/dports/biology/mothur/mothur-1.46.1/source/clearcut/ |
H A D | dmat.cpp | 464 dmat->size = dmat->ntaxa; in NJ_parse_distance_matrix() 507 expectedvalues = dmat->ntaxa * dmat->ntaxa; in NJ_parse_distance_matrix() 516 dmat->val[i+1] = dmat->val[i]; in NJ_parse_distance_matrix() 568 dmat->val[NJ_MAP(x, y, dmat->size)] = val; in NJ_parse_distance_matrix() 580 dmat->val[NJ_MAP(x, y, dmat->size)] = val; in NJ_parse_distance_matrix() 603 dmat->val[NJ_MAP(x, x+y+1, dmat->size)] = val; in NJ_parse_distance_matrix() 614 dmat->val[NJ_MAP(y, x, dmat->size)] = val; in NJ_parse_distance_matrix() 675 if(!dmat->r || !dmat->r2) { in NJ_parse_distance_matrix() 681 dmat->rhandle = dmat->r; in NJ_parse_distance_matrix() 682 dmat->r2handle = dmat->r2; in NJ_parse_distance_matrix() [all …]
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H A D | clearcut.cpp | 708 ( (dmat->val[NJ_MAP(a, b, dmat->size)]) + in NJ_check_additivity() 709 (dmat->r2[a] - dmat->r2[b]) ) / 2.0; in NJ_check_additivity() 713 ( (dmat->val[NJ_MAP(a, b, dmat->size)]) + in NJ_check_additivity() 714 (dmat->r2[b] - dmat->r2[a]) ) / 2.0; in NJ_check_additivity() 1430 if(dmat->r && dmat->r2) { in NJ_print_distance_matrix() 1440 printf(" %0.4f", dmat->val[NJ_MAP(i, j, dmat->size)] - (dmat->r2[i] + dmat->r2[j])); in NJ_print_distance_matrix() 1690 (dmat->val[NJ_MAP(x, y, dmat->size)]); in NJ_decompose() 1694 ((dmat->r2[x] - dmat->r2[y])/2); in NJ_decompose() 1701 (dmat->val[NJ_MAP(x, y, dmat->size)]); in NJ_decompose() 1705 ((dmat->r2[y] - dmat->r2[x])/2); in NJ_decompose() [all …]
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H A D | distclearcut.cpp | 95 dmat = in NJ_build_distance_matrix() 159 dmat->val = (float *)calloc(dmat->ntaxa*dmat->ntaxa, sizeof(float)); in NJ_compute_dmat() 171 dmat->rhandle = dmat->r; in NJ_compute_dmat() 172 dmat->r2handle = dmat->r2; in NJ_compute_dmat() 173 dmat->valhandle = dmat->val; in NJ_compute_dmat() 243 dmat->val[NJ_MAP(i, j, dmat->size)] = pdiff; in NJ_no_correction() 289 dmat->val[NJ_MAP(i, j, dmat->size)] = 0.0; in NJ_DNA_jc_correction() 291 dmat->val[NJ_MAP(i, j, dmat->size)] = dist; in NJ_DNA_jc_correction() 346 dmat->val[NJ_MAP(i, j, dmat->size)] = dist; in NJ_PROTEIN_jc_correction() 438 dmat->val[NJ_MAP(i, j, dmat->size)] = 0.0; in NJ_DNA_k2p_correction() [all …]
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H A D | clearcut.h | 200 NJ_print_distance_matrix(DMAT *dmat); 206 DMAT *dmat, 215 DMAT *dmat); 219 NJ_init_vertex(DMAT *dmat); 223 NJ_decompose(DMAT *dmat, 235 NJ_print_taxanames(DMAT *dmat); 239 NJ_init_r(DMAT *dmat); 243 NJ_print_r(DMAT *dmat); 247 NJ_shuffle_distance_matrix(DMAT *dmat); 264 NJ_free_dmat(DMAT *dmat); [all …]
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/data/ |
H A D | test_simple_dmatrix.cc | 20 EXPECT_EQ(dmat->Info().num_row_, 2); in TEST() 21 EXPECT_EQ(dmat->Info().num_col_, 5); in TEST() 23 EXPECT_EQ(dmat->Info().labels_.Size(), dmat->Info().num_row_); in TEST() 25 delete dmat; in TEST() 48 delete dmat; in TEST() 57 ASSERT_TRUE(dmat->SingleColBlock()); in TEST() 67 delete dmat; in TEST() 80 CHECK_EQ(dmat->Info().num_row_, 0); in TEST() 81 CHECK_EQ(dmat->Info().num_col_, 0); in TEST() 139 CHECK_EQ(dmat.Info().num_row_, 2); in TEST() [all …]
