="blast__traceback_8c_source.html#l01046">s_RPSComputeTraceback()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>, <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00287">s_SeqDbGetSequence()</a>, <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00417">s_SeqDbReleaseSequence()</a>, <a class="el" href="blast__kappa_8c_source.html#l01573">s_SequenceGetProteinRange()</a>, <a class="el" href="blast__kappa_8c_source.html#l01475">s_SequenceGetTranslatedRange()</a>, <a class="el" href="seqsrc__vdb_8c_source.html#l00137">s_VDBSRC_GetSequence()</a>, <a class="el" href="seqsrc__vdb_8c_source.html#l00273">s_VDBSRC_ReleaseSequence()</a>, and <a class="el" href="seqsrc__mock_8cpp_source.html#l00143">CRandomlyFailMockBlastSeqSrc::x_PopulateBLAST_SequenceBlk()</a>.</p>
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<hr/>The documentation for this struct was generated from the following file:<ul>
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<li>include/algo/blast/core/<a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a></li>
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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 14:57:29 2024 by modify_doxy.py rev. 669887</small></address>
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