/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | phiblast_unit_test.cpp | 220 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()
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H A D | blastoptions_unit_test.cpp | 749 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()
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H A D | scoreblk_unit_test.cpp | 222 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | phiblast_unit_test.cpp | 220 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()
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H A D | blastoptions_unit_test.cpp | 749 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()
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H A D | scoreblk_unit_test.cpp | 222 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()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | rpsutil.c | 815 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 …]
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H A D | blastconcat.c | 129 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()
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H A D | blast.c | 5094 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 …]
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H A D | blastutl.c | 2625 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 …]
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_parameters.c | 296 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()
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H A D | blast_traceback.c | 1095 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()
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H A D | blast_setup.c | 124 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()
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H A D | blast_kappa.c | 2060 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_parameters.c | 296 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()
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H A D | blast_traceback.c | 1111 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()
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H A D | blast_setup.c | 124 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()
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H A D | blast_kappa.c | 2072 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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_parameters.c | 296 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()
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H A D | blast_traceback.c | 1111 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()
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H A D | blast_setup.c | 124 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()
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H A D | blast_kappa.c | 2072 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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | blast_results.cpp | 102 if (sbp->kbp_gap) { in CBlastAncillaryData() 103 s_InitializeKarlinBlk(sbp->kbp_gap[ctx_index], &m_GappedKarlinBlk); in CBlastAncillaryData()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | blast_results.cpp | 102 if (sbp->kbp_gap) { in CBlastAncillaryData() 103 s_InitializeKarlinBlk(sbp->kbp_gap[ctx_index], &m_GappedKarlinBlk); in CBlastAncillaryData()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
H A D | blast_returns.c | 309 if (sbp->kbp_gap) { in s_SummaryKAParametersFill() 314 kbp = sbp->kbp_gap[context]; in s_SummaryKAParametersFill()
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