/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | lookup.c | 949 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() [all …]
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H A D | mblast.c | 1981 !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() [all …]
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H A D | lookup.h | 434 MbLookupTablePtr mb_lt; /* MegaBlast version of the lookup table */ member
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_nalookup.c | 682 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() [all …]
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H A D | blast_nascan.c | 1492 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() [all …]
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H A D | na_ungapped.c | 52 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()
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H A D | blast_nalookup.h | 296 BlastMBLookupTable* BlastMBLookupTableDestruct(BlastMBLookupTable* mb_lt);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_nalookup.c | 682 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() [all …]
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H A D | blast_nascan.c | 1492 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() [all …]
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H A D | na_ungapped.c | 52 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_nalookup.c | 682 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() [all …]
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H A D | blast_nascan.c | 1492 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() [all …]
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H A D | na_ungapped.c | 52 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | ntscan_unit_test.cpp | 392 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() [all …]
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H A D | nuclwordfinder_unit_test.cpp | 87 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | ntscan_unit_test.cpp | 392 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() [all …]
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H A D | nuclwordfinder_unit_test.cpp | 87 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
H A D | blast_nalookup.h | 296 BlastMBLookupTable* BlastMBLookupTableDestruct(BlastMBLookupTable* mb_lt);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_nalookup.h | 296 BlastMBLookupTable* BlastMBLookupTableDestruct(BlastMBLookupTable* mb_lt);
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