Changeset 1251
- Timestamp:
- Apr 3, 2008, 7:48:24 AM (14 years ago)
- Location:
- trunk
- Files:
-
- 21 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/test/alignment_test.cc
r1232 r1251 96 96 test::Suite suite(argc, argv); 97 97 98 std::ifstream s( std::string("data/isoform.peaks").c_str());98 std::ifstream s(test::filename("data/isoform.peaks").c_str()); 99 99 std::vector<std::vector<double> > peaksets; 100 100 s >> peaksets; -
trunk/test/averager_test.cc
r1234 r1251 235 235 delete apw2; 236 236 237 return !suite.ok();237 return suite.return_value(); 238 238 } 239 239 -
trunk/test/consensus_inputranker_test.cc
r1232 r1251 42 42 int main(int argc, char* argv[]) 43 43 { 44 using namespace theplu::yat; 44 45 theplu::yat::test::Suite suite(argc, argv); 45 46 suite.err() << "testing consensus_inputranker" << std::endl; 46 47 47 ifstream is( "data/rank_data.txt");48 ifstream is(test::filename("data/rank_data.txt").c_str()); 48 49 theplu::yat::utility::Matrix data_tmp(is); 49 50 theplu::yat::classifier::MatrixLookup data(data_tmp); 50 51 is.close(); 51 52 52 is.open( "data/rank_target.txt");53 is.open(test::filename("data/rank_target.txt").c_str()); 53 54 theplu::yat::classifier::Target target(is); 54 55 is.close(); -
trunk/test/data_lookup_1d_test.cc
r1233 r1251 120 120 121 121 // First with a vector with no missing values separated by ' '. 122 std::ofstream my_out(" data/tmp_test_datalookup1D.txt");122 std::ofstream my_out("/tmp/yat_test_datalookup1D.txt"); 123 123 my_out << v1; 124 124 my_out.close(); 125 std::ifstream is(" data/tmp_test_datalookup1D.txt");125 std::ifstream is("/tmp/yat_test_datalookup1D.txt"); 126 126 utility::Vector v5(is); 127 127 is.close(); … … 131 131 suite.err() << "\nERROR\n" << std::endl; 132 132 } 133 std::remove(" data/tmp_test_datalookup1D.txt");133 std::remove("/tmp/yat_test_datalookup1D.txt"); 134 134 135 135 // Second with a vector with a missing value separated by '\t'. 136 136 gsl_m1(3,0)=std::numeric_limits<double>::quiet_NaN(); 137 137 classifier::DataLookup1D v6(m1,1, true); 138 my_out.open(" data/tmp_test_datalookup1D.txt");138 my_out.open("/tmp/yat_test_datalookup1D.txt"); 139 139 char prev=my_out.fill('\t'); 140 140 my_out << v1; 141 141 my_out.fill(prev); 142 142 my_out.close(); 143 is.open(" data/tmp_test_datalookup1D.txt");143 is.open("/tmp/yat_test_datalookup1D.txt"); 144 144 utility::Vector v7(is,'\t'); 145 145 is.close(); … … 151 151 << std::endl; 152 152 } 153 std::remove("data/ tmp_test_datalookup1D.txt");153 std::remove("data/yat_test_datalookup1D.txt"); 154 154 suite.err() << "\n"; 155 155 -
trunk/test/ensemble_test.cc
r1236 r1251 56 56 57 57 suite.err() << "loading data" << std::endl; 58 std::ifstream is( "data/nm_data_centralized.txt");58 std::ifstream is(test::filename("data/nm_data_centralized.txt").c_str()); 59 59 utility::Matrix data_core(is); 60 60 is.close(); … … 68 68 69 69 suite.err() << "load target" << std::endl; 70 is.open( "data/nm_target_bin.txt");70 is.open(test::filename("data/nm_target_bin.txt").c_str()); 71 71 classifier::Target target(is); 72 72 is.close(); -
trunk/test/feature_selection_test.cc
r1237 r1251 53 53 54 54 suite.err() << "Reading in Sorlie data to identify top gene ..." << std::endl; 55 std::ifstream is( "data/sorlie_centroid_data.txt");55 std::ifstream is(test::filename("data/sorlie_centroid_data.txt").c_str()); 56 56 utility::Matrix data(is,'\t'); 57 57 is.close(); 58 58 59 is.open( "data/sorlie_centroid_classes.txt");59 is.open(test::filename("data/sorlie_centroid_classes.txt").c_str()); 60 60 classifier::Target targets(is); 61 61 is.close(); -
trunk/test/fileutil_test.cc
r1248 r1251 153 153 suite.err() << "\tfile does not exist: " << file.path() << std::endl; 154 154 suite.add(!testval); 155 utility::FileUtil file2( "fileutil_test.cc");155 utility::FileUtil file2(test::filename("fileutil_test.cc").c_str()); 156 156 if (!(testval=!file2.exists())) 157 157 suite.err() << "\tfile does exist: " << file2.path() << std::endl; -
trunk/test/inputranker_test.cc
r1237 r1251 42 42 suite.err() << "testing inputranker" << std::endl; 43 43 44 std::ifstream is( "data/rank_data.txt");44 std::ifstream is(test::filename("data/rank_data.txt").c_str()); 45 45 theplu::yat::utility::Matrix data_tmp(is); 46 46 theplu::yat::classifier::MatrixLookup data(data_tmp); 47 47 is.close(); 48 48 49 is.open( "data/rank_target.txt");49 is.open(test::filename("data/rank_target.txt").c_str()); 50 50 classifier::Target target(is); 51 51 is.close(); -
