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Searched refs:kbp_gap (Results 1 – 25 of 59) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dphiblast_unit_test.cpp220 BOOST_REQUIRE(m_ScoreBlk->kbp_gap == m_ScoreBlk->kbp_gap_std); in BOOST_FIXTURE_TEST_SUITE()
222 BOOST_REQUIRE_EQUAL(0.5, m_ScoreBlk->kbp_gap[0]->paramC); in BOOST_FIXTURE_TEST_SUITE()
223 BOOST_REQUIRE(m_ScoreBlk->kbp_gap[0]->H != 0); in BOOST_FIXTURE_TEST_SUITE()
225 m_ScoreBlk->kbp_gap[0]->Lambda); in BOOST_FIXTURE_TEST_SUITE()
226 BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->K, m_ScoreBlk->kbp_gap[0]->K); in BOOST_FIXTURE_TEST_SUITE()
242 BOOST_REQUIRE(m_ScoreBlk->kbp_gap == m_ScoreBlk->kbp_gap_std); in BOOST_AUTO_TEST_CASE()
244 BOOST_REQUIRE_EQUAL(0.5, m_ScoreBlk->kbp_gap[0]->paramC); in BOOST_AUTO_TEST_CASE()
245 BOOST_REQUIRE(m_ScoreBlk->kbp_gap[0]->H != 0); in BOOST_AUTO_TEST_CASE()
247 m_ScoreBlk->kbp_gap[0]->Lambda); in BOOST_AUTO_TEST_CASE()
248 BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->K, m_ScoreBlk->kbp_gap[0]->K); in BOOST_AUTO_TEST_CASE()
H A Dblastoptions_unit_test.cpp749 sb.kbp_gap = (Blast_KarlinBlk**) calloc(k_num_contexts, sizeof(Blast_KarlinBlk*)); in BOOST_AUTO_TEST_CASE()
751 MakeSomeInvalidKBP(sb.kbp_gap, k_num_contexts, 4, query_info); in BOOST_AUTO_TEST_CASE()
769 sb.kbp_gap[index] = Blast_KarlinBlkFree(sb.kbp_gap[index]); in BOOST_AUTO_TEST_CASE()
772 sfree(sb.kbp_gap); in BOOST_AUTO_TEST_CASE()
810 sb.kbp_gap = (Blast_KarlinBlk**) calloc(k_num_contexts, sizeof(Blast_KarlinBlk*)); in BOOST_AUTO_TEST_CASE()
812 MakeSomeValidKBP(sb.kbp_gap, k_num_contexts, query_info.Get()); in BOOST_AUTO_TEST_CASE()
841 sb.kbp_gap[index] = Blast_KarlinBlkFree(sb.kbp_gap[index]); in BOOST_AUTO_TEST_CASE()
844 sfree(sb.kbp_gap); in BOOST_AUTO_TEST_CASE()
902 MakeSomeInvalidKBP(sbp->kbp_gap, in BOOST_AUTO_TEST_CASE()
1282 MakeSomeInvalidKBP(sbp->kbp_gap, query_info->last_context+1, in BOOST_AUTO_TEST_CASE()
H A Dscoreblk_unit_test.cpp222 BOOST_REQUIRE(sbp->kbp_gap == sbp->kbp_gap_std); in BOOST_AUTO_TEST_CASE()
223 BOOST_REQUIRE(sbp->kbp_gap[0]->Lambda == kPhiLambda); in BOOST_AUTO_TEST_CASE()
224 BOOST_REQUIRE(sbp->kbp_gap[0]->K == kPhiK); in BOOST_AUTO_TEST_CASE()
225 BOOST_REQUIRE(sbp->kbp_gap[0]->H > 0); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dphiblast_unit_test.cpp220 BOOST_REQUIRE(m_ScoreBlk->kbp_gap == m_ScoreBlk->kbp_gap_std); in BOOST_FIXTURE_TEST_SUITE()
222 BOOST_REQUIRE_EQUAL(0.5, m_ScoreBlk->kbp_gap[0]->paramC); in BOOST_FIXTURE_TEST_SUITE()
223 BOOST_REQUIRE(m_ScoreBlk->kbp_gap[0]->H != 0); in BOOST_FIXTURE_TEST_SUITE()
225 m_ScoreBlk->kbp_gap[0]->Lambda); in BOOST_FIXTURE_TEST_SUITE()
226 BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->K, m_ScoreBlk->kbp_gap[0]->K); in BOOST_FIXTURE_TEST_SUITE()
242 BOOST_REQUIRE(m_ScoreBlk->kbp_gap == m_ScoreBlk->kbp_gap_std); in BOOST_AUTO_TEST_CASE()
244 BOOST_REQUIRE_EQUAL(0.5, m_ScoreBlk->kbp_gap[0]->paramC); in BOOST_AUTO_TEST_CASE()