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H A D | test_simple_dmatrix.cu | 31 EXPECT_EQ(dmat.Info().num_col_, 2); in TEST() 32 EXPECT_EQ(dmat.Info().num_row_, 16); in TEST() 33 EXPECT_EQ(dmat.Info().num_nonzero_, 32); in TEST() 47 ASSERT_EQ(dmat->Info().num_row_, n_rows); in TestDenseColumn() 48 ASSERT_EQ(dmat->Info().num_col_, n_cols); in TestDenseColumn() 70 TestDenseColumn(&dmat, kRows, kCols); in TEST() 78 ASSERT_EQ(dmat.Info().num_row_, kRows); in TEST() 176 ASSERT_EQ(dmat.Info().num_row_, kRows); in TEST() 177 ASSERT_EQ(dmat.Info().num_col_, kCols); in TEST() 305 EXPECT_EQ(dmat.Info().num_col_, 2); in TEST() [all …]
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/data/ |
H A D | test_simple_dmatrix.cc | 20 EXPECT_EQ(dmat->Info().num_row_, 2); in TEST() 21 EXPECT_EQ(dmat->Info().num_col_, 5); in TEST() 23 EXPECT_EQ(dmat->Info().labels_.Size(), dmat->Info().num_row_); in TEST() 25 delete dmat; in TEST() 48 delete dmat; in TEST() 57 ASSERT_TRUE(dmat->SingleColBlock()); in TEST() 67 delete dmat; in TEST() 80 CHECK_EQ(dmat->Info().num_row_, 0); in TEST() 81 CHECK_EQ(dmat->Info().num_col_, 0); in TEST() 139 CHECK_EQ(dmat.Info().num_row_, 2); in TEST() [all …]
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H A D | test_simple_dmatrix.cu | 31 EXPECT_EQ(dmat.Info().num_col_, 2); in TEST() 32 EXPECT_EQ(dmat.Info().num_row_, 16); in TEST() 33 EXPECT_EQ(dmat.Info().num_nonzero_, 32); in TEST() 47 ASSERT_EQ(dmat->Info().num_row_, n_rows); in TestDenseColumn() 48 ASSERT_EQ(dmat->Info().num_col_, n_cols); in TestDenseColumn() 70 TestDenseColumn(&dmat, kRows, kCols); in TEST() 78 ASSERT_EQ(dmat.Info().num_row_, kRows); in TEST() 176 ASSERT_EQ(dmat.Info().num_row_, kRows); in TEST() 177 ASSERT_EQ(dmat.Info().num_col_, kCols); in TEST() 305 EXPECT_EQ(dmat.Info().num_col_, 2); in TEST() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/unit_test/ |
H A D | clusterer_unit_test.cpp | 96 dmat(0, 1) = 0.1; in BOOST_AUTO_TEST_CASE() 97 dmat(1, 0) = dmat(0, 1); in BOOST_AUTO_TEST_CASE() 113 dmat(0, 1) = dmat(1, 0) = 0.1; in BOOST_AUTO_TEST_CASE() 114 dmat(0, 2) = dmat(2, 0) = 0.3; in BOOST_AUTO_TEST_CASE() 115 dmat(0, 3) = dmat(3, 0) = 0.2; in BOOST_AUTO_TEST_CASE() 116 dmat(1, 2) = dmat(2, 1) = 0.5; in BOOST_AUTO_TEST_CASE() 117 dmat(1, 3) = dmat(3, 1) = 0.2; in BOOST_AUTO_TEST_CASE() 118 dmat(2, 3) = dmat(3, 2) = 0.1; in BOOST_AUTO_TEST_CASE() 126 BOOST_CHECK_EQUAL(dmat.GetRows(), dmat.GetCols()); in BOOST_AUTO_TEST_CASE() 129 BOOST_CHECK_EQUAL(dmat.GetRows(), dmat.GetCols()); in BOOST_AUTO_TEST_CASE() [all …]
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H A D | kmer_unit_test.cpp | 200 TKMethods::TDistMatrix dmat; in BOOST_AUTO_TEST_CASE() local 225 BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size()); in BOOST_AUTO_TEST_CASE() 226 BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6); in BOOST_AUTO_TEST_CASE() 231 BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size()); in BOOST_AUTO_TEST_CASE() 232 BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6); in BOOST_AUTO_TEST_CASE() 244 BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size()); in BOOST_AUTO_TEST_CASE() 245 BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6); in BOOST_AUTO_TEST_CASE() 250 BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size()); in BOOST_AUTO_TEST_CASE() 251 BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6); in BOOST_AUTO_TEST_CASE() 263 BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6); in BOOST_AUTO_TEST_CASE() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/DataManip/MetricMatrixCalc/Wrap/ |
