/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_extend.c | 226 return init_hitlist; in BLAST_InitHitListNew() 235 init_hitlist->total = 0; in BlastInitHitListReset() 263 if (init_hitlist == NULL) in BLAST_InitHitListFree() 266 s_BlastInitHitListClean(init_hitlist); in BLAST_InitHitListFree() 267 sfree(init_hitlist); in BLAST_InitHitListFree() 308 qsort(init_hitlist->init_hsp_array, init_hitlist->total, in Blast_InitHitListSortByScore() 332 num = init_hitlist->total; in BLAST_SaveInitialHit() 333 num_avail = init_hitlist->allocated; in BLAST_SaveInitialHit() 335 match_array = init_hitlist->init_hsp_array; in BLAST_SaveInitialHit() 337 if (init_hitlist->do_not_reallocate) in BLAST_SaveInitialHit() [all …]
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H A D | phi_extend.c | 42 s_PHISaveInitialHit(BlastInitHitList* init_hitlist, BlastOffsetPair* offset_pair) in s_PHISaveInitialHit() argument 48 BLAST_SaveInitialHit(init_hitlist, offset_pair->phi_offsets.s_start, in s_PHISaveInitialHit() 59 Int4 max_hits, BlastInitHitList* init_hitlist, in PHIBlastWordFinder() argument 79 s_PHISaveInitialHit(init_hitlist, &offset_pairs[hit_index]); in PHIBlastWordFinder()
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H A D | blast_extend.h | 180 void BlastInitHitListReset(BlastInitHitList* init_hitlist); 184 BlastInitHitList* BLAST_InitHitListFree(BlastInitHitList* init_hitlist); 195 Boolean BLAST_SaveInitialHit(BlastInitHitList* init_hitlist, 217 Blast_InitHitListSortByScore(BlastInitHitList* init_hitlist); 224 Boolean Blast_InitHitListIsSortedByScore(BlastInitHitList* init_hitlist);
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H A D | na_ungapped.h | 60 BlastInitHitList* init_hitlist, 90 BlastInitHitList* init_hitlist, 135 BlastInitHitList* init_hitlist, 154 BlastInitHitList* init_hitlist,
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H A D | na_ungapped.c | 807 BlastInitHitList * init_hitlist, in s_BlastnDiagHashExtendInitialHit() argument 1056 BlastInitHitList * init_hitlist, in s_BlastNaExtend() argument 1443 init_hitlist, in s_BlastSmallNaExtendAlignedOneByte() 1686 init_hitlist->total); in BlastNaWordFinder() 1704 BlastInitHitList * init_hitlist, in MB_IndexedWordFinder() argument 1740 hsp_end = hsp + init_hitlist->total; in MB_IndexedWordFinder() 1778 init_hitlist->total = new_hsp - init_hitlist->init_hsp_array; in MB_IndexedWordFinder() 1938 BlastInitHitList* init_hitlist, in JumperNaWordFinder() argument 2170 BlastInitHitList* init_hitlist, in ShortRead_IndexedWordFinder() argument 2211 hsp = init_hitlist->init_hsp_array; in ShortRead_IndexedWordFinder() [all …]
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H A D | mb_indexed_lookup.h | 56 BlastInitHitList * init_hitlist); 92 BlastInitHitList * init_hitlist,
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H A D | aa_ungapped.h | 69 BlastInitHitList* init_hitlist, 95 BlastInitHitList* init_hitlist,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_extend.c | 226 return init_hitlist; in BLAST_InitHitListNew() 235 init_hitlist->total = 0; in BlastInitHitListReset() 263 if (init_hitlist == NULL) in BLAST_InitHitListFree() 266 s_BlastInitHitListClean(init_hitlist); in BLAST_InitHitListFree() 267 sfree(init_hitlist); in BLAST_InitHitListFree() 308 qsort(init_hitlist->init_hsp_array, init_hitlist->total, in Blast_InitHitListSortByScore() 332 num = init_hitlist->total; in BLAST_SaveInitialHit() 333 num_avail = init_hitlist->allocated; in BLAST_SaveInitialHit() 335 match_array = init_hitlist->init_hsp_array; in BLAST_SaveInitialHit() 337 if (init_hitlist->do_not_reallocate) in BLAST_SaveInitialHit() [all …]
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H A D | phi_extend.c | 42 s_PHISaveInitialHit(BlastInitHitList* init_hitlist, BlastOffsetPair* offset_pair) in s_PHISaveInitialHit() argument 48 BLAST_SaveInitialHit(init_hitlist, offset_pair->phi_offsets.s_start, in s_PHISaveInitialHit() 59 Int4 max_hits, BlastInitHitList* init_hitlist, in PHIBlastWordFinder() argument 79 s_PHISaveInitialHit(init_hitlist, &offset_pairs[hit_index]); in PHIBlastWordFinder()
