/* $Id: lookup_wrap.h 75675 2016-12-06 15:28:14Z boratyng $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Ilya Dondoshansky * */ /** @file lookup_wrap.h * Wrapper for all lookup tables used in BLAST */ #ifndef ALGO_BLAST_CORE__LOOKUP_WRAP__H #define ALGO_BLAST_CORE__LOOKUP_WRAP__H #include <algo/blast/core/ncbi_std.h> #include <algo/blast/core/blast_def.h> #include <algo/blast/core/blast_options.h> #include <algo/blast/core/blast_rps.h> #include <algo/blast/core/blast_stat.h> #include <algo/blast/core/blast_seqsrc.h> #ifdef __cplusplus extern "C" { #endif /** Wrapper structure for different types of BLAST lookup tables */ typedef struct LookupTableWrap { ELookupTableType lut_type; /**< What kind of a lookup table it is? */ void* lut; /**< Pointer to the actual lookup table structure */ void* read_indexed_db; /**< function used to retrieve hits from an indexed database */ void* check_index_oid; /**< function used to check if seeds for a given oid are present */ void * end_search_indication; /**< function used to report that a thread is done iterating over the database in preliminary search */ void* lookup_callback; /**< function used to look up an index->q_off pair */ } LookupTableWrap; /** Function pointer type to check the presence of index->q_off pair */ typedef Boolean (*T_Lookup_Callback)(const LookupTableWrap *, Int4, Int4); /** Create the lookup table for all query words. * @param query The query sequence [in] * @param lookup_options What kind of lookup table to build? [in] * @param query_options options for query setup [in] * @param lookup_segments Locations on query to be used for lookup table * construction [in] * @param sbp Scoring block containing matrix [in] * @param lookup_wrap_ptr The initialized lookup table [out] * @param rps_info Structure containing RPS blast setup information [in] * @param error_msg message with warning or errors [in|out] * @param seqsrc Database sequences [in] */ NCBI_XBLAST_EXPORT Int2 LookupTableWrapInit(BLAST_SequenceBlk* query, const LookupTableOptions* lookup_options, const QuerySetUpOptions* query_options, BlastSeqLoc* lookup_segments, BlastScoreBlk* sbp, LookupTableWrap** lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message* *error_msg, BlastSeqSrc* seqsrc); /** Create the lookup table for all query words (possibly multithreaded, depends on implementation). * @param query The query sequence [in] * @param lookup_options What kind of lookup table to build? [in] * @param query_options options for query setup [in] * @param lookup_segments Locations on query to be used for lookup table * construction [in] * @param sbp Scoring block containing matrix [in] * @param lookup_wrap_ptr The initialized lookup table [out] * @param rps_info Structure containing RPS blast setup information [in] * @param error_msg message with warning or errors [in|out] * @param seqsrc Database sequences [in] * @param num_threads Number of threads to use [in] */ NCBI_XBLAST_EXPORT Int2 LookupTableWrapInit_MT(BLAST_SequenceBlk* query, const LookupTableOptions* lookup_options, const QuerySetUpOptions* query_options, BlastSeqLoc* lookup_segments, BlastScoreBlk* sbp, LookupTableWrap** lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message* *error_msg, BlastSeqSrc* seqsrc, Uint4 num_threads); /** Deallocate memory for the lookup table */ NCBI_XBLAST_EXPORT LookupTableWrap* LookupTableWrapFree(LookupTableWrap* lookup); /** Default size of offset arrays filled in a single ScanSubject call. */ #define OFFSET_ARRAY_SIZE 4096 /** Determine the size of the offsets arrays to be filled by * the ScanSubject function. */ NCBI_XBLAST_EXPORT Int4 GetOffsetArraySize(LookupTableWrap* lookup); #ifdef __cplusplus } #endif #endif /* !ALGO_BLAST_CORE__LOOKUP_WRAP__H */
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