245 BOOST_REQUIRE(m_ScoreBlk->kbp_gap[0]->H != 0); in BOOST_AUTO_TEST_CASE()
247 m_ScoreBlk->kbp_gap[0]->Lambda); in BOOST_AUTO_TEST_CASE()
248 BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->K, m_ScoreBlk->kbp_gap[0]->K); in BOOST_AUTO_TEST_CASE()
H A Dblastoptions_unit_test.cpp749 sb.kbp_gap = (Blast_KarlinBlk**) calloc(k_num_contexts, sizeof(Blast_KarlinBlk*)); in BOOST_AUTO_TEST_CASE()
751 MakeSomeInvalidKBP(sb.kbp_gap, k_num_contexts, 4, query_info); in BOOST_AUTO_TEST_CASE()
769 sb.kbp_gap[index] = Blast_KarlinBlkFree(sb.kbp_gap[index]); in BOOST_AUTO_TEST_CASE()
772 sfree(sb.kbp_gap); in BOOST_AUTO_TEST_CASE()
810 sb.kbp_gap = (Blast_KarlinBlk**) calloc(k_num_contexts, sizeof(Blast_KarlinBlk*)); in BOOST_AUTO_TEST_CASE()
812 MakeSomeValidKBP(sb.kbp_gap, k_num_contexts, query_info.Get()); in BOOST_AUTO_TEST_CASE()
841 sb.kbp_gap[index] = Blast_KarlinBlkFree(sb.kbp_gap[index]); in BOOST_AUTO_TEST_CASE()
844 sfree(sb.kbp_gap); in BOOST_AUTO_TEST_CASE()
902 MakeSomeInvalidKBP(sbp->kbp_gap, in BOOST_AUTO_TEST_CASE()
1282 MakeSomeInvalidKBP(sbp->kbp_gap, query_info->last_context+1, in BOOST_AUTO_TEST_CASE()
H A Dscoreblk_unit_test.cpp222 BOOST_REQUIRE(sbp->kbp_gap == sbp->kbp_gap_std); in BOOST_AUTO_TEST_CASE()
223 BOOST_REQUIRE(sbp->kbp_gap[0]->Lambda == kPhiLambda); in BOOST_AUTO_TEST_CASE()
224 BOOST_REQUIRE(sbp->kbp_gap[0]->K == kPhiK); in BOOST_AUTO_TEST_CASE()
225 BOOST_REQUIRE(sbp->kbp_gap[0]->H > 0); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Drpsutil.c815 search->sbp->kbp_gap = search->sbp->kbp_gap_psi; in RPSubstituteQueryLookup()
1195 kbp = search->sbp->kbp_gap; in RPSCalcEValue()
1230 search->sbp->kbp_gap[0]->logK = log(search->sbp->kbp_gap[0]->K); in RPSCalcEValue()
1245 kbp = search->sbp->kbp_gap; in RPSCalcEValue()
1274 search->sbp->kbp_gap[0]->K /= PRO_K_MULTIPLIER; in RPSCalcEValue()
1275 search->sbp->kbp_gap[0]->logK = log(search->sbp->kbp_gap[0]->K); in RPSCalcEValue()
1405 search->sbp->kbp_gap[0]->logK = log(search->sbp->kbp_gap[0]->K); in RPSAlignTraceBack()
1447 search->sbp->kbp_gap[0]->K /= PRO_K_MULTIPLIER; in RPSAlignTraceBack()
1448 search->sbp->kbp_gap[0]->logK = log(search->sbp->kbp_gap[0]->K); in RPSAlignTraceBack()
1609 search->sbp->kbp_gap[0]->logK = log(search->sbp->kbp_gap[0]->K); in RPS_FIX()
[all …]
H A Dblastconcat.c129 kbp_gap; in GetNumSpacers() local
254 sbp->kbp_gap = sbp->kbp_gap_std; in GetNumSpacers()
257 kbp_gap = sbp->kbp[first_context]; in GetNumSpacers()
267 sbp->kbp_gap = sbp->kbp_gap_std; in GetNumSpacers()
269 kbp_gap = sbp->kbp_gap[first_context]; in GetNumSpacers()
270 Lambda = kbp_gap->Lambda; in GetNumSpacers()
H A Dblast.c5094 BLAST_KarlinBlkPtr kbp_gap = in BLASTSetUpSearchInternalByLoc() local
5104 BlastComputeLengthAdjustment(kbp_gap->K, in BLASTSetUpSearchInternalByLoc()
6473 kbp = search->sbp->kbp_gap; in BlastReapPartialHitlistByEvalue()
10189 BLAST_KarlinBlkPtr kbp, kbp_gap; in blast_set_parameters() local
10212 kbp_gap = sbp->kbp_gap[search->first_context]; in blast_set_parameters()
