1580 lines
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1580 lines
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<div class="title">blast_seqsrc.h File Reference</div> </div>
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<p>Declaration of ADT to retrieve sequences for the BLAST engine.
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<a href="#details">More...</a></p>
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<div class="textblock"><code>#include <<a class="el" href="ncbi__std_8h_source.html">algo/blast/core/ncbi_std.h</a>></code><br />
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<code>#include <<a class="el" href="blast__def_8h_source.html">algo/blast/core/blast_def.h</a>></code><br />
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<code>#include <<a class="el" href="blast__export_8h_source.html">algo/blast/core/blast_export.h</a>></code><br />
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<code>#include <<a class="el" href="blast__message_8h_source.html">algo/blast/core/blast_message.h</a>></code><br />
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<code>#include <<a class="el" href="blast__encoding_8h_source.html">algo/blast/core/blast_encoding.h</a>></code><br />
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</div><div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
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<img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for blast_seqsrc.h:</div>
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<div class="center"><img src="img__incl/blast__seqsrc_8h__incl.png" border="0" usemap="#ainclude_2algo_2blast_2core_2blast__seqsrc_8h" alt=""/></div>
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<p><a href="blast__seqsrc_8h_source.html">Go to the source code of this file.</a>
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<p><a href="/IEB/ToolBox/CPP_DOC/viewvc.cgi?p=include/algo/blast/core/blast_seqsrc.h">Go to the SVN repository for this file.</a></p></p>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
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Classes</h2></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Structure used as the argument to function SetRanges. <a href="structBlastSeqSrcSetRangesArg.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">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. <a href="structBlastSeqSrcGetSeqArg.html#details">More...</a><br /></td></tr>
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Macros</h2></td></tr>
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<tr class="memitem:ac5eee58a1ffa12e78c04364d025a4654"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#ac5eee58a1ffa12e78c04364d025a4654">BLAST_SEQSRC_MINGAP</a>   1024</td></tr>
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<tr class="memdesc:ac5eee58a1ffa12e78c04364d025a4654"><td class="mdescLeft"> </td><td class="mdescRight">Minimal gap allowed in range list. <a href="blast__seqsrc_8h.html#ac5eee58a1ffa12e78c04364d025a4654">More...</a><br /></td></tr>
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<tr class="separator:ac5eee58a1ffa12e78c04364d025a4654"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a52e800f662528d9fc42e8bd15a4a53a4"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a52e800f662528d9fc42e8bd15a4a53a4">BLAST_SEQSRC_OVERHANG</a>   1024</td></tr>
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<tr class="memdesc:a52e800f662528d9fc42e8bd15a4a53a4"><td class="mdescLeft"> </td><td class="mdescRight">Extension for each new range added. <a href="blast__seqsrc_8h.html#a52e800f662528d9fc42e8bd15a4a53a4">More...</a><br /></td></tr>
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<tr class="separator:a52e800f662528d9fc42e8bd15a4a53a4"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a5c1140ea892076940ee2dc6e599ac043"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a5c1140ea892076940ee2dc6e599ac043">BLAST_SEQSRC_MINLENGTH</a>   10</td></tr>
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<tr class="memdesc:a5c1140ea892076940ee2dc6e599ac043"><td class="mdescLeft"> </td><td class="mdescRight">Default minimal sequence length. <a href="blast__seqsrc_8h.html#a5c1140ea892076940ee2dc6e599ac043">More...</a><br /></td></tr>
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<tr class="separator:a5c1140ea892076940ee2dc6e599ac043"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a921049de0eaf40537268d8ea0be678ad"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a921049de0eaf40537268d8ea0be678ad">BLAST_SEQSRC_EXCLUDED</a>   -3</td></tr>
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<tr class="memdesc:a921049de0eaf40537268d8ea0be678ad"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="classSequence.html">Sequence</a> excluded due to filtering. <a href="blast__seqsrc_8h.html#a921049de0eaf40537268d8ea0be678ad">More...</a><br /></td></tr>
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<tr class="separator:a921049de0eaf40537268d8ea0be678ad"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0b466383c45148cb879445dc0905eb83"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a0b466383c45148cb879445dc0905eb83">BLAST_SEQSRC_ERROR</a>   -2</td></tr>
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<tr class="memdesc:a0b466383c45148cb879445dc0905eb83"><td class="mdescLeft"> </td><td class="mdescRight">Error while retrieving sequence. <a href="blast__seqsrc_8h.html#a0b466383c45148cb879445dc0905eb83">More...</a><br /></td></tr>
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<tr class="separator:a0b466383c45148cb879445dc0905eb83"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aee6932d14ba30995f78bf52628a7d689"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#aee6932d14ba30995f78bf52628a7d689">BLAST_SEQSRC_EOF</a>   -1</td></tr>
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<tr class="memdesc:aee6932d14ba30995f78bf52628a7d689"><td class="mdescLeft"> </td><td class="mdescRight">No more sequences available. <a href="blast__seqsrc_8h.html#aee6932d14ba30995f78bf52628a7d689">More...</a><br /></td></tr>
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<tr class="separator:aee6932d14ba30995f78bf52628a7d689"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4a8c5eb08476555d619c56d38fdcbe6d"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a4a8c5eb08476555d619c56d38fdcbe6d">BLAST_SEQSRC_SUCCESS</a>   0</td></tr>
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<tr class="memdesc:a4a8c5eb08476555d619c56d38fdcbe6d"><td class="mdescLeft"> </td><td class="mdescRight">Successful sequence retrieval. <a href="blast__seqsrc_8h.html#a4a8c5eb08476555d619c56d38fdcbe6d">More...</a><br /></td></tr>
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<tr class="separator:a4a8c5eb08476555d619c56d38fdcbe6d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="typedef-members"></a>
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Typedefs</h2></td></tr>
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<tr class="memitem:a86654b4777d19e87abfed1dee78d6c54"><td class="memItemLeft" align="right" valign="top">typedef struct <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a86654b4777d19e87abfed1dee78d6c54">BlastSeqSrc</a></td></tr>
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<tr class="memdesc:a86654b4777d19e87abfed1dee78d6c54"><td class="mdescLeft"> </td><td class="mdescRight">The <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> ADT is an opaque data type that defines an interface which is used by the core BLAST code to retrieve sequences. <a href="blast__seqsrc_8h.html#a86654b4777d19e87abfed1dee78d6c54">More...</a><br /></td></tr>
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<tr class="separator:a86654b4777d19e87abfed1dee78d6c54"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2e03de2714b53788153385fbe3785b46"><td class="memItemLeft" align="right" valign="top">typedef struct <a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a2e03de2714b53788153385fbe3785b46">BlastSeqSrcIterator</a></td></tr>
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<tr class="memdesc:a2e03de2714b53788153385fbe3785b46"><td class="mdescLeft"> </td><td class="mdescRight">Blast <a class="el" href="classSequence.html">Sequence</a> Source Iterator, designed to be used in conjunction with the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> to provide MT-safe iteration over the sequences in the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a>. <a href="blast__seqsrc_8h.html#a2e03de2714b53788153385fbe3785b46">More...</a><br /></td></tr>
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<tr class="separator:a2e03de2714b53788153385fbe3785b46"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3c94ce46e2ec046bcef60af5eb2d2179"><td class="memItemLeft" align="right" valign="top">typedef struct <a class="el" href="structBlastSeqSrcNewInfo.html">BlastSeqSrcNewInfo</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a3c94ce46e2ec046bcef60af5eb2d2179">BlastSeqSrcNewInfo</a></td></tr>
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<tr class="memdesc:a3c94ce46e2ec046bcef60af5eb2d2179"><td class="mdescLeft"> </td><td class="mdescRight">Structure that contains the information needed for BlastSeqSrcNew to fully populate the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure it returns. <a href="blast__seqsrc_8h.html#a3c94ce46e2ec046bcef60af5eb2d2179">More...</a><br /></td></tr>
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<tr class="separator:a3c94ce46e2ec046bcef60af5eb2d2179"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a96ef8c81fe14a71b09c09e4bb85c8a79"><td class="memItemLeft" align="right" valign="top">typedef struct <a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a96ef8c81fe14a71b09c09e4bb85c8a79">BlastSeqSrcSetRangesArg</a></td></tr>
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<tr class="memdesc:a96ef8c81fe14a71b09c09e4bb85c8a79"><td class="mdescLeft"> </td><td class="mdescRight">Structure used as the argument to function SetRanges. <a href="blast__seqsrc_8h.html#a96ef8c81fe14a71b09c09e4bb85c8a79">More...</a><br /></td></tr>
