Home
last modified time | relevance | path

Searched refs:kbp_ideal (Results 1 – 25 of 39) sorted by relevance

12

/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dscoreblk_unit_test.cpp383 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 …]
H A Dpssm_test_util.cpp94 BOOST_REQUIRE(retval->kbp_ideal); in InitializeBlastScoreBlk()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dscoreblk_unit_test.cpp383 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 …]
H A Dpssm_test_util.cpp94 BOOST_REQUIRE(retval->kbp_ideal); in InitializeBlastScoreBlk()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_posit.c133 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()
H A Dblast_stat.h216 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member
H A Dblast_psi_priv.c2409 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;
H A Dblast_stat.c984 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()
H A Dblast_kappa.c2215 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_posit.c133 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()
H A Dblast_psi_priv.c2409 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;
H A Dblast_stat.c984 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()
H A Dblast_kappa.c2227 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_posit.c133 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()
H A Dblast_psi_priv.c2409 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;
H A Dblast_stat.c984 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()
H A Dblast_kappa.c2227 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()
/dports/biology/ncbi-toolkit/ncbi/demo/
H A Dmakemat.c194 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()
H A Dformatrpsdb.c365 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()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dblastkar.c1275 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 …]
/dports/biology/ncbi-toolkit/ncbi/biostruc/cdd/
H A Dcddutil.c2434 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 …]
H A Dcddposutil.c1713 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()
/dports/biology/diamond/diamond-2.0.13/src/lib/blast/
H A Dblast_stat.h214 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_stat.h216 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_stat.h216 Blast_KarlinBlk* kbp_ideal; /**< Ideal values (for query with average database composition). */ member

12