NCBI C++ ToolKit
seqsrc_seqdb.hpp
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1 #ifndef ALGO_BLAST_API___SEQSRC_SEQDB__HPP
2 #define ALGO_BLAST_API___SEQSRC_SEQDB__HPP
3 
4 /* $Id: seqsrc_seqdb.hpp 49264 2011-04-11 14:49:23Z camacho $
5  * ===========================================================================
6  *
7  * PUBLIC DOMAIN NOTICE
8  * National Center for Biotechnology Information
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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
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14  * to the public for use. The National Library of Medicine and the U.S.
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27  * ===========================================================================
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29  * Author: Ilya Dondoshansky
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31  */
32 
33 /// @file seqsrc_seqdb.hpp
34 /// Implementation of the BlastSeqSrc interface using the C++ BLAST databases
35 /// API
36 
38 
42 
43 /** @addtogroup AlgoBlast
44  *
45  * @{
46  */
47 
49 BEGIN_SCOPE(blast)
50 
51 /** Initialize the sequence source structure.
52  * @param dbname BLAST database name [in]
53  * @param is_prot Is this a protein or nucleotide database? [in]
54  * @param first_seq First ordinal id in the database to search [in]
55  * @param last_seq Last ordinal id in the database to search
56  * (full database if 0) [in]
57  * @param mask_algo_id Database masking algorithm ID (-1 if not applicable) [in]
58  * @param mask_type Type of database masking [in]
59  */
62 SeqDbBlastSeqSrcInit(const string& dbname, bool is_prot,
63  Uint4 first_seq = 0, Uint4 last_seq = 0,
64  Int4 mask_algo_id = -1,
66 
67 /** Initialize the sequence source structure using an existing SeqDB object.
68  * @param seqdb CSeqDB object [in]
69  * @param mask_algo_id Database masking algorithm ID (-1 if not applicable) [in]
70  * @param mask_type Type of database masking [in]
71  */
75  Int4 mask_algo_id = -1,
77 
78 END_SCOPE(blast)
80 
81 /* @} */
82 
83 #endif /* ALGO_BLAST_API___SEQSRC_SEQDB__HPP */
Definitions used throughout BLAST.
ESubjectMaskingType
Define the possible subject masking types.
Definition: blast_def.h:235
@ eNoSubjMasking
Definition: blast_def.h:236
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
Declaration of ADT to retrieve sequences for the BLAST engine.
Definitions of special type used in BLAST.
CSeqDB.
Definition: seqdb.hpp:161
BlastSeqSrc * SeqDbBlastSeqSrcInit(const string &dbname, bool is_prot, Uint4 first_seq=0, Uint4 last_seq=0, Int4 mask_algo_id=-1, ESubjectMaskingType mask_type=eNoSubjMasking)
Initialize the sequence source structure.
int32_t Int4
4-byte (32-bit) signed integer
Definition: ncbitype.h:102
uint32_t Uint4
4-byte (32-bit) unsigned integer
Definition: ncbitype.h:103
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
char * dbname(DBPROCESS *dbproc)
Get name of current database.
Definition: dblib.c:6929
Defines BLAST database access classes.
Complete type definition of Blast Sequence Source ADT.
Definition: blast_seqsrc.c:43
Modified on Sun Apr 21 03:40:30 2024 by modify_doxy.py rev. 669887