/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | scoreblk_unit_test.cpp | 383 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 410 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 423 BOOST_REQUIRE_CLOSE(sbp->kbp_ideal->Lambda/sbp->kbp_ideal->H, in BOOST_AUTO_TEST_CASE() 436 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 455 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 474 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 490 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 502 BOOST_REQUIRE_CLOSE(sbp->kbp_ideal->Lambda/sbp->kbp_ideal->H, in BOOST_AUTO_TEST_CASE() 512 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 523 BOOST_REQUIRE_CLOSE(sbp->kbp_ideal->Lambda/sbp->kbp_ideal->H, in BOOST_AUTO_TEST_CASE() [all …]
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H A D | pssm_test_util.cpp | 94 BOOST_REQUIRE(retval->kbp_ideal); in InitializeBlastScoreBlk()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | scoreblk_unit_test.cpp | 383 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 410 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 423 BOOST_REQUIRE_CLOSE(sbp->kbp_ideal->Lambda/sbp->kbp_ideal->H, in BOOST_AUTO_TEST_CASE() 436 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 455 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 474 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 490 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 502 BOOST_REQUIRE_CLOSE(sbp->kbp_ideal->Lambda/sbp->kbp_ideal->H, in BOOST_AUTO_TEST_CASE() 512 score_opts->penalty, sbp->kbp_ideal, in BOOST_AUTO_TEST_CASE() 523 BOOST_REQUIRE_CLOSE(sbp->kbp_ideal->Lambda/sbp->kbp_ideal->H, in BOOST_AUTO_TEST_CASE() [all …]
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H A D | pssm_test_util.cpp | 94 BOOST_REQUIRE(retval->kbp_ideal); in InitializeBlastScoreBlk()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_posit.c | 133 retval->lambda_ideal = sbp->kbp_ideal->Lambda; in Kappa_compactSearchItemsNew() 134 retval->K_ideal = sbp->kbp_ideal->K; in Kappa_compactSearchItemsNew() 404 ASSERT(sbp->kbp_ideal->Lambda == compactSearch->lambda_ideal); in Kappa_impalaScaling() 405 ASSERT(sbp->kbp_ideal->K == compactSearch->K_ideal); in Kappa_impalaScaling()
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H A D | blast_stat.h | 216 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member
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H A D | blast_psi_priv.c | 2409 ideal_lambda = sbp->kbp_ideal->Lambda; 2505 ASSERT(sbp->kbp_ideal); 2509 ideal_lambda = sbp->kbp_ideal->Lambda; 2745 ASSERT(sbp->kbp_ideal); 2751 sbp->kbp_psi[0]->K * sbp->kbp_gap_std[0]->K / sbp->kbp_ideal->K;
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H A D | blast_stat.c | 984 if (sbp->kbp_ideal) in BlastScoreBlkFree() 985 sbp->kbp_ideal = Blast_KarlinBlkFree(sbp->kbp_ideal); in BlastScoreBlkFree() 2795 if (check_ideal && kbp->Lambda >= sbp->kbp_ideal->Lambda) in Blast_ScoreBlkKbpUngappedCalc() 2796 Blast_KarlinBlkCopy(kbp, sbp->kbp_ideal); in Blast_ScoreBlkKbpUngappedCalc() 2846 sbp->kbp_ideal = Blast_KarlinBlkNew(); in Blast_ScoreBlkKbpIdealCalc() 2847 Blast_KarlinBlkUngappedCalc(sbp->kbp_ideal, sfp); in Blast_ScoreBlkKbpIdealCalc()