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H A D | na_ungapped.c | 810 BlastInitHitList * init_hitlist, in s_BlastnDiagHashExtendInitialHit() argument 1059 BlastInitHitList * init_hitlist, in s_BlastNaExtend() argument 1446 init_hitlist, in s_BlastSmallNaExtendAlignedOneByte() 1689 init_hitlist->total); in BlastNaWordFinder() 1707 BlastInitHitList * init_hitlist, in MB_IndexedWordFinder() argument 1743 hsp_end = hsp + init_hitlist->total; in MB_IndexedWordFinder() 1781 init_hitlist->total = new_hsp - init_hitlist->init_hsp_array; in MB_IndexedWordFinder() 1941 BlastInitHitList* init_hitlist, in JumperNaWordFinder() argument 2174 BlastInitHitList* init_hitlist, in ShortRead_IndexedWordFinder() argument 2215 hsp = init_hitlist->init_hsp_array; in ShortRead_IndexedWordFinder() [all …]
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H A D | blast_engine.c | 98 BlastInitHitList* init_hitlist; /**< Placeholder for HSPs after member 115 BLAST_InitHitListFree(aux_struct->init_hitlist); in s_BlastCoreAuxStructFree() 326 BlastInitHitList* init_hitlist, in s_TranslateHSPsToDNAPCoord() argument 334 for(index = 0; index < init_hitlist->total; ++index) { in s_TranslateHSPsToDNAPCoord() 336 init_hsp = &init_hitlist->init_hsp_array[index]; in s_TranslateHSPsToDNAPCoord() 382 Blast_InitHitListSortByScore(init_hitlist); in s_TranslateHSPsToDNAPCoord() 441 BlastInitHitList* init_hitlist = aux_struct->init_hitlist; in s_BlastSearchEngineOneContext() local 492 BlastInitHitListReset(init_hitlist); in s_BlastSearchEngineOneContext() 501 if (init_hitlist->total == 0) continue; in s_BlastSearchEngineOneContext() 574 BlastInitHitListReset(init_hitlist); in s_BlastSearchEngineOneContext() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_extend.c | 226 return init_hitlist; in BLAST_InitHitListNew() 235 init_hitlist->total = 0; in BlastInitHitListReset() 263 if (init_hitlist == NULL) in BLAST_InitHitListFree() 266 s_BlastInitHitListClean(init_hitlist); in BLAST_InitHitListFree() 267 sfree(init_hitlist); in BLAST_InitHitListFree() 308 qsort(init_hitlist->init_hsp_array, init_hitlist->total, in Blast_InitHitListSortByScore() 332 num = init_hitlist->total; in BLAST_SaveInitialHit() 333 num_avail = init_hitlist->allocated; in BLAST_SaveInitialHit() 335 match_array = init_hitlist->init_hsp_array; in BLAST_SaveInitialHit() 337 if (init_hitlist->do_not_reallocate) in BLAST_SaveInitialHit() [all …]
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H A D | phi_extend.c | 42 s_PHISaveInitialHit(BlastInitHitList* init_hitlist, BlastOffsetPair* offset_pair) in s_PHISaveInitialHit() argument 48 BLAST_SaveInitialHit(init_hitlist, offset_pair->phi_offsets.s_start, in s_PHISaveInitialHit() 59 Int4 max_hits, BlastInitHitList* init_hitlist, in PHIBlastWordFinder() argument 79 s_PHISaveInitialHit(init_hitlist, &offset_pairs[hit_index]); in PHIBlastWordFinder()
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H A D | na_ungapped.c | 810 BlastInitHitList * init_hitlist, in s_BlastnDiagHashExtendInitialHit() argument 1059 BlastInitHitList * init_hitlist, in s_BlastNaExtend() argument 1446 init_hitlist, in s_BlastSmallNaExtendAlignedOneByte() 1689 init_hitlist->total); in BlastNaWordFinder() 1707 BlastInitHitList * init_hitlist, in MB_IndexedWordFinder() argument 1743 hsp_end = hsp + init_hitlist->total; in MB_IndexedWordFinder() 1781 init_hitlist->total = new_hsp - init_hitlist->init_hsp_array; in MB_IndexedWordFinder() 1941 BlastInitHitList* init_hitlist, in JumperNaWordFinder() argument 2174 BlastInitHitList* init_hitlist, in ShortRead_IndexedWordFinder() argument 2215 hsp = init_hitlist->init_hsp_array; in ShortRead_IndexedWordFinder() [all …]