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<tr class="separator:a96ef8c81fe14a71b09c09e4bb85c8a79"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac359a7474a0825eef63c0fe4ddaa1e57"><td class="memItemLeft" align="right" valign="top">typedef struct <a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#ac359a7474a0825eef63c0fe4ddaa1e57">BlastSeqSrcGetSeqArg</a></td></tr>
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<tr class="memdesc:ac359a7474a0825eef63c0fe4ddaa1e57"><td class="mdescLeft"> </td><td class="mdescRight">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. <a href="blast__seqsrc_8h.html#ac359a7474a0825eef63c0fe4ddaa1e57">More...</a><br /></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="func-members"></a>
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Functions</h2></td></tr>
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<tr class="memitem:a46401cf3a7e39b51523787ee918b6e65"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a46401cf3a7e39b51523787ee918b6e65">BlastSeqSrcNew</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrcNewInfo.html">BlastSeqSrcNewInfo</a> *bssn_info)</td></tr>
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<tr class="memdesc:a46401cf3a7e39b51523787ee918b6e65"><td class="mdescLeft"> </td><td class="mdescRight">Allocates memory for a <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure and then invokes the constructor function defined in its first argument, passing the ctor_argument member of that same structure. <a href="blast__seqsrc_8h.html#a46401cf3a7e39b51523787ee918b6e65">More...</a><br /></td></tr>
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<tr class="memitem:a65a3ba91c67a8cb770c42427481bd74d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a65a3ba91c67a8cb770c42427481bd74d">BlastSeqSrcCopy</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:a65a3ba91c67a8cb770c42427481bd74d"><td class="mdescLeft"> </td><td class="mdescRight">Copy function: needed to guarantee thread safety. <a href="blast__seqsrc_8h.html#a65a3ba91c67a8cb770c42427481bd74d">More...</a><br /></td></tr>
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<tr class="memitem:aab017f7f48cd04f1cb094b08df9e2d92"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#aab017f7f48cd04f1cb094b08df9e2d92">BlastSeqSrcFree</a> (<a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:aab017f7f48cd04f1cb094b08df9e2d92"><td class="mdescLeft"> </td><td class="mdescRight">Frees the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure by invoking the destructor function set by the user-defined constructor function when the structure is initialized (indirectly, by BlastSeqSrcNew). <a href="blast__seqsrc_8h.html#aab017f7f48cd04f1cb094b08df9e2d92">More...</a><br /></td></tr>
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<tr class="separator:aab017f7f48cd04f1cb094b08df9e2d92"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a906dc37859d57d3cb8bccf0b51da6115"><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="blast__seqsrc_8h.html#a906dc37859d57d3cb8bccf0b51da6115">BlastSeqSrcGetNumSeqs</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:a906dc37859d57d3cb8bccf0b51da6115"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of sequences contained in the sequence source. <a href="blast__seqsrc_8h.html#a906dc37859d57d3cb8bccf0b51da6115">More...</a><br /></td></tr>
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<tr class="separator:a906dc37859d57d3cb8bccf0b51da6115"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab25760d4a21dc5084c6fd9d8b89352bd"><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="blast__seqsrc_8h.html#ab25760d4a21dc5084c6fd9d8b89352bd">BlastSeqSrcGetNumSeqsStats</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:ab25760d4a21dc5084c6fd9d8b89352bd"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of sequences used for calculation of expect values etc. <a href="blast__seqsrc_8h.html#ab25760d4a21dc5084c6fd9d8b89352bd">More...</a><br /></td></tr>
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<tr class="separator:ab25760d4a21dc5084c6fd9d8b89352bd"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad2ee5f1a9af00d595fbd82d00af556fd"><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="blast__seqsrc_8h.html#ad2ee5f1a9af00d595fbd82d00af556fd">BlastSeqSrcGetMaxSeqLen</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:ad2ee5f1a9af00d595fbd82d00af556fd"><td class="mdescLeft"> </td><td class="mdescRight">Get the length of the longest sequence in the sequence source. <a href="blast__seqsrc_8h.html#ad2ee5f1a9af00d595fbd82d00af556fd">More...</a><br /></td></tr>
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<tr class="separator:ad2ee5f1a9af00d595fbd82d00af556fd"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af74443d9cdebc2cd3bae309183a1937e"><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="blast__seqsrc_8h.html#af74443d9cdebc2cd3bae309183a1937e">BlastSeqSrcGetMinSeqLen</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:af74443d9cdebc2cd3bae309183a1937e"><td class="mdescLeft"> </td><td class="mdescRight">Get the length of the longest sequence in the sequence source. <a href="blast__seqsrc_8h.html#af74443d9cdebc2cd3bae309183a1937e">More...</a><br /></td></tr>
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<tr class="separator:af74443d9cdebc2cd3bae309183a1937e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a776a73f9b3df3fc41d521583ea00e62b"><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="blast__seqsrc_8h.html#a776a73f9b3df3fc41d521583ea00e62b">BlastSeqSrcGetAvgSeqLen</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:a776a73f9b3df3fc41d521583ea00e62b"><td class="mdescLeft"> </td><td class="mdescRight">Get the average length of all sequences in the sequence source. <a href="blast__seqsrc_8h.html#a776a73f9b3df3fc41d521583ea00e62b">More...</a><br /></td></tr>
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<tr class="separator:a776a73f9b3df3fc41d521583ea00e62b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa47005077a0b50a4cebe3a449c7bfe7a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Portability.html#gac9cc73bc670c02eb6146e38650740642">Int8</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#aa47005077a0b50a4cebe3a449c7bfe7a">BlastSeqSrcGetTotLen</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:aa47005077a0b50a4cebe3a449c7bfe7a"><td class="mdescLeft"> </td><td class="mdescRight">Get the total length of all sequences in the sequence source. <a href="blast__seqsrc_8h.html#aa47005077a0b50a4cebe3a449c7bfe7a">More...</a><br /></td></tr>
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<tr class="separator:aa47005077a0b50a4cebe3a449c7bfe7a"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2807ac630ae01c215adfa4080ad92b52"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Portability.html#gac9cc73bc670c02eb6146e38650740642">Int8</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a2807ac630ae01c215adfa4080ad92b52">BlastSeqSrcGetTotLenStats</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:a2807ac630ae01c215adfa4080ad92b52"><td class="mdescLeft"> </td><td class="mdescRight">Get the total length of all sequences for calculation of expect value etc. <a href="blast__seqsrc_8h.html#a2807ac630ae01c215adfa4080ad92b52">More...</a><br /></td></tr>
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<tr class="separator:a2807ac630ae01c215adfa4080ad92b52"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ada455ff2e3b1dfffd4b530f4ce772384"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#ada455ff2e3b1dfffd4b530f4ce772384">BlastSeqSrcGetName</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:ada455ff2e3b1dfffd4b530f4ce772384"><td class="mdescLeft"> </td><td class="mdescRight">Get the Blast <a class="el" href="classSequence.html">Sequence</a> source name (e.g. <a href="blast__seqsrc_8h.html#ada455ff2e3b1dfffd4b530f4ce772384">More...</a><br /></td></tr>
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<tr class="separator:ada455ff2e3b1dfffd4b530f4ce772384"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a38f77869fa15212d20bcd7240810f870"><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="blast__seqsrc_8h.html#a38f77869fa15212d20bcd7240810f870">BlastSeqSrcGetIsProt</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:a38f77869fa15212d20bcd7240810f870"><td class="mdescLeft"> </td><td class="mdescRight">Find if the Blast <a class="el" href="classSequence.html">Sequence</a> Source contains protein or nucleotide sequences. <a href="blast__seqsrc_8h.html#a38f77869fa15212d20bcd7240810f870">More...</a><br /></td></tr>
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<tr class="separator:a38f77869fa15212d20bcd7240810f870"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad66ae0b63c1f008035c02e96ed64fa01"><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="blast__seqsrc_8h.html#ad66ae0b63c1f008035c02e96ed64fa01">BlastSeqSrcGetSupportsPartialFetching</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:ad66ae0b63c1f008035c02e96ed64fa01"><td class="mdescLeft"> </td><td class="mdescRight">Find if the Blast <a class="el" href="classSequence.html">Sequence</a> Source supports partial fetching. <a href="blast__seqsrc_8h.html#ad66ae0b63c1f008035c02e96ed64fa01">More...</a><br /></td></tr>
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<tr class="separator:ad66ae0b63c1f008035c02e96ed64fa01"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab5ff629359beef75b97a2879f622a148"><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="blast__seqsrc_8h.html#ab5ff629359beef75b97a2879f622a148">BlastSeqSrcSetRangesArgNew</a> (<a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> num_ranges)</td></tr>
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<tr class="memdesc:ab5ff629359beef75b97a2879f622a148"><td class="mdescLeft"> </td><td class="mdescRight">new setrangearg <a href="blast__seqsrc_8h.html#ab5ff629359beef75b97a2879f622a148">More...</a><br /></td></tr>