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H A D | blast_kappa.c | 2215 self->ungappedLambda = sbp->kbp_ideal->Lambda / scale_factor; in s_MatrixInfoInit() 2912 if (orig->kbp_ideal != NULL) { in s_BlastScoreBlk_Copy() 2913 copy->kbp_ideal = Blast_KarlinBlkNew(); in s_BlastScoreBlk_Copy() 2914 if (Blast_KarlinBlkCopy(copy->kbp_ideal, orig->kbp_ideal) != 0) { in s_BlastScoreBlk_Copy()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_posit.c | 133 retval->lambda_ideal = sbp->kbp_ideal->Lambda; in Kappa_compactSearchItemsNew() 134 retval->K_ideal = sbp->kbp_ideal->K; in Kappa_compactSearchItemsNew() 404 ASSERT(sbp->kbp_ideal->Lambda == compactSearch->lambda_ideal); in Kappa_impalaScaling() 405 ASSERT(sbp->kbp_ideal->K == compactSearch->K_ideal); in Kappa_impalaScaling()
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H A D | blast_psi_priv.c | 2409 ideal_lambda = sbp->kbp_ideal->Lambda; 2505 ASSERT(sbp->kbp_ideal); 2509 ideal_lambda = sbp->kbp_ideal->Lambda; 2745 ASSERT(sbp->kbp_ideal); 2751 sbp->kbp_psi[0]->K * sbp->kbp_gap_std[0]->K / sbp->kbp_ideal->K;
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H A D | blast_stat.c | 984 if (sbp->kbp_ideal) in BlastScoreBlkFree() 985 sbp->kbp_ideal = Blast_KarlinBlkFree(sbp->kbp_ideal); in BlastScoreBlkFree() 2795 if (check_ideal && kbp->Lambda >= sbp->kbp_ideal->Lambda) in Blast_ScoreBlkKbpUngappedCalc() 2796 Blast_KarlinBlkCopy(kbp, sbp->kbp_ideal); in Blast_ScoreBlkKbpUngappedCalc() 2846 sbp->kbp_ideal = Blast_KarlinBlkNew(); in Blast_ScoreBlkKbpIdealCalc() 2847 Blast_KarlinBlkUngappedCalc(sbp->kbp_ideal, sfp); in Blast_ScoreBlkKbpIdealCalc()
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H A D | blast_kappa.c | 2227 self->ungappedLambda = sbp->kbp_ideal->Lambda / scale_factor; in s_MatrixInfoInit() 2918 if (orig->kbp_ideal != NULL) { in s_BlastScoreBlk_Copy() 2919 copy->kbp_ideal = Blast_KarlinBlkNew(); in s_BlastScoreBlk_Copy() 2920 if (Blast_KarlinBlkCopy(copy->kbp_ideal, orig->kbp_ideal) != 0) { in s_BlastScoreBlk_Copy()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_posit.c | 133 retval->lambda_ideal = sbp->kbp_ideal->Lambda; in Kappa_compactSearchItemsNew() 134 retval->K_ideal = sbp->kbp_ideal->K; in Kappa_compactSearchItemsNew() 404 ASSERT(sbp->kbp_ideal->Lambda == compactSearch->lambda_ideal); in Kappa_impalaScaling() 405 ASSERT(sbp->kbp_ideal->K == compactSearch->K_ideal); in Kappa_impalaScaling()
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H A D | blast_psi_priv.c | 2409 ideal_lambda = sbp->kbp_ideal->Lambda; 2505 ASSERT(sbp->kbp_ideal); 2509 ideal_lambda = sbp->kbp_ideal->Lambda; 2745 ASSERT(sbp->kbp_ideal); 2751 sbp->kbp_psi[0]->K * sbp->kbp_gap_std[0]->K / sbp->kbp_ideal->K;
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H A D | blast_stat.c | 984 if (sbp->kbp_ideal) in BlastScoreBlkFree() 985 sbp->kbp_ideal = Blast_KarlinBlkFree(sbp->kbp_ideal); in BlastScoreBlkFree() 2795 if (check_ideal && kbp->Lambda >= sbp->kbp_ideal->Lambda) in Blast_ScoreBlkKbpUngappedCalc() 2796 Blast_KarlinBlkCopy(kbp, sbp->kbp_ideal); in Blast_ScoreBlkKbpUngappedCalc() 2846 sbp->kbp_ideal = Blast_KarlinBlkNew(); in Blast_ScoreBlkKbpIdealCalc() 2847 Blast_KarlinBlkUngappedCalc(sbp->kbp_ideal, sfp); in Blast_ScoreBlkKbpIdealCalc()
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H A D | blast_kappa.c | 2227 self->ungappedLambda = sbp->kbp_ideal->Lambda / scale_factor; in s_MatrixInfoInit() 2918 if (orig->kbp_ideal != NULL) { in s_BlastScoreBlk_Copy() 2919 copy->kbp_ideal = Blast_KarlinBlkNew(); in s_BlastScoreBlk_Copy() 2920 if (Blast_KarlinBlkCopy(copy->kbp_ideal, orig->kbp_ideal) != 0) { in s_BlastScoreBlk_Copy()