10214 if (kbp == NULL && kbp_gap == NULL) in blast_set_parameters()
10244 BlastCutoffs( &s, &e, kbp_gap, in blast_set_parameters()
10280 BlastCutoffs( &s2, &e2, kbp_gap, in blast_set_parameters()
11086 kbp_array = search->sbp->kbp_gap; in new_link_hsps()
11302 kbp = search->sbp->kbp_gap; in link_hsps()
[all …]
H A Dblastutl.c2625 sbp->kbp_gap = sbp->kbp_gap_psi; in BlastTwoSequencesCoreEx()
2834 search->sbp->kbp_gap[0]->K = in BlastTwoSequencesCore()
2836 search->sbp->kbp_gap[0]->logK = log(search->sbp->kbp_gap[0]->K); in BlastTwoSequencesCore()
2837 search->sbp->kbp_gap[0]->Lambda /= search->pbp->scalingFactor; in BlastTwoSequencesCore()
2955 search->sbp->kbp_gap[0]->K = search->sbp->karlinK; in BlastTwoSequencesCore()
2956 search->sbp->kbp_gap[0]->logK = log(search->sbp->kbp_gap[0]->K); in BlastTwoSequencesCore()
4590 search->sbp->kbp_gap = search->sbp->kbp_gap_psi; in BioseqBlastEngineCore()
4726 kbp = search1->sbp->kbp_gap[search1->first_context]; in BioseqBlastEngineCore()
5167 search->sbp->kbp_gap = search->sbp->kbp_gap_psi; in BioseqBlastEngineByLocWithCallbackMult()
5517 if (search->sbp->kbp_gap && search->sbp->kbp_gap[search->first_context]) { in BlastOtherReturnsPrepare()
[all …]
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_parameters.c296 if (sbp->kbp_gap) { in BlastInitialWordParametersUpdate()
297 kbp_array = sbp->kbp_gap; in BlastInitialWordParametersUpdate()
453 if (sbp->kbp_gap) { in BlastExtensionParametersNew()
454 double min_lambda = s_BlastFindSmallestLambda(sbp->kbp_gap, query_info, NULL); in BlastExtensionParametersNew()
750 if (!sbp->kbp_gap) in BlastHitSavingParametersNew()
854 if (sbp->kbp_gap) { in BlastHitSavingParametersUpdate()
855 kbp_array = sbp->kbp_gap; in BlastHitSavingParametersUpdate()
H A Dblast_traceback.c1095 if (sbp->kbp_gap[index] != NULL) { in s_RPSComputeTraceback()
1105 if (sbp->kbp_gap[index] == NULL) { in s_RPSComputeTraceback()
1106 sbp->kbp_gap[index] = Blast_KarlinBlkNew(); in s_RPSComputeTraceback()
1107 Blast_KarlinBlkCopy(sbp->kbp_gap[index], sbp->kbp_gap[valid_kb_index]); in s_RPSComputeTraceback()
1176 sbp->kbp_gap[0]->K = RPS_K_MULT * karlin_k[hsp_list->oid]; in s_RPSComputeTraceback()
1177 sbp->kbp_gap[0]->logK = log(RPS_K_MULT * karlin_k[hsp_list->oid]); in s_RPSComputeTraceback()
1218 sbp->kbp_gap[0]->K = RPS_K_MULT * karlin_k[hsp_list->oid]; in s_RPSComputeTraceback()
1219 sbp->kbp_gap[0]->logK = log(RPS_K_MULT * karlin_k[hsp_list->oid]); in s_RPSComputeTraceback()
1277 sbp->kbp_gap[0] = NULL; in s_RPSComputeTraceback()
H A Dblast_setup.c124 sbp->kbp_gap = Blast_QueryIsPssm(program) ? in Blast_ScoreBlkKbpGappedCalc()
150 sbp->kbp_gap = sbp->kbp_gap_std; in s_PHIScoreBlkFill()
449 sbp->kbp_gap = sbp->kbp_gap_std; in s_JumperScoreBlkFill()
522 ASSERT(sbp->kbp_gap == NULL); in BlastSetup_ScoreBlkInit()
550 if (score_blk->kbp_gap) { in BlastSetup_Validate()
551 ASSERT(score_blk->kbp_gap[index] == NULL); in BlastSetup_Validate()
H A Dblast_kappa.c2060 if (sbp->kbp_gap[i] != NULL) { in s_RecordInitialSearch()