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<tr class="separator:ab5ff629359beef75b97a2879f622a148"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a139969750a141eca61d7a01b3399ba96"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Portability.html#ga4c5ce3be47003f4087cbd9b202a8492d">Int2</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a139969750a141eca61d7a01b3399ba96">BlastSeqSrcSetRangesArgAddRange</a> (<a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> *arg, <a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> begin, <a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> end, <a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> <a class="el" href="ftds14_2freetds_2tds_2iconv_8c.html#a96bbf959016e4411c9e6b9812a8be60a">len</a>)</td></tr>
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<tr class="memdesc:a139969750a141eca61d7a01b3399ba96"><td class="mdescLeft"> </td><td class="mdescRight">add new range <a href="blast__seqsrc_8h.html#a139969750a141eca61d7a01b3399ba96">More...</a><br /></td></tr>
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<tr class="separator:a139969750a141eca61d7a01b3399ba96"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae5442b1145f38442fd4354fc08b173b9"><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="blast__seqsrc_8h.html#ae5442b1145f38442fd4354fc08b173b9">BlastSeqSrcSetRangesArgFree</a> (<a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> *arg)</td></tr>
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<tr class="memdesc:ae5442b1145f38442fd4354fc08b173b9"><td class="mdescLeft"> </td><td class="mdescRight">free setrangearg <a href="blast__seqsrc_8h.html#ae5442b1145f38442fd4354fc08b173b9">More...</a><br /></td></tr>
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<tr class="separator:ae5442b1145f38442fd4354fc08b173b9"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a54539d5f0e9e253498d2d6bddc1d1bd6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a54539d5f0e9e253498d2d6bddc1d1bd6">BlastSeqSrcSetRangesArgBuild</a> (<a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> *arg)</td></tr>
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<tr class="memdesc:a54539d5f0e9e253498d2d6bddc1d1bd6"><td class="mdescLeft"> </td><td class="mdescRight">build <a class="el" href="structBlastSeqSrcSetRangesArg.html" title="Structure used as the argument to function SetRanges.">BlastSeqSrcSetRangesArg</a> from range list <a href="blast__seqsrc_8h.html#a54539d5f0e9e253498d2d6bddc1d1bd6">More...</a><br /></td></tr>
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<tr class="separator:a54539d5f0e9e253498d2d6bddc1d1bd6"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a6f886124dbb2fdcc48dd96d26eb55885"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a6f886124dbb2fdcc48dd96d26eb55885">BlastSeqSrcSetSeqRanges</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src, <a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> *setranges_arg)</td></tr>
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<tr class="memdesc:a6f886124dbb2fdcc48dd96d26eb55885"><td class="mdescLeft"> </td><td class="mdescRight">Setting the ranges for partial fetching. <a href="blast__seqsrc_8h.html#a6f886124dbb2fdcc48dd96d26eb55885">More...</a><br /></td></tr>
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<tr class="separator:a6f886124dbb2fdcc48dd96d26eb55885"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae1bf3c99343c9fe13452dd6bdd1534da"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Portability.html#ga4c5ce3be47003f4087cbd9b202a8492d">Int2</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#ae1bf3c99343c9fe13452dd6bdd1534da">BlastSeqSrcGetSequence</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src, <a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a> *getseq_arg)</td></tr>
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<tr class="memdesc:ae1bf3c99343c9fe13452dd6bdd1534da"><td class="mdescLeft"> </td><td class="mdescRight">Retrieve an individual sequence. <a href="blast__seqsrc_8h.html#ae1bf3c99343c9fe13452dd6bdd1534da">More...</a><br /></td></tr>
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<tr class="separator:ae1bf3c99343c9fe13452dd6bdd1534da"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a353f24339b726ee3bbab30adcb11ab09"><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="blast__seqsrc_8h.html#a353f24339b726ee3bbab30adcb11ab09">BlastSeqSrcGetSeqLen</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src, void *oid)</td></tr>
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<tr class="memdesc:a353f24339b726ee3bbab30adcb11ab09"><td class="mdescLeft"> </td><td class="mdescRight">Retrieve sequence length (number of residues/bases) <a href="blast__seqsrc_8h.html#a353f24339b726ee3bbab30adcb11ab09">More...</a><br /></td></tr>
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<tr class="separator:a353f24339b726ee3bbab30adcb11ab09"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a5909bb7ccc99229678dee036626dc618"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a5909bb7ccc99229678dee036626dc618">BlastSeqSrcReleaseSequence</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src, <a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a> *getseq_arg)</td></tr>
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<tr class="memdesc:a5909bb7ccc99229678dee036626dc618"><td class="mdescLeft"> </td><td class="mdescRight">Deallocate individual sequence. <a href="blast__seqsrc_8h.html#a5909bb7ccc99229678dee036626dc618">More...</a><br /></td></tr>
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<tr class="separator:a5909bb7ccc99229678dee036626dc618"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a7dc64768dc2c656e226264055d43a5c2"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a7dc64768dc2c656e226264055d43a5c2">BlastSeqSrcGetInitError</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:a7dc64768dc2c656e226264055d43a5c2"><td class="mdescLeft"> </td><td class="mdescRight">Function to retrieve NULL terminated string containing the description of an initialization error or NULL. <a href="blast__seqsrc_8h.html#a7dc64768dc2c656e226264055d43a5c2">More...</a><br /></td></tr>
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<tr class="separator:a7dc64768dc2c656e226264055d43a5c2"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a5cfb590abfe225628fc0827007cac612"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a5cfb590abfe225628fc0827007cac612">BlastSeqSrcIteratorNew</a> (void)</td></tr>
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<tr class="memdesc:a5cfb590abfe225628fc0827007cac612"><td class="mdescLeft"> </td><td class="mdescRight">Allocate and initialize an iterator over a <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> with a default chunk size for MT-safe iteration. <a href="blast__seqsrc_8h.html#a5cfb590abfe225628fc0827007cac612">More...</a><br /></td></tr>
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<tr class="separator:a5cfb590abfe225628fc0827007cac612"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a343bfa5ab569faf981307b4161e49a74"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a343bfa5ab569faf981307b4161e49a74">BlastSeqSrcIteratorNewEx</a> (unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> chunk_sz)</td></tr>
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<tr class="memdesc:a343bfa5ab569faf981307b4161e49a74"><td class="mdescLeft"> </td><td class="mdescRight">Allocate and initialize an iterator over a <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a>. <a href="blast__seqsrc_8h.html#a343bfa5ab569faf981307b4161e49a74">More...</a><br /></td></tr>
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<tr class="separator:a343bfa5ab569faf981307b4161e49a74"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2db9709fa1a1af3f3986254bf6f0acda"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#a2db9709fa1a1af3f3986254bf6f0acda">BlastSeqSrcIteratorFree</a> (<a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> *itr)</td></tr>
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<tr class="memdesc:a2db9709fa1a1af3f3986254bf6f0acda"><td class="mdescLeft"> </td><td class="mdescRight">Frees the <a class="el" href="structBlastSeqSrcIterator.html" title="Complete type definition of Blast Sequence Source Iterator.">BlastSeqSrcIterator</a> structure. <a href="blast__seqsrc_8h.html#a2db9709fa1a1af3f3986254bf6f0acda">More...</a><br /></td></tr>
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<tr class="separator:a2db9709fa1a1af3f3986254bf6f0acda"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a258f37f685e0315c4d807cfccb899d04"><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="blast__seqsrc_8h.html#a258f37f685e0315c4d807cfccb899d04">BlastSeqSrcIteratorNext</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src, <a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> *itr)</td></tr>
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<tr class="memdesc:a258f37f685e0315c4d807cfccb899d04"><td class="mdescLeft"> </td><td class="mdescRight">Increments the <a class="el" href="structBlastSeqSrcIterator.html" title="Complete type definition of Blast Sequence Source Iterator.">BlastSeqSrcIterator</a>. <a href="blast__seqsrc_8h.html#a258f37f685e0315c4d807cfccb899d04">More...</a><br /></td></tr>
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<tr class="separator:a258f37f685e0315c4d807cfccb899d04"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:afc6eda40980bc24c81420d47b3fe3078"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#afc6eda40980bc24c81420d47b3fe3078">BlastSeqSrcResetChunkIterator</a> (<a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src)</td></tr>
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<tr class="memdesc:afc6eda40980bc24c81420d47b3fe3078"><td class="mdescLeft"> </td><td class="mdescRight">Reset the internal "bookmark" of the last chunk for iteration provided by this object. <a href="blast__seqsrc_8h.html#afc6eda40980bc24c81420d47b3fe3078">More...</a><br /></td></tr>