H A D | testMatricCalc.py | 28 dmat = rdmmc.GetEuclideanDistMat(desc) 29 for i in range(numpy.shape(dmat)[0]): 30 assert feq(dmat[i], exp[i]) 39 for i in range(numpy.shape(dmat)[0]): 40 assert feq(dmat[i], exp[i]) 50 assert feq(dmat[i], exp[i]) 60 assert feq(dmat[i], exp[i]) 67 assert feq(dmat[i], exp[i]) 73 assert feq(dmat[i], exp[i]) 81 assert feq(dmat[i], exp[i]) [all …]
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/dports/misc/rump/buildrump.sh-b914579/src/sys/dev/ieee1394/ |
H A D | fwdma.c | 80 bus_dmamem_free(dmat, &segs, nsegs); in fwdma_malloc() 85 err = bus_dmamap_create(dmat, size, nsegs, in fwdma_malloc() 90 bus_dmamem_unmap(dmat, v_addr, size); in fwdma_malloc() 91 bus_dmamem_free(dmat, &segs, nsegs); in fwdma_malloc() 99 bus_dmamap_destroy(dmat, *dmamap); in fwdma_malloc() 100 bus_dmamem_unmap(dmat, v_addr, size); in fwdma_malloc() 101 bus_dmamem_free(dmat, &segs, nsegs); in fwdma_malloc() 112 bus_dmamap_unload(dmat, dmamap); in fwdma_free() 115 bus_dmamap_destroy(dmat, dmamap); in fwdma_free() 127 dma->dma_tag = dmat; in fwdma_alloc_setup() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/DistGeom/ |
H A D | testDistGeom.cpp | 92 dmat.setVal(0, 0, 0.0); in testIssue216() 93 dmat.setVal(0, 1, 1.0); in testIssue216() 94 dmat.setVal(0, 2, 1.0); in testIssue216() 95 dmat.setVal(0, 3, 1.0); in testIssue216() 96 dmat.setVal(1, 1, 0.0); in testIssue216() 97 dmat.setVal(1, 2, 1.0); in testIssue216() 98 dmat.setVal(1, 3, 1.0); in testIssue216() 99 dmat.setVal(2, 2, 0.0); in testIssue216() 100 dmat.setVal(2, 3, 1.0); in testIssue216() 101 dmat.setVal(3, 3, 0.0); in testIssue216() [all …]
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/plugin/ |
H A D | test_predictor_oneapi.cc | 29 auto dmat = RandomDataGenerator(kRows, kCols, 0).GenerateDMatrix(); in TEST() local 33 oneapi_predictor->PredictBatch(dmat.get(), &out_predictions, model, 0); in TEST() 41 auto const &batch = *dmat->GetBatches<xgboost::SparsePage>().begin(); in TEST() 50 oneapi_predictor->PredictLeaf(dmat.get(), &leaf_out_predictions, model); in TEST() 92 param.num_feature = dmat->Info().num_col_; in TEST() 101 ASSERT_EQ(out_predictions.predictions.Size(), dmat->Info().num_row_); in TEST() 109 ASSERT_EQ(leaf_out_predictions.size(), dmat->Info().num_row_); in TEST() 117 ASSERT_EQ(out_contribution.size(), dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() 121 if ((i + 1) % (dmat->Info().num_col_ + 1) == 0) { in TEST() 132 dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() [all …]
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/plugin/ |
H A D | test_predictor_oneapi.cc | 29 auto dmat = RandomDataGenerator(kRows, kCols, 0).GenerateDMatrix(); in TEST() local 33 oneapi_predictor->PredictBatch(dmat.get(), &out_predictions, model, 0); in TEST() 41 auto const &batch = *dmat->GetBatches<xgboost::SparsePage>().begin(); in TEST() 50 oneapi_predictor->PredictLeaf(dmat.get(), &leaf_out_predictions, model); in TEST() 92 param.num_feature = dmat->Info().num_col_; in TEST() 101 ASSERT_EQ(out_predictions.predictions.Size(), dmat->Info().num_row_); in TEST() 109 ASSERT_EQ(leaf_out_predictions.size(), dmat->Info().num_row_); in TEST() 117 ASSERT_EQ(out_contribution.size(), dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() 121 if ((i + 1) % (dmat->Info().num_col_ + 1) == 0) { in TEST() 132 dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() [all …]
