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Searched refs:mb_lt (Results 1 – 19 of 19) sorted by relevance

/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dlookup.c949 mb_lt->hashsize = (1<<(8*mb_lt->width)); in MegaBlastBuildLookupTable()
960 mask = mb_lt->mask = (1 << (8*mb_lt->width - 2)) - 1; in MegaBlastBuildLookupTable()
982 mb_lt->hashtable2 = mb_lt->hashtable; in MegaBlastBuildLookupTable()
1105 mb_lt->next_pos[index] = mb_lt->hashtable[ecode1]; in MegaBlastBuildLookupTable()
1166 mb_lt->next_pos[index] = mb_lt->hashtable[ecode1]; in MegaBlastBuildLookupTable()
1186 mb_lt->next_pos[index] = mb_lt->hashtable[ecode]; in MegaBlastBuildLookupTable()
1213 4*mb_lt->width); in MegaBlastBuildLookupTable()
1218 mb_lt->mask = (1 << mb_lt->width*8) - 1; in MegaBlastBuildLookupTable()
1220 mb_lt->mask = (1 << (mb_lt->width*8 - 8)) - 1; in MegaBlastBuildLookupTable()
1277 lookup->mb_lt = mb_lt; in MegaBlastBuildLookupTable()
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H A Dmblast.c1981 !search->wfp->lookup->mb_lt) in MegaBlastSaveExactMatch()
2070 mask = lookup->mb_lt->mask; in MegaBlastWordFinder_disc()
2073 if (lookup->mb_lt->estack) in MegaBlastWordFinder_disc()
2350 if (!lookup->mb_lt->estack) in MegaBlastWordFinder_disc()
2421 mask = lookup->mb_lt->mask; in MegaBlastWordFinder_disc_1b()
2424 if (lookup->mb_lt->estack) in MegaBlastWordFinder_disc_1b()
2720 if (!lookup->mb_lt->estack) in MegaBlastWordFinder_disc_1b()
2764 mask = lookup->mb_lt->mask; in MegaBlastWordFinder()
2767 if (lookup->mb_lt->estack) in MegaBlastWordFinder()
2799 if (!lookup->mb_lt->estack) in MegaBlastWordFinder()
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H A Dlookup.h434 MbLookupTablePtr mb_lt; /* MegaBlast version of the lookup table */ member
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_nalookup.c682 ASSERT(mb_lt); in s_FillDiscMBTable()
777 mb_lt->next_pos[index] = mb_lt->hashtable[ecode1]; in s_FillDiscMBTable()
795 mb_lt->next_pos2[index] = mb_lt->hashtable2[ecode2]; in s_FillDiscMBTable()
835 ASSERT(mb_lt); in s_FillPV()
1075 mb_lt->next_pos[index] = mb_lt->hashtable[ecode]; in s_FillContigMBTable()
1253 mb_lt->word_length > mb_lt->lut_word_length && in BlastMBLookupTableNew()
1288 mb_lt->pv_array_bts = ilog2(mb_lt->hashsize / pv_size); in BlastMBLookupTableNew()
1317 mb_lt->scan_step = mb_lt->word_length - mb_lt->lut_word_length + 1; in BlastMBLookupTableNew()
1356 if (!mb_lt) in BlastMBLookupTableDestruct()
1366 sfree(mb_lt); in BlastMBLookupTableDestruct()
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H A Dblast_nascan.c1492 Int8 mask = mb_lt->hashsize - 1; in s_MBScanSubject_Any()
1506 max_hits -= mb_lt->longest_chain; in s_MBScanSubject_Any()
1655 ASSERT(mb_lt->scan_step == 1); in s_MBScanSubject_9_1()
1731 ASSERT(mb_lt->scan_step == 2); in s_MBScanSubject_9_2()
1784 ASSERT(mb_lt->scan_step == 1); in s_MBScanSubject_10_1()
1861 ASSERT(mb_lt->scan_step == 2); in s_MBScanSubject_10_2()
1914 ASSERT(mb_lt->scan_step == 3); in s_MBScanSubject_10_3()
2216 max_hits -= mb_lt->longest_chain; in s_MB_DiscWordScanSubject_1()
2305 max_hits -= mb_lt->longest_chain; in s_MB_DiscWordScanSubject_TwoTemplates_1()
2617 if (mb_lt->discontiguous) { in s_MBChooseScanSubject()
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H A Dna_ungapped.c52 BlastMBLookupTable* mb_lt = (BlastMBLookupTable *) lookup_wrap->lut; in s_MBLookup() local