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<tr class="separator:afc6eda40980bc24c81420d47b3fe3078"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:acb1644f9782e2de7bf9410d248232efc"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#acb1644f9782e2de7bf9410d248232efc">BlastSeqSrcSetNumberOfThreads</a> (<a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> *seq_src, <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> nthreads)</td></tr>
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<tr class="memdesc:acb1644f9782e2de7bf9410d248232efc"><td class="mdescLeft"> </td><td class="mdescRight">Set the number of threads for MT mode. <a href="blast__seqsrc_8h.html#acb1644f9782e2de7bf9410d248232efc">More...</a><br /></td></tr>
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<tr class="separator:acb1644f9782e2de7bf9410d248232efc"><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="var-members"></a>
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Variables</h2></td></tr>
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<tr class="memitem:ab7c5991d3a46ea3e664de1487203e33c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="blast__seqsrc_8h.html#ab7c5991d3a46ea3e664de1487203e33c">kBlastSeqSrcDefaultChunkSize</a></td></tr>
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<tr class="memdesc:ab7c5991d3a46ea3e664de1487203e33c"><td class="mdescLeft"> </td><td class="mdescRight">How many database sequences to process in one database chunk. <a href="blast__seqsrc_8h.html#ab7c5991d3a46ea3e664de1487203e33c">More...</a><br /></td></tr>
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<tr class="separator:ab7c5991d3a46ea3e664de1487203e33c"><td class="memSeparator" colspan="2"> </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>Declaration of ADT to retrieve sequences for the BLAST engine. </p>
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<p class="definition">Definition in file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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</div><h2 class="groupheader">Macro Definition Documentation</h2>
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<a id="aee6932d14ba30995f78bf52628a7d689"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#aee6932d14ba30995f78bf52628a7d689">◆ </a></span>BLAST_SEQSRC_EOF</h2>
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<td class="memname">#define BLAST_SEQSRC_EOF   -1</td>
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<p>No more sequences available. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00292">292</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0b466383c45148cb879445dc0905eb83">◆ </a></span>BLAST_SEQSRC_ERROR</h2>
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<td class="memname">#define BLAST_SEQSRC_ERROR   -2</td>
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<p>Error while retrieving sequence. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00291">291</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a921049de0eaf40537268d8ea0be678ad">◆ </a></span>BLAST_SEQSRC_EXCLUDED</h2>
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<td class="memname">#define BLAST_SEQSRC_EXCLUDED   -3</td>
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<p><a class="el" href="classSequence.html">Sequence</a> excluded due to filtering. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00290">290</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac5eee58a1ffa12e78c04364d025a4654">◆ </a></span>BLAST_SEQSRC_MINGAP</h2>
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<td class="memname">#define BLAST_SEQSRC_MINGAP   1024</td>
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<p>Minimal gap allowed in range list. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00203">203</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a5c1140ea892076940ee2dc6e599ac043">◆ </a></span>BLAST_SEQSRC_MINLENGTH</h2>
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<td class="memname">#define BLAST_SEQSRC_MINLENGTH   10</td>
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<p>Default minimal sequence length. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00205">205</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a52e800f662528d9fc42e8bd15a4a53a4">◆ </a></span>BLAST_SEQSRC_OVERHANG</h2>
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<td class="memname">#define BLAST_SEQSRC_OVERHANG   1024</td>
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<p>Extension for each new range added. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00204">204</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4a8c5eb08476555d619c56d38fdcbe6d">◆ </a></span>BLAST_SEQSRC_SUCCESS</h2>
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<td class="memname">#define BLAST_SEQSRC_SUCCESS   0</td>
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<p>Successful sequence retrieval. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00293">293</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="groupheader">Typedef Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a86654b4777d19e87abfed1dee78d6c54">◆ </a></span>BlastSeqSrc</h2>
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<td class="memname">typedef struct <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a></td>
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<p>The <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> ADT is an opaque data type that defines an interface which is used by the core BLAST code to retrieve sequences. </p>
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<p>The interface currently provides the following services:</p><ul>
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<li>Retrieving number of sequences in a set</li>
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<li>Retrieving the total length (in bases/residues) of sequences in a set.</li>
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<li>Retrieving the length of the longest sequence in a set</li>
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<li>Retrieving an individual sequence in a user-specified encoding by ordinal id (index into a set)</li>
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<li>Retrieving the length of a given sequence in a set by ordinal id</li>
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<li>Allow MT-safe iteration over sequences in a set through the <a class="el" href="structBlastSeqSrcIterator.html" title="Complete type definition of Blast Sequence Source Iterator.">BlastSeqSrcIterator</a> abstraction, as well as resetting of any applicable implementation internal 'bookmarks' which keep track of the iteration progress, as to allow multiple passes over the set of sequences (<dl class="section see"><dt>See also</dt><dd><a class="el" href="blast__seqsrc_8h.html#afc6eda40980bc24c81420d47b3fe3078" title="Reset the internal "bookmark" of the last chunk for iteration provided by this object.">BlastSeqSrcResetChunkIterator</a>). Currently <a class="el" href="introspection__html_8hpp.html#aee59723ff290c25c3c24460df26c75b8">available</a> <a class="el" href="smart__save__to__client_8cpp.html#af34ed20b67d023f9bcbacc616d6e05be">client</a> implementations of the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> API include:</dd></dl>
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<li>ReaddbBlastSeqSrcInit (C toolkit)</li>
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<li>SeqDbBlastSeqSrcInit (C++ toolkit)</li>
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<li>MultiSeqBlastSeqSrcInit (C/C++ toolkit)</li>
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<p>For more details, see also <a class="el" href="_impl_blast_seqsrc_howto.html">Implementing the BlastSeqSrc interface</a> </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00001">1</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac359a7474a0825eef63c0fe4ddaa1e57">◆ </a></span>BlastSeqSrcGetSeqArg</h2>
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<td class="memname">typedef struct <a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a> <a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a></td>
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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. </p>
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<p>Index-based implementations include BLAST databases or an array/vector of sequences. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2e03de2714b53788153385fbe3785b46">◆ </a></span>BlastSeqSrcIterator</h2>
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<td class="memname">typedef struct <a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> <a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a></td>
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<p>Blast <a class="el" href="classSequence.html">Sequence</a> Source Iterator, designed to be used in conjunction with the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> to provide MT-safe iteration over the sequences in the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a>. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00001">1</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a3c94ce46e2ec046bcef60af5eb2d2179">◆ </a></span>BlastSeqSrcNewInfo</h2>
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<td class="memname">typedef struct <a class="el" href="structBlastSeqSrcNewInfo.html">BlastSeqSrcNewInfo</a> <a class="el" href="structBlastSeqSrcNewInfo.html">BlastSeqSrcNewInfo</a></td>
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<p>Structure that contains the information needed for BlastSeqSrcNew to fully populate the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure it returns. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8h_source.html#l00001">1</a> of file <a class="el" href="blast__seqsrc_8h_source.html">blast_seqsrc.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a96ef8c81fe14a71b09c09e4bb85c8a79">◆ </a></span>BlastSeqSrcSetRangesArg</h2>
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<td class="memname">typedef struct <a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> <a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a></td>
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<p>Structure used as the argument to function SetRanges. </p>