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/predictor/ |
H A D | test_cpu_predictor.cc | 30 auto dmat = RandomDataGenerator(kRows, kCols, 0).GenerateDMatrix(); in TEST() local 35 cpu_predictor->PredictBatch(dmat.get(), &out_predictions, model, 0); in TEST() 98 std::unique_ptr<DMatrix> dmat = CreateSparsePageDMatrix(kEntries); in TEST() local 106 param.num_feature = dmat->Info().num_col_; in TEST() 125 ASSERT_EQ(h_leaf_out_predictions.size(), dmat->Info().num_row_); in TEST() 134 ASSERT_EQ(out_contribution.size(), dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() 138 if ((i + 1) % (dmat->Info().num_col_ + 1) == 0) { in TEST() 151 dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() 155 if ((i + 1) % (dmat->Info().num_col_ + 1) == 0) { in TEST() 221 gbm->DoBoost(dmat.get(), &gpair, &predtion_cache); in TestUpdatePredictionCache() [all …]
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/predictor/ |
H A D | test_cpu_predictor.cc | 30 auto dmat = RandomDataGenerator(kRows, kCols, 0).GenerateDMatrix(); in TEST() local 35 cpu_predictor->PredictBatch(dmat.get(), &out_predictions, model, 0); in TEST() 98 std::unique_ptr<DMatrix> dmat = CreateSparsePageDMatrix(kEntries); in TEST() local 106 param.num_feature = dmat->Info().num_col_; in TEST() 125 ASSERT_EQ(h_leaf_out_predictions.size(), dmat->Info().num_row_); in TEST() 134 ASSERT_EQ(out_contribution.size(), dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() 138 if ((i + 1) % (dmat->Info().num_col_ + 1) == 0) { in TEST() 151 dmat->Info().num_row_ * (dmat->Info().num_col_ + 1)); in TEST() 155 if ((i + 1) % (dmat->Info().num_col_ + 1) == 0) { in TEST() 221 gbm->DoBoost(dmat.get(), &gpair, &predtion_cache); in TestUpdatePredictionCache() [all …]
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/dports/science/afni/afni-AFNI_21.3.16/src/R_scripts/ |
H A D | AFNIplot.R | 401 if (!is.null(ll$dmat) && is.character(ll$dmat)) { 402 dmatv <- ll$dmat 429 ll$dmat <- cbind(ll$dmat, dmatc) 506 if (dim(ll$dmat)[2] == dim(ll$dmat)[1] ) { 565 if (is.null(P$dmat)) { 569 dmatv <- P$dmat 593 P$dmat <- cbind(P$dmat, dmatc) 598 if (is.null(P$dmat)) { 721 P$col.plot.char <- rep(P$col.plot.char,ncol(P$dmat))[1:ncol(P$dmat)] 871 P$dmat[is.na(P$dmat)] = P$NAval [all …]
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/common/ |
H A D | test_hist_util.cu | 30 data::SimpleDMatrix dmat(adapter, missing, 1); in GetHostCuts() local 125 auto dmat = GetDMatrixFromData(x, n, 1); in TEST() local 127 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 178 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 193 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 230 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 255 auto dmat = in TEST() local 298 ValidateCuts(batched_cuts, dmat, num_bins); in ValidateBatchedCuts() 589 dmat->Info().num_col_ = kCols; in TestAdapterSketchFromWeights() 590 dmat->Info().num_row_ = kRows; in TestAdapterSketchFromWeights() [all …]
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/common/ |