53 PV_ARRAY_TYPE *pv = mb_lt->pv_array; in s_MBLookup()
56 index &= (mb_lt->hashsize-1); in s_MBLookup()
59 if (! PV_TEST(pv, index, mb_lt->pv_array_bts)) { in s_MBLookup()
63 q_off = mb_lt->hashtable[index]; in s_MBLookup()
66 q_off = mb_lt->next_pos[q_off]; in s_MBLookup()
H A Dblast_nalookup.h296 BlastMBLookupTable* BlastMBLookupTableDestruct(BlastMBLookupTable* mb_lt);
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_nalookup.c682 ASSERT(mb_lt); in s_FillDiscMBTable()
777 mb_lt->next_pos[index] = mb_lt->hashtable[ecode1]; in s_FillDiscMBTable()
795 mb_lt->next_pos2[index] = mb_lt->hashtable2[ecode2]; in s_FillDiscMBTable()
835 ASSERT(mb_lt); in s_FillPV()
1078 mb_lt->next_pos[index] = mb_lt->hashtable[ecode]; in s_FillContigMBTable()
1257 mb_lt->word_length > mb_lt->lut_word_length && in BlastMBLookupTableNew()
1292 mb_lt->pv_array_bts = ilog2(mb_lt->hashsize / pv_size); in BlastMBLookupTableNew()
1322 mb_lt->scan_step = mb_lt->word_length - mb_lt->lut_word_length + 1; in BlastMBLookupTableNew()
1361 if (!mb_lt) in BlastMBLookupTableDestruct()
1371 sfree(mb_lt); in BlastMBLookupTableDestruct()
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H A Dblast_nascan.c1492 Int8 mask = mb_lt->hashsize - 1; in s_MBScanSubject_Any()
1506 max_hits -= mb_lt->longest_chain; in s_MBScanSubject_Any()
1655 ASSERT(mb_lt->scan_step == 1); in s_MBScanSubject_9_1()
1731 ASSERT(mb_lt->scan_step == 2); in s_MBScanSubject_9_2()
1784 ASSERT(mb_lt->scan_step == 1); in s_MBScanSubject_10_1()
1861 ASSERT(mb_lt->scan_step == 2); in s_MBScanSubject_10_2()
1914 ASSERT(mb_lt->scan_step == 3); in s_MBScanSubject_10_3()
2216 max_hits -= mb_lt->longest_chain; in s_MB_DiscWordScanSubject_1()
2305 max_hits -= mb_lt->longest_chain; in s_MB_DiscWordScanSubject_TwoTemplates_1()
2617 if (mb_lt->discontiguous) { in s_MBChooseScanSubject()
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H A Dna_ungapped.c52 BlastMBLookupTable* mb_lt = (BlastMBLookupTable *) lookup_wrap->lut; in s_MBLookup() local
53 PV_ARRAY_TYPE *pv = mb_lt->pv_array; in s_MBLookup()
56 index &= (mb_lt->hashsize-1); in s_MBLookup()
59 if (! PV_TEST(pv, index, mb_lt->pv_array_bts)) { in s_MBLookup()
63 q_off = mb_lt->hashtable[index]; in s_MBLookup()
66 q_off = mb_lt->next_pos[q_off]; in s_MBLookup()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_nalookup.c682 ASSERT(mb_lt); in s_FillDiscMBTable()
777 mb_lt->next_pos[index] = mb_lt->hashtable[ecode1]; in s_FillDiscMBTable()
795 mb_lt->next_pos2[index] = mb_lt->hashtable2[ecode2]; in s_FillDiscMBTable()
835 ASSERT(mb_lt); in s_FillPV()
1078 mb_lt->next_pos[index] = mb_lt->hashtable[ecode]; in s_FillContigMBTable()
1257 mb_lt->word_length > mb_lt->lut_word_length && in BlastMBLookupTableNew()
1292 mb_lt->pv_array_bts = ilog2(mb_lt->hashsize / pv_size); in BlastMBLookupTableNew()
1322 mb_lt->scan_step = mb_lt->word_length - mb_lt->lut_word_length + 1; in BlastMBLookupTableNew()
1361 if (!mb_lt) in BlastMBLookupTableDestruct()
1371 sfree(mb_lt); in BlastMBLookupTableDestruct()
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H A Dblast_nascan.c1492 Int8 mask = mb_lt->hashsize - 1; in s_MBScanSubject_Any()
1506 max_hits -= mb_lt->longest_chain; in s_MBScanSubject_Any()
1655 ASSERT(mb_lt->scan_step == 1); in s_MBScanSubject_9_1()
1731 ASSERT(mb_lt->scan_step == 2); in s_MBScanSubject_9_2()
1784 ASSERT(mb_lt->scan_step == 1); in s_MBScanSubject_10_1()