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<h2 class="groupheader">Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a65a3ba91c67a8cb770c42427481bd74d">◆ </a></span>BlastSeqSrcCopy()</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a>* BlastSeqSrcCopy </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Copy function: needed to guarantee thread safety. </p>
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<p>Copies the contents of an input <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a>, then calls a copier function, provided by the implementation, to achieve multi-thread safety. </p><dl class="params"><dt>Parameters</dt><dd>
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<dl class="section return"><dt>Returns</dt><dd>An MT-safe copy of the structure passed in, NULL in case of memory allocation failure, or, if no copy function was provided by the implementation, a bitwise copy of the input. </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00138">138</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8c_source.html#l00035">BlastMemDup()</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00047">BlastSeqSrc::CopyFnPtr</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__kappa_8c_source.html#l02981">Blast_RedoAlignmentCore_MT()</a>, <a class="el" href="traceback__unit__test_8cpp_source.html#l01147">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="prelim__search__runner_8hpp_source.html#l00111">CPrelimSearchThread::CPrelimSearchThread()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01725">NaHashLookupThreadDataNew()</a>, <a class="el" href="split__query__aux__priv_8cpp_source.html#l00185">SplitQuery_CreateChunkData()</a>, and <a class="el" href="blast__traceback__mt__priv_8c_source.html#l00202">SThreadLocalDataArraySetup()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aab017f7f48cd04f1cb094b08df9e2d92">◆ </a></span>BlastSeqSrcFree()</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a>* BlastSeqSrcFree </td>
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<p>Frees the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure by invoking the destructor function set by the user-defined constructor function when the structure is initialized (indirectly, by BlastSeqSrcNew). </p>
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<p>If the destructor function pointer is not set, a memory leak could occur. Note that it is the implementation's destructor responsibility to free the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure by calling sfree. </p><dl class="params"><dt>Parameters</dt><dd>
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<dl class="section return"><dt>Returns</dt><dd>NULL </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00112">112</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00046">BlastSeqSrc::DeleteFnPtr</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00084">BlastSeqSrc::InitErrorStr</a>, <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>, and <a class="el" href="blast__def_8h_source.html#l00112">sfree</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__kappa_8c_source.html#l02981">Blast_RedoAlignmentCore_MT()</a>, <a class="el" href="blastengine__unit__test_8cpp_source.html#l00148">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="prelim__stage_8cpp_source.html#l00062">CBlastPrelimSearch::CBlastPrelimSearch()</a>, <a class="el" href="prelim__search__runner_8hpp_source.html#l00111">CPrelimSearchThread::CPrelimSearchThread()</a>, <a class="el" href="setup__factory_8cpp_source.html#l00414">CSetupFactory::CreateBlastSeqSrc()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01672">NaHashLookupThreadDataFree()</a>, <a class="el" href="kblastapi_8cpp_source.html#l00154">CBlastKmerSearch::Run()</a>, <a class="el" href="split__query__aux__priv_8cpp_source.html#l00185">SplitQuery_CreateChunkData()</a>, <a class="el" href="blast__traceback__mt__priv_8c_source.html#l00042">SThreadLocalDataFree()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00219">CVDBBlastUtil::x_MakeVDBSeqSrc()</a>, <a class="el" href="local__db__adapter_8cpp_source.html#l00092">CLocalDbAdapter::~CLocalDbAdapter()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00293">CVDBBlastUtil::~CVDBBlastUtil()</a>, and <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00053">FailingMockSeqSrcTestFixture::~FailingMockSeqSrcTestFixture()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a776a73f9b3df3fc41d521583ea00e62b">◆ </a></span>BlastSeqSrcGetAvgSeqLen()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcGetAvgSeqLen </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em></td><td>)</td>
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<p>Get the average length of all sequences in the sequence source. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00211">211</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00057">BlastSeqSrc::GetAvgSeqLen</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00074">BOOST_AUTO_TEST_CASE()</a>, and <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a7dc64768dc2c656e226264055d43a5c2">◆ </a></span>BlastSeqSrcGetInitError()</h2>
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<td class="memname">char* BlastSeqSrcGetInitError </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Function to retrieve NULL terminated string containing the description of an initialization error or NULL. </p>
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<p>This function MUST ALWAYS be called after calling one of the client implementation's Init functions. If the return value is not NULL, invoking any other functionality from the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> will result in undefined behavior. Caller is responsible for deallocating the return value. </p><dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td><a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> from which to get an error [in] </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>error message or NULL </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00159">159</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="blast__seqsrc_8c_source.html#l00084">BlastSeqSrc::InitErrorStr</a>, <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>, and <a class="el" href="ncbi__ansi__ext_8h_source.html#l00070">strdup</a>.</p>
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<p class="reference">Referenced by <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00109">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="algo_2blast_2unit__tests_2api_2blast__test__util_8cpp_source.html#l00226">TestUtil::CheckForBlastSeqSrcErrors()</a>, <a class="el" href="setup__factory_8cpp_source.html#l00414">CSetupFactory::CreateBlastSeqSrc()</a>, <a class="el" href="local__db__adapter_8cpp_source.html#l00110">s_CheckForBlastSeqSrcErrors()</a>, and <a class="el" href="vdb2blast__util_8cpp_source.html#l00219">CVDBBlastUtil::x_MakeVDBSeqSrc()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a38f77869fa15212d20bcd7240810f870">◆ </a></span>BlastSeqSrcGetIsProt()</h2>
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<td class="memname"><a class="el" href="ncbi__std_8h.html#a9f6121a7aa37a7e5487a28839b1f44a7">Boolean</a> BlastSeqSrcGetIsProt </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em></td><td>)</td>
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<p>Find if the Blast <a class="el" href="classSequence.html">Sequence</a> Source contains protein or nucleotide sequences. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00243">243</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00062">BlastSeqSrc::GetIsProt</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00089">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="local__db__adapter_8cpp_source.html#l00178">CLocalDbAdapter::IsProtein()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>, and <a class="el" href="local__blast_8cpp_source.html#l00150">s_InitSeqInfoSrc()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ad2ee5f1a9af00d595fbd82d00af556fd">◆ </a></span>BlastSeqSrcGetMaxSeqLen()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcGetMaxSeqLen </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Get the length of the longest sequence in the sequence source. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00193">193</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00055">BlastSeqSrc::GetMaxSeqLen</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__setup_8c_source.html#l00888">BLAST_GapAlignSetUp()</a>, <a class="el" href="blast__kappa_8c_source.html#l02981">Blast_RedoAlignmentCore_MT()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00069">BOOST_AUTO_TEST_CASE()</a>, and <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af74443d9cdebc2cd3bae309183a1937e">◆ </a></span>BlastSeqSrcGetMinSeqLen()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcGetMinSeqLen </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Get the length of the longest sequence in the sequence source. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00201">201</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00205">BLAST_SEQSRC_MINLENGTH</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00056">BlastSeqSrc::GetMinSeqLen</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__setup_8c_source.html#l00888">BLAST_GapAlignSetUp()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ada455ff2e3b1dfffd4b530f4ce772384">◆ </a></span>BlastSeqSrcGetName()</h2>
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<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> char* BlastSeqSrcGetName </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Get the Blast <a class="el" href="classSequence.html">Sequence</a> source name (e.g. </p>
