NCBI C++ ToolKit
seqsrc_vdb.h
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1 #ifndef ALGO_BLAST_VDB___SEQSRC_VDB__H
2 #define ALGO_BLAST_VDB___SEQSRC_VDB__H
3 
4 /* $Id: seqsrc_vdb.h 101102 2023-10-30 13:07:22Z fongah2 $
5  * ===========================================================================
6  *
7  * PUBLIC DOMAIN NOTICE
8  * National Center for Biotechnology Information
9  *
10  * This software/database is a "United States Government Work" under the
11  * terms of the United States Copyright Act. It was written as part of
12  * the author's official duties as a United States Government employee and
13  * thus cannot be copyrighted. This software/database is freely available
14  * to the public for use. The National Library of Medicine and the U.S.
15  * Government have not placed any restriction on its use or reproduction.
16  *
17  * Although all reasonable efforts have been taken to ensure the accuracy
18  * and reliability of the software and data, the NLM and the U.S.
19  * Government do not and cannot warrant the performance or results that
20  * may be obtained by using this software or data. The NLM and the U.S.
21  * Government disclaim all warranties, express or implied, including
22  * warranties of performance, merchantability or fitness for any particular
23  * purpose.
24  *
25  * Please cite the author in any work or product based on this material.
26  *
27  * ===========================================================================
28  *
29  * Author: Vahram Avagyan
30  *
31  */
32 
33 /// @file blastseqsrc_sra.h
34 /// Blast Sequence Source implementation for the Sequence Read Archive databases.
35 ///
36 /// BlastSeqSrc is an abstract data type used by Blast as a layer between
37 /// the Blast engine and the physical source of biological sequence data.
38 /// This implementation of BlastSeqSrc uses the SRA (Sequence Read Archive)
39 /// databases to extract and convert the nucleotide sequence data and
40 /// provide it to Blast through the standard BlastSeqSrc interface.
41 ///
42 /// This is the top-level header file for the SRA BlastSeqSrc library.
43 /// It contains the main function for initializing the SRA BlastSeqSrc
44 /// object, which takes care of setting up the BlastSeqSrc with all the
45 /// correct function pointers and data structures.
46 
47 // ==========================================================================//
48 
49 // Blast includes
50 
51 #include <common/ncbi_export.h>
55 
56 #ifdef __cplusplus
57 extern "C" {
58 #endif
59 
60 // ==========================================================================//
61 // BlastSeqSrc initialization
62 
63 /// Allocate and initialize the SRA BlastSeqSrc object.
64 /// @param sraRunAccessions Array of SRA run accessions to open. [in]
65 /// @param numRuns Number of SRA run accessions to open. [in]
66 /// @return Pointer to a properly initialized BlastSeqSrc object.
67 
69 SRABlastSeqSrcInit(const char** sraRunAccessions, Uint4 numRuns,
70  Boolean isProtein, Boolean* excluded_runs, Uint4 * status,
71  Boolean isCSRA, Boolean include_filtered_reads);
72 
73 // ==========================================================================//
74 
75 #ifdef __cplusplus
76 }
77 #endif
78 
79 #endif /* ALGO_BLAST_VDB___SEQSRC_VDB__H */
Definitions used throughout BLAST.
Declaration of ADT to retrieve sequences for the BLAST engine.
uint32_t Uint4
4-byte (32-bit) unsigned integer
Definition: ncbitype.h:103
Defines to provide correct exporting from DLLs in some configurations.
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Uint1 Boolean
bool replacment for C
Definition: ncbi_std.h:94
BlastSeqSrc * SRABlastSeqSrcInit(const char **sraRunAccessions, Uint4 numRuns, Boolean isProtein, Boolean *excluded_runs, Uint4 *status, Boolean isCSRA, Boolean include_filtered_reads)
Allocate and initialize the SRA BlastSeqSrc object.
Definition: seqsrc_vdb.c:546
Complete type definition of Blast Sequence Source ADT.
Definition: blast_seqsrc.c:43
Modified on Thu Jun 13 17:26:19 2024 by modify_doxy.py rev. 669887