2067 sbp->kbp_gap[i]); in s_RecordInitialSearch()
2110 if (sbp->kbp_gap[i] != NULL) { in s_RescaleSearch()
2111 Blast_KarlinBlk * kbp = sbp->kbp_gap[i]; in s_RescaleSearch()
2148 if (sbp->kbp_gap[i] != NULL) { in s_RestoreSearch()
2149 Blast_KarlinBlkCopy(sbp->kbp_gap[i], in s_RestoreSearch()
2361 if (context->sbp->kbp_gap[i] != NULL && in s_GappingParamsNew()
2431 / context->sbp->kbp_gap[index]->Lambda; in s_GetAlignParams()
2852 copy->kbp_gap = copy->kbp_gap_psi; in s_BlastScoreBlk_Copy()
2855 copy->kbp_gap = copy->kbp_gap_std; in s_BlastScoreBlk_Copy()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_parameters.c296 if (sbp->kbp_gap) { in BlastInitialWordParametersUpdate()
297 kbp_array = sbp->kbp_gap; in BlastInitialWordParametersUpdate()
453 if (sbp->kbp_gap) { in BlastExtensionParametersNew()
454 double min_lambda = s_BlastFindSmallestLambda(sbp->kbp_gap, query_info, NULL); in BlastExtensionParametersNew()
754 if (!sbp->kbp_gap) in BlastHitSavingParametersNew()
858 if (sbp->kbp_gap) { in BlastHitSavingParametersUpdate()
859 kbp_array = sbp->kbp_gap; in BlastHitSavingParametersUpdate()
H A Dblast_traceback.c1111 if (sbp->kbp_gap[index] != NULL) { in s_RPSComputeTraceback()
1121 if (sbp->kbp_gap[index] == NULL) { in s_RPSComputeTraceback()
1122 sbp->kbp_gap[index] = Blast_KarlinBlkNew(); in s_RPSComputeTraceback()
1123 Blast_KarlinBlkCopy(sbp->kbp_gap[index], sbp->kbp_gap[valid_kb_index]); in s_RPSComputeTraceback()
1192 sbp->kbp_gap[0]->K = RPS_K_MULT * karlin_k[hsp_list->oid]; in s_RPSComputeTraceback()
1193 sbp->kbp_gap[0]->logK = log(RPS_K_MULT * karlin_k[hsp_list->oid]); in s_RPSComputeTraceback()
1234 sbp->kbp_gap[0]->K = RPS_K_MULT * karlin_k[hsp_list->oid]; in s_RPSComputeTraceback()
1235 sbp->kbp_gap[0]->logK = log(RPS_K_MULT * karlin_k[hsp_list->oid]); in s_RPSComputeTraceback()
1293 sbp->kbp_gap[0] = NULL; in s_RPSComputeTraceback()
H A Dblast_setup.c124 sbp->kbp_gap = Blast_QueryIsPssm(program) ? in Blast_ScoreBlkKbpGappedCalc()
150 sbp->kbp_gap = sbp->kbp_gap_std; in s_PHIScoreBlkFill()
449 sbp->kbp_gap = sbp->kbp_gap_std; in s_JumperScoreBlkFill()
522 ASSERT(sbp->kbp_gap == NULL); in BlastSetup_ScoreBlkInit()
550 if (score_blk->kbp_gap) { in BlastSetup_Validate()
551 ASSERT(score_blk->kbp_gap[index] == NULL); in BlastSetup_Validate()
H A Dblast_kappa.c2072 if (sbp->kbp_gap[i] != NULL) { in s_RecordInitialSearch()
2079 sbp->kbp_gap[i]); in s_RecordInitialSearch()
2122 if (sbp->kbp_gap[i] != NULL) { in s_RescaleSearch()
2123 Blast_KarlinBlk * kbp = sbp->kbp_gap[i]; in s_RescaleSearch()
2160 if (sbp->kbp_gap[i] != NULL) { in s_RestoreSearch()
2161 Blast_KarlinBlkCopy(sbp->kbp_gap[i], in s_RestoreSearch()
2373 if (context->sbp->kbp_gap[i] != NULL && in s_GappingParamsNew()
2443 / context->sbp->kbp_gap[index]->Lambda; in s_GetAlignParams()
2858 copy->kbp_gap = copy->kbp_gap_psi; in s_BlastScoreBlk_Copy()
2861 copy->kbp_gap = copy->kbp_gap_std; in s_BlastScoreBlk_Copy()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_parameters.c296 if (sbp->kbp_gap) { in BlastInitialWordParametersUpdate()
