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* Structures and API used for saving BLAST hits
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#ifndef __BLAST_HITS__
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#define __BLAST_HITS__
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#ifndef ALGO_BLAST_CORE__BLAST_HITS__H
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#define ALGO_BLAST_CORE__BLAST_HITS__H
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#include <algo/blast/core/ncbi_std.h>
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#include <algo/blast/core/blast_export.h>
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#include <algo/blast/core/blast_program.h>
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#include <algo/blast/core/blast_query_info.h>
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#include <algo/blast/core/blast_options.h>
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#include <algo/blast/core/blast_parameters.h>
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#include <algo/blast/core/blast_stat.h>
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#include <algo/blast/core/gapinfo.h>
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#include <algo/blast/core/blast_seqsrc.h>
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#include <algo/blast/core/pattern.h>
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const BlastInitialWordParameters* word_params,
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BlastScoreBlk* sbp, Boolean translated);
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/** Calculate number of identities in an HSP.
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* @param query The query sequence [in]
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* @param subject The uncompressed subject sequence [in]
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* @param hsp All information about the HSP [in]
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* @param num_ident_ptr Number of identities [out]
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* @param align_length_ptr The alignment length, including gaps [out]
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Blast_HSPGetNumIdentities(Uint1* query, Uint1* subject, BlastHSP* hsp,
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Int4* num_ident_ptr, Int4* align_length_ptr);
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/** Calculate number of identities in an HSP for an out-of-frame alignment.
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* @param query The query sequence [in]
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* @param subject The uncompressed subject sequence [in]
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* @param hsp All information about the HSP [in]
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* @param program BLAST program (blastx or tblastn) [in]
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* @param num_ident_ptr Number of identities [out]
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* @param align_length_ptr The alignment length, including gaps [out]
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Blast_HSPGetOOFNumIdentities(Uint1* query, Uint1* subject, BlastHSP* hsp,
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EBlastProgramType program, Int4* num_ident_ptr,
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Int4* align_length_ptr);
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/** Calculates number of identities and alignment lengths of an HSP and
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* determines whether this HSP should be kept or deleted. The num_ident
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* field of the BlastHSP structure is filled here.
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/** Calculate number of identities in an HSP and set the BlastHSP::num_ident
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* field (unconditionally)
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* @param query The query sequence [in]
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* @param subject The uncompressed subject sequence [in]
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* @param hsp All information about the HSP, the output of this function will
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* be stored in its num_ident field [in|out]
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* @param score_options Scoring options [in]
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* @param align_length_ptr The alignment length, including gaps (optional) [out]
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* @return 0 on success, -1 on invalid parameters or error
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Blast_HSPGetNumIdentities(const Uint1* query,
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const Uint1* subject,
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const BlastScoringOptions* score_options,
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Int4* align_length_ptr);
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/** Calculates number of identities and alignment lengths of an HSP via
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* Blast_HSPGetNumIdentities and determines whether this HSP should be kept or
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* @param program_number Type of BLAST program [in]
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* @param hsp An HSP structure [in] [out]
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* @param query Query sequence [in]
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Blast_HSPList_IsEmpty(const BlastHSPList* hsp_list);
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/** Returns a duplicate (deep copy) of the given hsp list. */
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BlastHSPList* BlastHSPListDup(const BlastHSPList* hsp_list);
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/** Swaps the two HSP lists via structure assignment */
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void Blast_HSPListSwap(BlastHSPList* list1, BlastHSPList* list2);
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/** Saves HSP information into a BlastHSPList structure
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* @param hsp_list Structure holding all HSPs with full gapped alignment
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* information [in] [out]
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Blast_HSPListPurgeHSPsWithCommonEndpoints(EBlastProgramType program,
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BlastHSPList* hsp_list);
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/** Reevaluate all HSPs in an HSP list, using ambiguity information.
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/** Reevaluate all ungapped HSPs in an HSP list, using ambiguity information.
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* This is/can only done either for an ungapped search, or if traceback is
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* already available.
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* Subject sequence is uncompressed and saved here. Number of identities is
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NCBI_XBLAST_EXPORT
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Blast_HSPListReevaluateWithAmbiguities(EBlastProgramType program,
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Blast_HSPListReevaluateWithAmbiguitiesUngapped(EBlastProgramType program,
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BlastHSPList* hsp_list, BLAST_SequenceBlk* query_blk,
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BLAST_SequenceBlk* subject_blk,
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const BlastInitialWordParameters* word_params,
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* @param hsp_list Contains HSPs from the new chunk [in]
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* @param combined_hsp_list_ptr Contains HSPs from previous chunks [in] [out]
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* @param hsp_num_max Maximal allowed number of HSPs to save (unlimited if INT4_MAX) [in]
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* @param start Offset where the current subject chunk starts [in]
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* @param merge_hsps Should the overlapping HSPs be merged into one? [in]
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* @param split_points Offset The sequence offset (query or subject) that is
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* the boundary between HSPs in combined_hsp_list and hsp_list. [in]
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* @param contexts_per_query If positive, the number of query contexts
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* that hits can contain. If negative, the (one) split
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* point occurs on the subject sequence [in]
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* @param chunk_overlap_size The length of the overlap region between the
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* sequence region containing hsp_list and that
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* containing combined_hsp_list [in]
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* @return 0 if HSP lists have been merged successfully, -1 otherwise.
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NCBI_XBLAST_EXPORT
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Int2 Blast_HSPListsMerge(BlastHSPList** hsp_list,
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BlastHSPList** combined_hsp_list_ptr,
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Int4 hsp_num_max, Int4 start, Boolean merge_hsps);
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Int4 hsp_num_max, Int4* split_points,
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Int4 contexts_per_query,
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Int4 chunk_overlap_size);
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/** Adjust subject offsets in an HSP list if only part of the subject sequence
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* was searched. Used when long subject sequence is split into more manageable
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NCBI_XBLAST_EXPORT
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Int2 Blast_HitListUpdate(BlastHitList* hit_list, BlastHSPList* hsp_list);
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/** Combine two hitlists; both HitLists must contain HSPs that
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* represent alignments to the same query sequence
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* @param old_hit_list_ptr Pointer to original HitList, will be NULLed
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* out on return [in|out]
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* @param combined_hit_list_ptr Pointer to the combined HitList [in|out]
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* @param contexts_per_query The number of different contexts that can
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* occur in hits from old_hit_list and combined_hit_list [in]
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* @param split_offsets the query offset that marks the boundary between
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* combined_hit_list and old_hit_list. HSPs in old_hit_list
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* that hit to context i are assumed to lie to the right
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* of split_offsets[i] [in]
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* @param chunk_overlap_size The length of the overlap region between the
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* sequence region containing hit_list and that
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* containing combined_hit_list [in]
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Int2 Blast_HitListMerge(BlastHitList** old_hit_list_ptr,
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BlastHitList** combined_hit_list_ptr,
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Int4 contexts_per_query, Int4 *split_offsets,
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Int4 chunk_overlap_size);
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/** Purges a BlastHitList of NULL HSP lists.
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* @param hit_list BLAST hit list to purge. [in] [out]
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removed
algo/blast/core/blast_hits.h
