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/dports/biology/mothur/mothur-1.46.1/source/clearcut/
H A Ddmat.cpp464 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()
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H A Dclearcut.cpp708 ( (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()
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H A Ddistclearcut.cpp95 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()
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H A Dclearcut.h200 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);
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/data/
H A Dtest_simple_dmatrix.cc20 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()
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H A Dtest_simple_dmatrix.cu31 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()
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/data/
H A Dtest_simple_dmatrix.cc20 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()
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H A Dtest_simple_dmatrix.cu31 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/unit_test/
H A Dclusterer_unit_test.cpp96 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()
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H A Dkmer_unit_test.cpp200 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/DataManip/MetricMatrixCalc/Wrap/
H A DtestMatricCalc.py28 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])
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/dports/misc/rump/buildrump.sh-b914579/src/sys/dev/ieee1394/
H A Dfwdma.c80 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/DistGeom/
H A DtestDistGeom.cpp92 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()
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/plugin/
H A Dtest_predictor_oneapi.cc29 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()
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/plugin/
H A Dtest_predictor_oneapi.cc29 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()
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/predictor/
H A Dtest_cpu_predictor.cc30 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()
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/predictor/
H A Dtest_cpu_predictor.cc30 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()
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/dports/science/afni/afni-AFNI_21.3.16/src/R_scripts/
H A DAFNIplot.R401 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
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/dports/misc/py-xgboost/xgboost-1.5.1/tests/cpp/common/
H A Dtest_hist_util.cu30 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()
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/dports/misc/xgboost/xgboost-1.5.1/tests/cpp/common/
H A Dtest_hist_util.cu30 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()
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/dports/math/scilab/scilab-6.1.1/scilab/modules/optimization/src/fortran/
H A Dqpgen2.f107 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)
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/src/tests/
H A Dtest_incrementalfockbuilder.cc37 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()
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/xtp-2a31d70/src/tests/
H A Dtest_incrementalfockbuilder.cc37 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);
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/dports/math/R-cran-quadprog/quadprog/src/
H A Dsolve.QP.compact.f132 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)
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H A Dsolve.QP.f123 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)
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