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<p>: BLAST database name). Here the full name (path and file name) should be returned. If an alias file is present the return value should be the full name of the alias file. </p><dl class="params"><dt>Parameters</dt><dd>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00235">235</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00061">BlastSeqSrc::GetName</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__aux__priv_8cpp_source.html#l00132">BlastSetupPreliminarySearchEx()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00084">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="traceback__stage_8cpp_source.html#l00060">CBlastTracebackSearch::CBlastTracebackSearch()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00644">CVDBBlastUtil::FillVDBInfo()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>, and <a class="el" href="local__blast_8cpp_source.html#l00150">s_InitSeqInfoSrc()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a906dc37859d57d3cb8bccf0b51da6115">◆ </a></span>BlastSeqSrcGetNumSeqs()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcGetNumSeqs </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Get the number of sequences contained in the sequence source. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00177">177</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00053">BlastSeqSrc::GetNumSeqs</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__setup_8c_source.html#l00888">BLAST_GapAlignSetUp()</a>, <a class="el" href="blast__setup_8c_source.html#l00853">BLAST_GetSubjectTotals()</a>, <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00064">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__format_8cpp_source.html#l00068">CBlastFormat::CBlastFormat()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00280">CVDBBlastUtil::CVDBBlastUtil()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00644">CVDBBlastUtil::FillVDBInfo()</a>, <a class="el" href="prelim__stage_8cpp_source.html#l00206">CBlastPrelimSearch::Run()</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="magicblast__app_8cpp_source.html#l00226">s_InitializeSubject()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01827">s_NaHashLookupScanSubjectForWordCounts()</a>, <a class="el" href="blast__engine_8c_source.html#l01096">s_RPSPreliminarySearchEngine()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00160">CVDBSeqInfoSrc::Size()</a>, and <a class="el" href="split__query__aux__priv_8cpp_source.html#l00150">SplitQuery_SetEffectiveSearchSpace()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab25760d4a21dc5084c6fd9d8b89352bd">◆ </a></span>BlastSeqSrcGetNumSeqsStats()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcGetNumSeqsStats </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em></td><td>)</td>
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<p>Get the number of sequences used for calculation of expect values etc. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00185">185</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00054">BlastSeqSrc::GetNumSeqsStats</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__setup_8c_source.html#l00888">BLAST_GapAlignSetUp()</a>, <a class="el" href="blast__setup_8c_source.html#l00853">BLAST_GetSubjectTotals()</a>, and <a class="el" href="split__query__aux__priv_8cpp_source.html#l00150">SplitQuery_SetEffectiveSearchSpace()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a353f24339b726ee3bbab30adcb11ab09">◆ </a></span>BlastSeqSrcGetSeqLen()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcGetSeqLen </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Retrieve sequence length (number of residues/bases) </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<tr><td class="paramname">oid</td><td>ordinal id of the sequence desired (should be Uint4) [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00281">281</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, and <a class="el" href="blast__seqsrc_8c_source.html#l00071">BlastSeqSrc::GetSeqLen</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__setup_8c_source.html#l00888">BLAST_GapAlignSetUp()</a>, <a class="el" href="blast__setup_8c_source.html#l00853">BLAST_GetSubjectTotals()</a>, <a class="el" href="blast__traceback_8c_source.html#l01324">BLAST_SetupPartialFetching()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00103">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00151">CVDBSeqInfoSrc::GetLength()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>, and <a class="el" href="blast__kappa_8c_source.html#l01357">s_MatchingSequenceInitialize()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae1bf3c99343c9fe13452dd6bdd1534da">◆ </a></span>BlastSeqSrcGetSequence()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga4c5ce3be47003f4087cbd9b202a8492d">Int2</a> BlastSeqSrcGetSequence </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a> * </td>
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<p>Retrieve an individual sequence. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<tr><td class="paramname">getseq_arg</td><td>arguments to aid retrieval of sequence data from the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> [in|out] </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>one of the BLAST_SEQSRC_* defined in <a class="el" href="blast__seqsrc_8h.html" title="Declaration of ADT to retrieve sequences for the BLAST engine.">blast_seqsrc.h</a> </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00271">271</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, and <a class="el" href="blast__seqsrc_8c_source.html#l00070">BlastSeqSrc::GetSequence</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#l00097">BOOST_AUTO_TEST_CASE()</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#l00459">s_ComputeNumIdentities()</a>, <a class="el" href="blast__kappa_8c_source.html#l01357">s_MatchingSequenceInitialize()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01827">s_NaHashLookupScanSubjectForWordCounts()</a>, <a class="el" href="blast__traceback_8c_source.html#l01046">s_RPSComputeTraceback()</a>, and <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ad66ae0b63c1f008035c02e96ed64fa01">◆ </a></span>BlastSeqSrcGetSupportsPartialFetching()</h2>
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<td class="memname"><a class="el" href="ncbi__std_8h.html#a9f6121a7aa37a7e5487a28839b1f44a7">Boolean</a> BlastSeqSrcGetSupportsPartialFetching </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Find if the Blast <a class="el" href="classSequence.html">Sequence</a> Source supports partial fetching. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00251">251</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="ncbi__std_8h_source.html#l00101">FALSE</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00066">BlastSeqSrc::GetSupportsPartialFetching</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</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__kappa_8c_source.html#l02981">Blast_RedoAlignmentCore_MT()</a>, and <a class="el" href="blast__traceback_8c_source.html#l01324">BLAST_SetupPartialFetching()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa47005077a0b50a4cebe3a449c7bfe7a">◆ </a></span>BlastSeqSrcGetTotLen()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#gac9cc73bc670c02eb6146e38650740642">Int8</a> BlastSeqSrcGetTotLen </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Get the total length of all sequences in the sequence source. </p>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00219">219</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00059">BlastSeqSrc::GetTotLen</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</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__setup_8c_source.html#l00888">BLAST_GapAlignSetUp()</a>, <a class="el" href="blast__setup_8c_source.html#l00853">BLAST_GetSubjectTotals()</a>, <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00079">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__format_8cpp_source.html#l00068">CBlastFormat::CBlastFormat()</a>, <a class="el" href="vdb2blast__util_8cpp_source.html#l00644">CVDBBlastUtil::FillVDBInfo()</a>, <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>, <a class="el" href="magicblast__app_8cpp_source.html#l00226">s_InitializeSubject()</a>, <a class="el" href="blast__engine_8c_source.html#l01096">s_RPSPreliminarySearchEngine()</a>, and <a class="el" href="split__query__aux__priv_8cpp_source.html#l00150">SplitQuery_SetEffectiveSearchSpace()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2807ac630ae01c215adfa4080ad92b52">◆ </a></span>BlastSeqSrcGetTotLenStats()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#gac9cc73bc670c02eb6146e38650740642">Int8</a> BlastSeqSrcGetTotLenStats </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<p>Get the total length of all sequences for calculation of expect value etc. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00227">227</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00060">BlastSeqSrc::GetTotLenStats</a>, and <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__setup_8c_source.html#l00888">BLAST_GapAlignSetUp()</a>, <a class="el" href="blast__setup_8c_source.html#l00853">BLAST_GetSubjectTotals()</a>, and <a class="el" href="split__query__aux__priv_8cpp_source.html#l00150">SplitQuery_SetEffectiveSearchSpace()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2db9709fa1a1af3f3986254bf6f0acda">◆ </a></span>BlastSeqSrcIteratorFree()</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a>* BlastSeqSrcIteratorFree </td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> * </td>
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<p>Frees the <a class="el" href="structBlastSeqSrcIterator.html" title="Complete type definition of Blast Sequence Source Iterator.">BlastSeqSrcIterator</a> structure. </p>
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<tr><td class="paramname">itr</td><td><a class="el" href="structBlastSeqSrcIterator.html" title="Complete type definition of Blast Sequence Source Iterator.">BlastSeqSrcIterator</a> to free [in] </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>NULL </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00412">412</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>, <a class="el" href="blast__seqsrc__impl_8h_source.html#l00175">BlastSeqSrcIterator::oid_list</a>, and <a class="el" href="blast__def_8h_source.html#l00112">sfree</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00115">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01672">NaHashLookupThreadDataFree()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l00848">PrintSAMHeader()</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>, and <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a5cfb590abfe225628fc0827007cac612">◆ </a></span>BlastSeqSrcIteratorNew()</h2>