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/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | makemat.c | 194 putMatrixKbp(checkFile, sbp->kbp_ideal, scaleScores, 1/scalingFactor); in takeMatrixCheckpoint() 353 if (sbp->kbp_ideal == NULL) in convertToMatrices() 354 sbp->kbp_ideal = BlastKarlinBlkStandardCalcEx(sbp); in convertToMatrices() 360 compactSearch->lambda_ideal = sbp->kbp_ideal->Lambda; in convertToMatrices() 361 compactSearch->K_ideal = sbp->kbp_ideal->K; in convertToMatrices()
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H A D | formatrpsdb.c | 365 if (sbp->kbp_ideal == NULL) in RPSUpdateStatistics() 366 sbp->kbp_ideal = BlastKarlinBlkStandardCalcEx(sbp); in RPSUpdateStatistics() 375 compactSearch->lambda_ideal = sbp->kbp_ideal->Lambda; in RPSUpdateStatistics() 376 compactSearch->K_ideal = sbp->kbp_ideal->K; in RPSUpdateStatistics()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | blastkar.c | 1275 if (sbp->kbp_ideal) in BLAST_ScoreBlkDestruct() 1276 sbp->kbp_ideal = BlastKarlinBlkDestruct(sbp->kbp_ideal); in BLAST_ScoreBlkDestruct() 1759 BLAST_KarlinBlkPtr kbp_ideal; in BlastKarlinBlkStandardCalcEx() local 1767 kbp_ideal = BlastKarlinBlkCreate(); in BlastKarlinBlkStandardCalcEx() 1773 return kbp_ideal; in BlastKarlinBlkStandardCalcEx() 1780 BLAST_KarlinBlkPtr kbp_ideal, kbp; in BlastKarlinBlkStandardCalc() local 1790 kbp->Lambda = kbp_ideal->Lambda; in BlastKarlinBlkStandardCalc() 1791 kbp->K = kbp_ideal->K; in BlastKarlinBlkStandardCalc() 1792 kbp->logK = kbp_ideal->logK; in BlastKarlinBlkStandardCalc() 1793 kbp->H = kbp_ideal->H; in BlastKarlinBlkStandardCalc() [all …]
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/dports/biology/ncbi-toolkit/ncbi/biostruc/cdd/ |
H A D | cddutil.c | 2434 sbp->kbp_ideal->Lambda = lambda[index]; in CddDenDiagCposComputation() 2435 sbp->kbp_ideal->K = K[index]; in CddDenDiagCposComputation() 2436 sbp->kbp_ideal->H = H[index]; in CddDenDiagCposComputation() 2445 if (sbp->kbp_ideal == NULL) { in CddDenDiagCposComputation() 2634 sbp->kbp_ideal->Lambda = lambda[index]; in CddCposComputation() 2635 sbp->kbp_ideal->K = K[index]; in CddCposComputation() 2636 sbp->kbp_ideal->H = H[index]; in CddCposComputation() 2645 if (sbp->kbp_ideal == NULL) { in CddCposComputation() 4321 sbp->kbp_ideal->K = K[index]; in CddCposCompPart1() 4322 sbp->kbp_ideal->H = H[index]; in CddCposCompPart1() [all …]
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H A D | cddposutil.c | 1713 search->sbp->kbp_ideal = BlastKarlinBlkCreate(); in CddSetUpSearchInternalByLoc() 1714 search->sbp->kbp_ideal->Lambda = lambda[index]; in CddSetUpSearchInternalByLoc() 1715 search->sbp->kbp_ideal->K = K[index]; in CddSetUpSearchInternalByLoc() 1716 search->sbp->kbp_ideal->H = H[index]; in CddSetUpSearchInternalByLoc() 1725 if (search->sbp->kbp_ideal == NULL) in CddSetUpSearchInternalByLoc() 1726 search->sbp->kbp_ideal = BlastKarlinBlkStandardCalcEx(search->sbp); in CddSetUpSearchInternalByLoc()
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/dports/biology/diamond/diamond-2.0.13/src/lib/blast/ |
H A D | blast_stat.h | 214 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
H A D | blast_stat.h | 216 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_stat.h | 216 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member
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