/* $Id: phi_gapalign.h 41431 2009-03-27 15:03:32Z camacho $ * =========================================================================== * * 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 phi_gapalign.h * Function prototypes used for PHI BLAST gapped extension and gapped extension * with traceback. */ #ifndef ALGO_BLAST_CORE__PHI_GAPALIGN_H #define ALGO_BLAST_CORE__PHI_GAPALIGN_H #include <algo/blast/core/ncbi_std.h> #include <algo/blast/core/blast_def.h> #include <algo/blast/core/blast_query_info.h> #include <algo/blast/core/blast_parameters.h> #include <algo/blast/core/gapinfo.h> #include <algo/blast/core/blast_hits.h> #include <algo/blast/core/blast_gapalign.h> #include <algo/blast/core/pattern.h> #ifdef __cplusplus extern "C" { #endif /** Perform a gapped alignment with traceback for PHI BLAST * @param query The query sequence [in] * @param subject The subject sequence [in] * @param gap_align The gapped alignment structure [in] [out] * @param score_params Scoring parameters [in] * @param q_start Offset in query where to start alignment [in] * @param s_start Offset in subject where to start alignment [in] * @param query_length Maximal allowed extension in query [in] * @param subject_length Maximal allowed extension in subject [in] * @param q_pat_length Length of this pattern in query. [in] * @param s_pat_length Length of this pattern in subject. [in] * @param pattern_blk Detailed pattern information. [in] * @return Status, 0 on success, -1 on failure. */ NCBI_XBLAST_EXPORT Int2 PHIGappedAlignmentWithTraceback(Uint1* query, Uint1* subject, BlastGapAlignStruct* gap_align, const BlastScoringParameters* score_params, Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length, Int4 q_pat_length, Int4 s_pat_length, SPHIPatternSearchBlk *pattern_blk); /** Preliminary gapped alignment for PHI BLAST. * @param program_number Type of BLAST program [in] * @param query The query sequence block [in] * @param query_info Query information structure, containing offsets into * the concatenated sequence [in] * @param subject The subject sequence block [in] * @param gap_align The auxiliary structure for gapped alignment [in] * @param score_params Parameters related to scoring [in] * @param ext_params Parameters related to extensions (not used) [in] * @param hit_params Parameters related to saving hits [in] * @param init_hitlist List of initial HSPs, including offset pairs and * pattern match lengths [in] * @param hsp_list_ptr Structure containing all saved HSPs [out] * @param gapped_stats Return statistics (not filled if NULL) [out] * @param fence_hit Not curently supported for PHI-blast but here * for compatiability. Normally true here indicates that an * overrun was detected. [out] * @return Status, 0 on success, -1 on failure. */ NCBI_XBLAST_EXPORT Int2 PHIGetGappedScore (EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, BLAST_SequenceBlk* subject, BlastGapAlignStruct* gap_align, const BlastScoringParameters* score_params, const BlastExtensionParameters* ext_params, const BlastHitSavingParameters* hit_params, BlastInitHitList* init_hitlist, BlastHSPList** hsp_list_ptr, BlastGappedStats* gapped_stats, Boolean * fence_hit); #ifdef __cplusplus } #endif #endif /* !ALGO_BLAST_CORE__PHI_GAPALIGN_H */
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