query_offset,
Int4query_length,
Int4* start_shift);
Definitions used throughout BLAST.
Various diagnostics (hit counts, etc.) returned from the BLAST engine.
Defines to provide correct exporting from BLAST DLL in Windows.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Ungapped extension structures that are common to nucleotide and protein extension routines.
Boolean BlastGetOffsetsForGappedAlignment(const Uint1 *query, const Uint1 *subject, const BlastScoreBlk *sbp, BlastHSP *hsp, Int4 *q_retval, Int4 *s_retval)
Function to look for the highest scoring window (of size HSP_MAX_WINDOW) in an HSP and return the mid...
Int2 BLAST_GappedAlignmentWithTraceback(EBlastProgramType program, const Uint1 *query, const Uint1 *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length, Boolean *fence_hit)
Perform a gapped alignment with traceback.
Int4 BlastGetStartForGappedAlignment(const Uint1 *query, const Uint1 *subject, const BlastScoreBlk *sbp, Uint4 q_start, Uint4 q_length, Uint4 s_start, Uint4 s_length)
Function to look for the highest scoring window (of size HSP_MAX_WINDOW) in an HSP and return the mid...
Int2 BLAST_GetGappedScore(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, const BlastInitialWordParameters *word_params, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit)
Performs gapped extension for all non-Mega BLAST programs, given that ungapped extension has been don...
Int2 BLAST_GetUngappedHSPList(BlastInitHitList *init_hitlist, BlastQueryInfo *query_info, BLAST_SequenceBlk *subject, const BlastHitSavingOptions *hit_options, BlastHSPList **hsp_list_ptr)
Convert initial HSP list to an HSP list: to be used in ungapped search.
struct BlastGapAlignStruct BlastGapAlignStruct
Structure supporting the gapped alignment.
Int2 BLAST_GreedyGappedAlignment(const Uint1 *query, const Uint1 *subject, Int4 query_length, Int4 subject_length, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, Int4 q_off, Int4 s_off, Boolean compressed_subject, Boolean do_traceback, Boolean *fence_hit)
Greedy gapped alignment, with or without traceback.
void AdjustSubjectRange(Int4 *subject_offset_ptr, Int4 *subject_length_ptr, Int4 query_offset, Int4 query_length, Int4 *start_shift)
Adjusts range of subject sequence to be passed for gapped extension, taking into account the length a...
void BlastGetStartForGappedAlignmentNucl(const Uint1 *query, const Uint1 *subject, BlastHSP *hsp)
Function to look for the longest identity match run (up to size HSP_MAX_IDENT_RUN) in an HSP and retu...
Int2 BLAST_GapAlignStructNew(const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, Uint4 max_subject_length, BlastScoreBlk *sbp, BlastGapAlignStruct **gap_align_ptr)
Initializes the BlastGapAlignStruct structure.
BlastGapAlignStruct * BLAST_GapAlignStructFree(BlastGapAlignStruct *gap_align)
Deallocates memory in the BlastGapAlignStruct structure.
Structures and API used for saving BLAST hits.
Structure and function definitions for BLAST parameter structures, which are internal to the CORE of ...
EBlastProgramType
Defines the engine's notion of the different applications of the BLAST algorithm.
Definitions and functions associated with the BlastQueryInfo structure.
Definitions of structures used for saving traceback information.
Prototypes and structures for greedy gapped alignment.
uint8_t Uint1
1-byte (8-bit) unsigned integer
int16_t Int2
2-byte (16-bit) signed integer
int32_t Int4
4-byte (32-bit) signed integer
uint32_t Uint4
4-byte (32-bit) unsigned integer
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Uint1 Boolean
bool replacment for C
Structure to hold a sequence.
Computed values used as parameters for gapped alignments.
Structure supporting the gapped alignment.
GapPrelimEditBlock * fwd_prelim_tback
traceback from right extensions
Int4 gap_x_dropoff
X-dropoff parameter to use.
GapPrelimEditBlock * rev_prelim_tback
traceback from left extensions
Boolean positionBased
Is this PSI-BLAST?
Int4 query_stop
query end offseet of current alignment
ChainingStruct * chaining
data for chaining
Int4 dp_mem_alloc
current number of structures allocated
Int4 subject_start
subject start offset current alignment
Int4 greedy_subject_seed_start
for greedy alignments, the subject offset of the gapped start point
BlastScoreBlk * sbp
Pointer to the scoring information block.
SGreedyAlignMem * greedy_align_mem
Preallocated memory for the greedy gapped extension.
GapStateArrayStruct * state_struct
Structure to keep extension state information.
Int4 query_start
query start offset of current alignment
Int4 subject_stop
subject end offset of current alignment
Int4 max_mismatches
Max number of mismatches for jumper.
Int4 greedy_query_seed_start
for greedy alignments, the query offset of the gapped start point
Int4 mismatch_window
Window sie for mismatches for jumper.
BlastGapDP * dp_mem
scratch structures for dynamic programming
JumperGapAlign * jumper
data for jumper alignment
Int4 score
Return value: alignment score.
GapEditScript * edit_script
The traceback (gap) information.
Auxiliary structure for dynamic programming gapped extension.
Int4 best_gap
score of best path that ends in a gap at this position
Int4 best
score of best path that ends in a match at this position
Structure containing hit counts from the gapped stage of a BLAST search.
The structure to hold all HSPs for a given sequence after the gapped alignment.
Structure holding all information about an HSP.
Options used when evaluating and saving hits These include: a.
Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.
Structure to hold all initial HSPs for a given subject sequence.
Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.
The query related information.
Structure used for scoring calculations.
Scoring parameters block Contains scoring-related information that is actually used for the blast sea...
Workspace used for chaining.
Edit script: linked list of correspondencies between two sequences.
Preliminary version of GapEditBlock, used directly by the low- level dynamic programming routines.
Structure to keep memory for state structure.
Gapped alignment data needed for jumper.
All auxiliary memory needed for the greedy extension algorithm.
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