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<td>(</td>
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<td class="paramtype">void </td>
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<p>Allocate and initialize an iterator over a <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> with a default chunk size for MT-safe iteration. </p>
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<dl class="section return"><dt>Returns</dt><dd>pointer to initialized iterator for <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00380">380</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="blast__seqsrc_8c_source.html#l00387">BlastSeqSrcIteratorNewEx()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="mockseqsrc1__unit__test_8cpp_source.html#l00115">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="magicblast__util_8cpp_source.html#l00848">PrintSAMHeader()</a>, and <a class="el" href="seqsrc__unit__test_8cpp_source.html#l00242">s_checkDbSeqSrcFunctions()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a343bfa5ab569faf981307b4161e49a74">◆ </a></span>BlastSeqSrcIteratorNewEx()</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a>* BlastSeqSrcIteratorNewEx </td>
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<td>(</td>
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<td class="paramtype">unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
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<td class="paramname"><em>chunk_sz</em></td><td>)</td>
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<p>Allocate and initialize an iterator over a <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a>. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">chunk_sz</td><td>sets the chunk size of the iterator, if zero use kBlastSeqSrcDefaultChunkSize (above). [in] </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>pointer to initialized iterator for <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00387">387</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="zlib__cloudflare_2zutil_8c.html#a0659e28c2a1d3b0b2f8c3564c6645f9c">calloc()</a>, <a class="el" href="blast__seqsrc__impl_8h_source.html#l00185">BlastSeqSrcIterator::chunk_sz</a>, <a class="el" href="blast__seqsrc__impl_8h_source.html#l00181">BlastSeqSrcIterator::current_pos</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00385">kBlastSeqSrcDefaultChunkSize</a>, <a class="el" href="zlib__cloudflare_2gzguts_8h.html#adacbf80ddc99f9a9e0f6aa2bbf1fb0e9">malloc()</a>, <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>, <a class="el" href="blast__seqsrc__impl_8h_source.html#l00175">BlastSeqSrcIterator::oid_list</a>, <a class="el" href="blast__def_8h_source.html#l00112">sfree</a>, and <a class="el" href="ncbi__std_8h_source.html#l00136">UINT4_MAX</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__engine_8c_source.html#l01335">BLAST_PreliminarySearchEngine()</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00380">BlastSeqSrcIteratorNew()</a>, <a class="el" href="blast__vdb__cmd_8cpp_source.html#l00268">CVdbFastaExtractor::DumpAll()</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>, and <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a258f37f685e0315c4d807cfccb899d04">◆ </a></span>BlastSeqSrcIteratorNext()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> BlastSeqSrcIteratorNext </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em>, </td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcIterator.html">BlastSeqSrcIterator</a> * </td>
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<td class="paramname"><em>itr</em> </td>
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<td>)</td>
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<p>Increments the <a class="el" href="structBlastSeqSrcIterator.html" title="Complete type definition of Blast Sequence Source Iterator.">BlastSeqSrcIterator</a>. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">itr</td><td>the <a class="el" href="structBlastSeqSrcIterator.html" title="Complete type definition of Blast Sequence Source Iterator.">BlastSeqSrcIterator</a> to increment. </td></tr>
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<tr><td class="paramname">seq_src</td><td>the underlying <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>one of the BLAST_SEQSRC_* defined in <a class="el" href="blast__seqsrc_8h.html" title="Declaration of ADT to retrieve sequences for the BLAST engine.">blast_seqsrc.h</a> </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00425">425</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, and <a class="el" href="blast__seqsrc_8c_source.html#l00076">BlastSeqSrc::IterNext</a>.</p>
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<p class="reference">Referenced by <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="magicblast__util_8cpp_source.html#l00848">PrintSAMHeader()</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__nalookup_8c_source.html#l01827">s_NaHashLookupScanSubjectForWordCounts()</a>, and <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a46401cf3a7e39b51523787ee918b6e65">◆ </a></span>BlastSeqSrcNew()</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a>* BlastSeqSrcNew </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrcNewInfo.html">BlastSeqSrcNewInfo</a> * </td>
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<td class="paramname"><em>bssn_info</em></td><td>)</td>
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<p>Allocates memory for a <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure and then invokes the constructor function defined in its first argument, passing the ctor_argument member of that same structure. </p>
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<p>If the constructor function pointer is not set or there is a memory allocation failure, NULL is returned. </p><dl class="section note"><dt>Note</dt><dd>This function need not be called directly by client code as all the implementations of the <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> interface provide a function(s) which call this function (<a class="el" href="group__AlgoBlast.html#ga70b55cf5c641192214ba4c9b2447f004">MultiSeqBlastSeqSrcInit</a>, <a class="el" href="group__AlgoBlast.html#ga045dc78649700bcca0e283ebd5249142">SeqDbBlastSeqSrcInit</a>) </dd></dl>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">bssn_info</td><td>Structure defining constructor and its argument to be invoked from this function [in] </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>a properly initialized <a class="el" href="structBlastSeqSrc.html" title="Complete type definition of Blast Sequence Source ADT.">BlastSeqSrc</a> structure or NULL. </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00090">90</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="zlib__cloudflare_2zutil_8c.html#a0659e28c2a1d3b0b2f8c3564c6645f9c">calloc()</a>, <a class="el" href="blast__seqsrc__impl_8h_source.html#l00070">BlastSeqSrcNewInfo::constructor</a>, <a class="el" href="blast__seqsrc__impl_8h_source.html#l00072">BlastSeqSrcNewInfo::ctor_argument</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00045">BlastSeqSrc::NewFnPtr</a>, <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>, and <a class="el" href="blast__def_8h_source.html#l00112">sfree</a>.</p>
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<p class="reference">Referenced by <a class="el" href="seqsrc__mock_8cpp_source.html#l00314">MockBlastSeqSrcInit()</a>, <a class="el" href="seqsrc__multiseq_8cpp_source.html#l00555">MultiSeqBlastSeqSrcInit()</a>, <a class="el" href="seqsrc__query__factory_8cpp_source.html#l00540">s_QueryFactoryBlastSeqSrcInit()</a>, <a class="el" href="seqsrc__seqdb_8cpp_source.html#l00764">SeqDbBlastSeqSrcInit()</a>, and <a class="el" href="seqsrc__vdb_8c_source.html#l00546">SRABlastSeqSrcInit()</a>.</p>
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<a id="a5909bb7ccc99229678dee036626dc618"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a5909bb7ccc99229678dee036626dc618">◆ </a></span>BlastSeqSrcReleaseSequence()</h2>
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<td class="memname">void BlastSeqSrcReleaseSequence </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em>, </td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcGetSeqArg.html">BlastSeqSrcGetSeqArg</a> * </td>
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<td class="paramname"><em>getseq_arg</em> </td>
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<td></td>
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<p>Deallocate individual sequence. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<tr><td class="paramname">getseq_arg</td><td>contains sequence to deallocate [in|out] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00289">289</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, and <a class="el" href="blast__seqsrc_8c_source.html#l00072">BlastSeqSrc::ReleaseSequence</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="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#l00459">s_ComputeNumIdentities()</a>, <a class="el" href="blast__kappa_8c_source.html#l00908">s_MatchingSequenceRelease()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01827">s_NaHashLookupScanSubjectForWordCounts()</a>, <a class="el" href="blast__traceback_8c_source.html#l01046">s_RPSComputeTraceback()</a>, and <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#afc6eda40980bc24c81420d47b3fe3078">◆ </a></span>BlastSeqSrcResetChunkIterator()</h2>
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<td class="memname">void BlastSeqSrcResetChunkIterator </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em></td><td>)</td>