1861 ASSERT(mb_lt->scan_step == 2); in s_MBScanSubject_10_2()
1914 ASSERT(mb_lt->scan_step == 3); in s_MBScanSubject_10_3()
2216 max_hits -= mb_lt->longest_chain; in s_MB_DiscWordScanSubject_1()
2305 max_hits -= mb_lt->longest_chain; in s_MB_DiscWordScanSubject_TwoTemplates_1()
2617 if (mb_lt->discontiguous) { in s_MBChooseScanSubject()
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H A Dna_ungapped.c52 BlastMBLookupTable* mb_lt = (BlastMBLookupTable *) lookup_wrap->lut; in s_MBLookup() local
53 PV_ARRAY_TYPE *pv = mb_lt->pv_array; in s_MBLookup()
56 index &= (mb_lt->hashsize-1); in s_MBLookup()
59 if (! PV_TEST(pv, index, mb_lt->pv_array_bts)) { in s_MBLookup()
63 q_off = mb_lt->hashtable[index]; in s_MBLookup()
66 q_off = mb_lt->next_pos[q_off]; in s_MBLookup()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dntscan_unit_test.cpp392 BlastMBLookupTable *mb_lt = NULL; in ScanOffsetTestCore() local
409 discontig = mb_lt->discontiguous; in ScanOffsetTestCore()
466 if (mb_lt) { in ScanOffsetTestCore()
496 BlastMBLookupTable *mb_lt = NULL; in ScanMaxHitsTestCore() local
512 discontig = mb_lt->discontiguous; in ScanMaxHitsTestCore()
539 if (mb_lt) in ScanMaxHitsTestCore()
541 mb_lt->longest_chain); in ScanMaxHitsTestCore()
565 BlastMBLookupTable *mb_lt = NULL; in ScanCheckHitsCore() local
582 discontig = mb_lt->discontiguous; in ScanCheckHitsCore()
621 switch (mb_lt->template_type) { in ScanCheckHitsCore()
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H A Dnuclwordfinder_unit_test.cpp87 BlastMBLookupTable* mb_lt = in setupLookupTable() local
89 m_pLookup->lut = (void*) mb_lt; in setupLookupTable()
91 mb_lt->word_length = 12; in setupLookupTable()
92 mb_lt->lut_word_length = 12; in setupLookupTable()
94 mb_lt->discontiguous = TRUE; in setupLookupTable()
95 mb_lt->scan_step = 4; in setupLookupTable()
96 mb_lt->template_length = 21; in setupLookupTable()
98 mb_lt->scan_step = word_size - 11; in setupLookupTable()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dntscan_unit_test.cpp392 BlastMBLookupTable *mb_lt = NULL; in ScanOffsetTestCore() local
409 discontig = mb_lt->discontiguous; in ScanOffsetTestCore()
466 if (mb_lt) { in ScanOffsetTestCore()
496 BlastMBLookupTable *mb_lt = NULL; in ScanMaxHitsTestCore() local
512 discontig = mb_lt->discontiguous; in ScanMaxHitsTestCore()
539 if (mb_lt) in ScanMaxHitsTestCore()
541 mb_lt->longest_chain); in ScanMaxHitsTestCore()
565 BlastMBLookupTable *mb_lt = NULL; in ScanCheckHitsCore() local
582 discontig = mb_lt->discontiguous; in ScanCheckHitsCore()
621 switch (mb_lt->template_type) { in ScanCheckHitsCore()
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H A Dnuclwordfinder_unit_test.cpp87 BlastMBLookupTable* mb_lt = in setupLookupTable() local
89 m_pLookup->lut = (void*) mb_lt; in setupLookupTable()
91 mb_lt->word_length = 12; in setupLookupTable()
92 mb_lt->lut_word_length = 12; in setupLookupTable()
94 mb_lt->discontiguous = TRUE; in setupLookupTable()
95 mb_lt->scan_step = 4; in setupLookupTable()
96 mb_lt->template_length = 21; in setupLookupTable()
98 mb_lt->scan_step = word_size - 11; in setupLookupTable()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_nalookup.h296 BlastMBLookupTable* BlastMBLookupTableDestruct(BlastMBLookupTable* mb_lt);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_nalookup.h296 BlastMBLookupTable* BlastMBLookupTableDestruct(BlastMBLookupTable* mb_lt);