H A D | test_hist_util.cu | 30 data::SimpleDMatrix dmat(adapter, missing, 1); in GetHostCuts() local 125 auto dmat = GetDMatrixFromData(x, n, 1); in TEST() local 127 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 178 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 193 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 230 ValidateCuts(cuts, dmat.get(), num_bins); in TEST() 255 auto dmat = in TEST() local 298 ValidateCuts(batched_cuts, dmat, num_bins); in ValidateBatchedCuts() 589 dmat->Info().num_col_ = kCols; in TestAdapterSketchFromWeights() 590 dmat->Info().num_row_ = kRows; in TestAdapterSketchFromWeights() [all …]
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/dports/math/scilab/scilab-6.1.1/scilab/modules/optimization/src/fortran/ |
H A D | qpgen2.f | 107 call dpofa(dmat,fddmat,n,info) 113 call dpori(dmat,fddmat,n) 143 dmat(i,j) = 0.d0 409 dmat(j,i-1) = dmat(j,i) 416 temp = gc*dmat(j,i-1) + gs*dmat(j,i) 417 dmat(j,i) = nu*(dmat(j,i-1)+temp) - dmat(j,i) 501 dmat(i,it1) = dmat(i,it1+1) 502 dmat(i,it1+1) = temp 513 temp = gc*dmat(i,it1) + gs*dmat(i,it1+1) 514 dmat(i,it1+1) = nu*(dmat(i,it1)+temp) - dmat(i,it1+1) [all …]
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/src/tests/ |
H A D | test_incrementalfockbuilder.cc | 37 Eigen::MatrixXd dmat = Eigen::MatrixXd::Random(10, 10); in BOOST_AUTO_TEST_CASE() local 38 fb.Configure(dmat); in BOOST_AUTO_TEST_CASE() 43 fb.resetMatrices(J, K, dmat); in BOOST_AUTO_TEST_CASE() 47 BOOST_CHECK(fb.getDmat_diff().isApprox(dmat)); in BOOST_AUTO_TEST_CASE() 49 fb.UpdateDmats(dmat, 1e-5, 2); in BOOST_AUTO_TEST_CASE() 62 fb.Configure(dmat); in BOOST_AUTO_TEST_CASE() 71 fb.resetMatrices(J, K, dmat); in BOOST_AUTO_TEST_CASE() 76 fb.UpdateDmats(dmat, 1e-6, iteration); in BOOST_AUTO_TEST_CASE() 81 fb.UpdateDmats(dmat, 1e-6, iteration); in BOOST_AUTO_TEST_CASE() 84 fb.UpdateDmats(dmat, 1e-6, iteration); in BOOST_AUTO_TEST_CASE() [all …]
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/xtp-2a31d70/src/tests/ |
H A D | test_incrementalfockbuilder.cc | 37 Eigen::MatrixXd dmat = Eigen::MatrixXd::Random(10, 10); 38 fb.Configure(dmat); 43 fb.resetMatrices(J, K, dmat); 47 BOOST_CHECK(fb.getDmat_diff().isApprox(dmat)); 49 fb.UpdateDmats(dmat, 1e-5, 2); 62 fb.Configure(dmat); 71 fb.resetMatrices(J, K, dmat); 76 fb.UpdateDmats(dmat, 1e-6, iteration); 81 fb.UpdateDmats(dmat, 1e-6, iteration); 84 fb.UpdateDmats(dmat, 1e-6, iteration); [all …]
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/dports/math/R-cran-quadprog/quadprog/src/ |
H A D | solve.QP.compact.f | 132 call dpofa(dmat,fddmat,n,info) 138 call dpori(dmat,fddmat,n) 168 dmat(i,j) = 0.d0 440 dmat(j,i-1) = dmat(j,i) 447 temp = gc*dmat(j,i-1) + gs*dmat(j,i) 448 dmat(j,i) = nu*(dmat(j,i-1)+temp) - dmat(j,i) 532 dmat(i,it1) = dmat(i,it1+1) 533 dmat(i,it1+1) = temp 544 temp = gc*dmat(i,it1) + gs*dmat(i,it1+1) 545 dmat(i,it1+1) = nu*(dmat(i,it1)+temp) - dmat(i,it1+1) [all …]
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H A D | solve.QP.f | 123 call dpofa(dmat,fddmat,n,info) 129 call dpori(dmat,fddmat,n) 159 dmat(i,j) = 0.d0 431 dmat(j,i-1) = dmat(j,i) 438 temp = gc*dmat(j,i-1) + gs*dmat(j,i) 439 dmat(j,i) = nu*(dmat(j,i-1)+temp) - dmat(j,i) 523 dmat(i,it1) = dmat(i,it1+1) 524 dmat(i,it1+1) = temp 535 temp = gc*dmat(i,it1) + gs*dmat(i,it1+1) 536 dmat(i,it1+1) = nu*(dmat(i,it1)+temp) - dmat(i,it1+1) [all …]
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