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<p>Reset the internal "bookmark" of the last chunk for iteration provided by this object. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">seq_src</td><td>the BLAST sequence source [in] </td></tr>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00436">436</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, and <a class="el" href="blast__seqsrc_8c_source.html#l00078">BlastSeqSrc::ResetChunkIterator</a>.</p>
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<p class="reference">Referenced by <a class="el" href="magicblast__util_8cpp_source.html#l00848">PrintSAMHeader()</a>, <a class="el" href="local__db__adapter_8cpp_source.html#l00100">CLocalDbAdapter::ResetBlastSeqSrcIteration()</a>, <a class="el" href="prelim__stage_8cpp_source.html#l00206">CBlastPrelimSearch::Run()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01827">s_NaHashLookupScanSubjectForWordCounts()</a>, <a class="el" href="blast__nalookup_8c_source.html#l01179">s_ScanSubjectForWordCounts()</a>, and <a class="el" href="split__query__aux__priv_8cpp_source.html#l00185">SplitQuery_CreateChunkData()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#acb1644f9782e2de7bf9410d248232efc">◆ </a></span>BlastSeqSrcSetNumberOfThreads()</h2>
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<td class="memname">void BlastSeqSrcSetNumberOfThreads </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em>, </td>
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<td class="paramtype"><a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td>
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<p>Set the number of threads for MT mode. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00168">168</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, and <a class="el" href="blast__seqsrc_8c_source.html#l00050">BlastSeqSrc::SetNumberOfThreads</a>.</p>
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<p class="reference">Referenced by <a class="el" href="prelim__stage_8cpp_source.html#l00142">CBlastPrelimSearch::x_LaunchMultiThreadedSearch()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a139969750a141eca61d7a01b3399ba96">◆ </a></span>BlastSeqSrcSetRangesArgAddRange()</h2>
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<td class="memname"><a class="el" href="group__Portability.html#ga4c5ce3be47003f4087cbd9b202a8492d">Int2</a> BlastSeqSrcSetRangesArgAddRange </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> * </td>
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<td class="paramname"><em>arg</em>, </td>
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<td class="paramtype"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> </td>
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<td class="paramname"><em>begin</em>, </td>
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<td class="paramtype"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> </td>
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<td class="paramname"><em>end</em>, </td>
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<td class="paramtype"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> </td>
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<td class="paramname"><em>len</em> </td>
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<td>)</td>
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<p>add new range </p>
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<dl class="section return"><dt>Returns</dt><dd>0 in case of success, otherwise 1 </dd></dl>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00467">467</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00204">BLAST_SEQSRC_OVERHANG</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00213">BlastSeqSrcSetRangesArg::capacity</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01450">len</a>, <a class="el" href="ncbi__std_8h_source.html#l00117">MAX</a>, <a class="el" href="ncbi__std_8h_source.html#l00112">MIN</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00216">BlastSeqSrcSetRangesArg::num_ranges</a>, and <a class="el" href="blast__seqsrc_8h_source.html#l00219">BlastSeqSrcSetRangesArg::ranges</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01324">BLAST_SetupPartialFetching()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a54539d5f0e9e253498d2d6bddc1d1bd6">◆ </a></span>BlastSeqSrcSetRangesArgBuild()</h2>
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<td class="memname">void BlastSeqSrcSetRangesArgBuild </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> * </td>
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<td class="paramname"><em>arg</em></td><td>)</td>
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<p>build <a class="el" href="structBlastSeqSrcSetRangesArg.html" title="Structure used as the argument to function SetRanges.">BlastSeqSrcSetRangesArg</a> from range list </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00496">496</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00488">BeginCompareHSPs()</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00203">BLAST_SEQSRC_MINGAP</a>, <a class="el" href="lex_8newick_8cpp_source.html#l01456">i</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00216">BlastSeqSrcSetRangesArg::num_ranges</a>, and <a class="el" href="blast__seqsrc_8h_source.html#l00219">BlastSeqSrcSetRangesArg::ranges</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01324">BLAST_SetupPartialFetching()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae5442b1145f38442fd4354fc08b173b9">◆ </a></span>BlastSeqSrcSetRangesArgFree()</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a>* BlastSeqSrcSetRangesArgFree </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> * </td>
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<td class="paramname"><em>arg</em></td><td>)</td>
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<p>free setrangearg </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00455">455</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ctools_2ctransition_2ncbistd_8hpp_source.html#l00225">NULL</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00219">BlastSeqSrcSetRangesArg::ranges</a>, and <a class="el" href="blast__def_8h_source.html#l00112">sfree</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__traceback_8c_source.html#l01324">BLAST_SetupPartialFetching()</a>, <a class="el" href="traceback__unit__test_8cpp_source.html#l01147">BOOST_AUTO_TEST_CASE()</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="#ab5ff629359beef75b97a2879f622a148">◆ </a></span>BlastSeqSrcSetRangesArgNew()</h2>
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<td class="memname"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a>* BlastSeqSrcSetRangesArgNew </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="group__Portability.html#ga51b761affa74cf9aa661229a74bc91f7">Int4</a> </td>
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<td class="paramname"><em>num_ranges</em></td><td>)</td>
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<p>new setrangearg </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00444">444</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="blast__seqsrc_8h_source.html#l00213">BlastSeqSrcSetRangesArg::capacity</a>, <a class="el" href="zlib__cloudflare_2gzguts_8h.html#adacbf80ddc99f9a9e0f6aa2bbf1fb0e9">malloc()</a>, <a class="el" href="blast__seqsrc_8h_source.html#l00216">BlastSeqSrcSetRangesArg::num_ranges</a>, and <a class="el" href="blast__seqsrc_8h_source.html#l00219">BlastSeqSrcSetRangesArg::ranges</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__traceback_8c_source.html#l01324">BLAST_SetupPartialFetching()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a6f886124dbb2fdcc48dd96d26eb55885">◆ </a></span>BlastSeqSrcSetSeqRanges()</h2>
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<td class="memname">void BlastSeqSrcSetSeqRanges </td>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="structBlastSeqSrc.html">BlastSeqSrc</a> * </td>
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<td class="paramname"><em>seq_src</em>, </td>
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<td class="paramtype"><a class="el" href="structBlastSeqSrcSetRangesArg.html">BlastSeqSrcSetRangesArg</a> * </td>
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<td class="paramname"><em>setranges_arg</em> </td>
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<p>Setting the ranges for partial fetching. </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00261">261</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">References <a class="el" href="ncbi__std_8h_source.html#l00107">ASSERT</a>, <a class="el" href="blast__seqsrc_8c_source.html#l00082">BlastSeqSrc::DataStructure</a>, and <a class="el" href="blast__seqsrc_8c_source.html#l00067">BlastSeqSrc::SetSeqRange</a>.</p>
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<h2 class="groupheader">Variable Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ab7c5991d3a46ea3e664de1487203e33c">◆ </a></span>kBlastSeqSrcDefaultChunkSize</h2>
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<td class="memname"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> kBlastSeqSrcDefaultChunkSize</td>
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<p>How many database sequences to process in one database chunk. </p>
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<p>this value is overriden in seqdb implementation, where the number of sequences is determined by the mmaped slice size </p>
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<p class="definition">Definition at line <a class="el" href="blast__seqsrc_8c_source.html#l00385">385</a> of file <a class="el" href="blast__seqsrc_8c_source.html">blast_seqsrc.c</a>.</p>
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<p class="reference">Referenced by <a class="el" href="blast__seqsrc_8c_source.html#l00387">BlastSeqSrcIteratorNewEx()</a>.</p>
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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 14:58:01 2024 by modify_doxy.py rev. 669887</small></address>
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