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H A D | blast_engine.c | 98 BlastInitHitList* init_hitlist; /**< Placeholder for HSPs after member 115 BLAST_InitHitListFree(aux_struct->init_hitlist); in s_BlastCoreAuxStructFree() 326 BlastInitHitList* init_hitlist, in s_TranslateHSPsToDNAPCoord() argument 334 for(index = 0; index < init_hitlist->total; ++index) { in s_TranslateHSPsToDNAPCoord() 336 init_hsp = &init_hitlist->init_hsp_array[index]; in s_TranslateHSPsToDNAPCoord() 382 Blast_InitHitListSortByScore(init_hitlist); in s_TranslateHSPsToDNAPCoord() 441 BlastInitHitList* init_hitlist = aux_struct->init_hitlist; in s_BlastSearchEngineOneContext() local 492 BlastInitHitListReset(init_hitlist); in s_BlastSearchEngineOneContext() 501 if (init_hitlist->total == 0) continue; in s_BlastSearchEngineOneContext() 574 BlastInitHitListReset(init_hitlist); in s_BlastSearchEngineOneContext() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
H A D | blast_extend.h | 180 void BlastInitHitListReset(BlastInitHitList* init_hitlist); 184 BlastInitHitList* BLAST_InitHitListFree(BlastInitHitList* init_hitlist); 195 Boolean BLAST_SaveInitialHit(BlastInitHitList* init_hitlist, 217 Blast_InitHitListSortByScore(BlastInitHitList* init_hitlist); 224 Boolean Blast_InitHitListIsSortedByScore(BlastInitHitList* init_hitlist);
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H A D | na_ungapped.h | 60 BlastInitHitList* init_hitlist, 90 BlastInitHitList* init_hitlist, 135 BlastInitHitList* init_hitlist, 154 BlastInitHitList* init_hitlist,
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H A D | mb_indexed_lookup.h | 56 BlastInitHitList * init_hitlist); 92 BlastInitHitList * init_hitlist,
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H A D | aa_ungapped.h | 69 BlastInitHitList* init_hitlist, 95 BlastInitHitList* init_hitlist,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_extend.h | 180 void BlastInitHitListReset(BlastInitHitList* init_hitlist); 184 BlastInitHitList* BLAST_InitHitListFree(BlastInitHitList* init_hitlist); 195 Boolean BLAST_SaveInitialHit(BlastInitHitList* init_hitlist, 217 Blast_InitHitListSortByScore(BlastInitHitList* init_hitlist); 224 Boolean Blast_InitHitListIsSortedByScore(BlastInitHitList* init_hitlist);
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H A D | na_ungapped.h | 60 BlastInitHitList* init_hitlist, 90 BlastInitHitList* init_hitlist, 135 BlastInitHitList* init_hitlist, 154 BlastInitHitList* init_hitlist,
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H A D | mb_indexed_lookup.h | 56 BlastInitHitList * init_hitlist); 92 BlastInitHitList * init_hitlist,
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H A D | aa_ungapped.h | 69 BlastInitHitList* init_hitlist, 95 BlastInitHitList* init_hitlist,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | blast_dbindex.cpp | 81 BlastInitHitList * init_hitlist ); 322 BlastInitHitList * init_hitlist ) const; 902 BlastInitHitList * init_hitlist ) const in GetResults() 914 BlastInitHitListMove( init_hitlist, res ); in GetResults() 918 BlastInitHitListReset( init_hitlist ); in GetResults() 1051 BlastInitHitList * init_hitlist ) const in GetResults() 1059 BlastInitHitListMove( init_hitlist, res ); in GetResults() 1062 BlastInitHitListReset( init_hitlist ); in GetResults() 1171 BlastInitHitList * init_hitlist ) in s_MB_IdbGetResults() argument 1175 _ASSERT( init_hitlist != 0 ); in s_MB_IdbGetResults() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | blast_dbindex.cpp | 81 BlastInitHitList * init_hitlist ); 322 BlastInitHitList * init_hitlist ) const; 902 BlastInitHitList * init_hitlist ) const in GetResults() 914 BlastInitHitListMove( init_hitlist, res ); in GetResults() 918 BlastInitHitListReset( init_hitlist ); in GetResults() 1051 BlastInitHitList * init_hitlist ) const in GetResults() 1059 BlastInitHitListMove( init_hitlist, res ); in GetResults() 1062 BlastInitHitListReset( init_hitlist ); in GetResults() 1171 BlastInitHitList * init_hitlist ) in s_MB_IdbGetResults() argument 1175 _ASSERT( init_hitlist != 0 ); in s_MB_IdbGetResults() [all …]
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