297 kbp_array = sbp->kbp_gap; in BlastInitialWordParametersUpdate()
453 if (sbp->kbp_gap) { in BlastExtensionParametersNew()
454 double min_lambda = s_BlastFindSmallestLambda(sbp->kbp_gap, query_info, NULL); in BlastExtensionParametersNew()
754 if (!sbp->kbp_gap) in BlastHitSavingParametersNew()
858 if (sbp->kbp_gap) { in BlastHitSavingParametersUpdate()
859 kbp_array = sbp->kbp_gap; in BlastHitSavingParametersUpdate()
H A Dblast_traceback.c1111 if (sbp->kbp_gap[index] != NULL) { in s_RPSComputeTraceback()
1121 if (sbp->kbp_gap[index] == NULL) { in s_RPSComputeTraceback()
1122 sbp->kbp_gap[index] = Blast_KarlinBlkNew(); in s_RPSComputeTraceback()
1123 Blast_KarlinBlkCopy(sbp->kbp_gap[index], sbp->kbp_gap[valid_kb_index]); in s_RPSComputeTraceback()
1192 sbp->kbp_gap[0]->K = RPS_K_MULT * karlin_k[hsp_list->oid]; in s_RPSComputeTraceback()
1193 sbp->kbp_gap[0]->logK = log(RPS_K_MULT * karlin_k[hsp_list->oid]); in s_RPSComputeTraceback()
1234 sbp->kbp_gap[0]->K = RPS_K_MULT * karlin_k[hsp_list->oid]; in s_RPSComputeTraceback()
1235 sbp->kbp_gap[0]->logK = log(RPS_K_MULT * karlin_k[hsp_list->oid]); in s_RPSComputeTraceback()
1293 sbp->kbp_gap[0] = NULL; in s_RPSComputeTraceback()
H A Dblast_setup.c124 sbp->kbp_gap = Blast_QueryIsPssm(program) ? in Blast_ScoreBlkKbpGappedCalc()
150 sbp->kbp_gap = sbp->kbp_gap_std; in s_PHIScoreBlkFill()
449 sbp->kbp_gap = sbp->kbp_gap_std; in s_JumperScoreBlkFill()
522 ASSERT(sbp->kbp_gap == NULL); in BlastSetup_ScoreBlkInit()
550 if (score_blk->kbp_gap) { in BlastSetup_Validate()
551 ASSERT(score_blk->kbp_gap[index] == NULL); in BlastSetup_Validate()
H A Dblast_kappa.c2072 if (sbp->kbp_gap[i] != NULL) { in s_RecordInitialSearch()
2079 sbp->kbp_gap[i]); in s_RecordInitialSearch()
2122 if (sbp->kbp_gap[i] != NULL) { in s_RescaleSearch()
2123 Blast_KarlinBlk * kbp = sbp->kbp_gap[i]; in s_RescaleSearch()
2160 if (sbp->kbp_gap[i] != NULL) { in s_RestoreSearch()
2161 Blast_KarlinBlkCopy(sbp->kbp_gap[i], in s_RestoreSearch()
2373 if (context->sbp->kbp_gap[i] != NULL && in s_GappingParamsNew()
2443 / context->sbp->kbp_gap[index]->Lambda; in s_GetAlignParams()
2858 copy->kbp_gap = copy->kbp_gap_psi; in s_BlastScoreBlk_Copy()
2861 copy->kbp_gap = copy->kbp_gap_std; in s_BlastScoreBlk_Copy()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_results.cpp102 if (sbp->kbp_gap) { in CBlastAncillaryData()
103 s_InitializeKarlinBlk(sbp->kbp_gap[ctx_index], &m_GappedKarlinBlk); in CBlastAncillaryData()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_results.cpp102 if (sbp->kbp_gap) { in CBlastAncillaryData()
103 s_InitializeKarlinBlk(sbp->kbp_gap[ctx_index], &m_GappedKarlinBlk); in CBlastAncillaryData()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dblast_returns.c309 if (sbp->kbp_gap) { in s_SummaryKAParametersFill()
314 kbp = sbp->kbp_gap[context]; in s_SummaryKAParametersFill()

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