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Searched refs:init_hitlist (Results 1 – 25 of 52) sorted by relevance

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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_extend.c226 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 …]
H A Dphi_extend.c42 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()
H A Dblast_extend.h180 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);
H A Dna_ungapped.h60 BlastInitHitList* init_hitlist,
90 BlastInitHitList* init_hitlist,
135 BlastInitHitList* init_hitlist,
154 BlastInitHitList* init_hitlist,
H A Dna_ungapped.c807 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 …]
H A Dmb_indexed_lookup.h56 BlastInitHitList * init_hitlist);
92 BlastInitHitList * init_hitlist,
H A Daa_ungapped.h69 BlastInitHitList* init_hitlist,
95 BlastInitHitList* init_hitlist,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_extend.c226 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 …]
H A Dphi_extend.c42 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()
H A Dna_ungapped.c810 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 …]
H A Dblast_engine.c98 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_extend.c226 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 …]
H A Dphi_extend.c42 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()
H A Dna_ungapped.c810 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 …]
H A Dblast_engine.c98 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_extend.h180 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);
H A Dna_ungapped.h60 BlastInitHitList* init_hitlist,
90 BlastInitHitList* init_hitlist,
135 BlastInitHitList* init_hitlist,
154 BlastInitHitList* init_hitlist,
H A Dmb_indexed_lookup.h56 BlastInitHitList * init_hitlist);
92 BlastInitHitList * init_hitlist,
H A Daa_ungapped.h69 BlastInitHitList* init_hitlist,
95 BlastInitHitList* init_hitlist,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_extend.h180 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);
H A Dna_ungapped.h60 BlastInitHitList* init_hitlist,
90 BlastInitHitList* init_hitlist,
135 BlastInitHitList* init_hitlist,
154 BlastInitHitList* init_hitlist,
H A Dmb_indexed_lookup.h56 BlastInitHitList * init_hitlist);
92 BlastInitHitList * init_hitlist,
H A Daa_ungapped.h69 BlastInitHitList* init_hitlist,
95 BlastInitHitList* init_hitlist,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_dbindex.cpp81 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_dbindex.cpp81 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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