trunk/test/kernel_test.cc
r1238 r1251 90 90 // containing kernel matrices calculated in matlab. 91 91 double error_bound = 1e-6; 92 std::ifstream is( "data/nm_data_centralized.txt");92 std::ifstream is(test::filename("data/nm_data_centralized.txt").c_str()); 93 93 utility::Matrix data_core(is); 94 94 is.close(); … … 96 96 classifier::MatrixLookup data(data_core); 97 97 98 is.open( "data/nm_kernel.txt");98 is.open(test::filename("data/nm_kernel.txt").c_str()); 99 99 utility::Matrix kernel_matlab(is); 100 100 is.close(); … … 104 104 delete kf; 105 105 106 is.open( "data/nm_kernel2.txt");106 is.open(test::filename("data/nm_kernel2.txt").c_str()); 107 107 utility::Matrix kernel_matlab2(is); 108 108 is.close(); … … 114 114 // Checking that GaussianKernelFunction. 115 115 suite.err() << "Checking GaussianKernelFunction.\n"; 116 is.open( "data/nm_kernel_gaussian.txt");116 is.open(test::filename("data/nm_kernel_gaussian.txt").c_str()); 117 117 utility::Matrix kernel_gaussian(is); 118 118 is.close(); -
trunk/test/matrix_test.cc
r1240 r1251 67 67 // Checking that the matrix output operator writes a file that the 68 68 // input operator can read. 69 std::ofstream my_out(" data/tmp_test_matrix.txt");69 std::ofstream my_out("/tmp/yat_test_matrix.txt"); 70 70 my_out << m2; 71 71 my_out.close(); 72 std::ifstream is(" data/tmp_test_matrix.txt");72 std::ifstream is("/tmp/yat_test_matrix.txt"); 73 73 utility::Matrix m3(is); 74 74 is.close(); 75 75 if (m3!=m2) 76 76 suite.add(false); 77 std::remove(" data/tmp_test_matrix.txt");77 std::remove("/tmp/yat_test_matrix.txt"); 78 78 79 79 suite.err() << "\toperator*=(double)" << std::endl; … … 85 85 } 86 86 87 is.open( "data/knni_matrix.data");87 is.open(test::filename("data/knni_matrix.data").c_str()); 88 88 // The stream input is a proper matrix file, with some stray empty 89 89 // lines and other whitespaces. The file is not expected to break … … 195 195 196 196 suite.err() << "\tmatrix::nan()" << std::endl; 197 is.open( "data/sorlie_centroid_data.txt");197 is.open(test::filename("data/sorlie_centroid_data.txt").c_str()); 198 198 utility::Matrix* m_nan = new utility::Matrix(is,'\t'); 199 199 utility::Matrix m_weight; -
trunk/test/nbc_test.cc
r1241 r1251 42 42 suite.err() << "testing ncc" << std::endl; 43 43 44 std::ifstream is( "data/nm_data_centralized.txt");44 std::ifstream is(test::filename("data/nm_data_centralized.txt").c_str()); 45 45 utility::Matrix data_core(is); 46 46 is.close(); 47 47 classifier::MatrixLookup data(data_core); 48 48 49 is.open( "data/nm_target_bin.txt");49 is.open(test::filename("data/nm_target_bin.txt").c_str()); 50 50 classifier::Target target(is); 51 51 is.close(); -
trunk/test/ncc_test.cc
r1241 r1251 197 197 ////////////////////////////////////////////////////////////////////////// 198 198 suite.err() << "test with Sorlie data\n"; 199 std::ifstream is( "data/sorlie_centroid_data.txt");199 std::ifstream is(test::filename("data/sorlie_centroid_data.txt").c_str()); 200 200 utility::Matrix data(is,'\t'); 201 201 is.close(); 202 202 203 is.open( "data/sorlie_centroid_classes.txt");203 is.open(test::filename("data/sorlie_centroid_classes.txt").c_str()); 204 204 classifier::Target targets(is); 205 205 is.close(); … … 215 215 216 216 // Comparing the centroids to stored result 217 is.open( "data/sorlie_centroids.txt");217 is.open(test::filename("data/sorlie_centroids.txt").c_str()); 218 218 utility::Matrix centroids(is); 219 219 is.close(); … … 239 239 240 240 // Comparing the prediction to stored result 241 is.open( "data/sorlie_centroid_predictions.txt");241 is.open(test::filename("data/sorlie_centroid_predictions.txt").c_str()); 242 242 utility::Matrix result(is,'\t'); 243 243 is.close(); -
trunk/test/nni_test.cc
r1242 r1251 51 51 52 52 uint neighbours=3; 53 std::string knni_data( "data/knni_matrix.data");54 std::string knni_result( "data/knni_result.data");55 std::string knni_weight( "data/knni_weight.data");56 std::string wenni_data( "data/knni_matrix.data");57 std::string wenni_result( "data/wenni_result.data");58 std::string wenni_weight( "data/wenni_weight.data");53 std::string knni_data(test::filename("data/knni_matrix.data")); 54 std::string knni_result(test::filename("data/knni_result.data")); 55 std::string knni_weight(test::filename("data/knni_weight.data")); 56 std::string wenni_data(test::filename("data/knni_matrix.data")); 57 std::string wenni_result(test::filename("data/wenni_result.data")); 58 std::string wenni_weight(test::filename("data/wenni_weight.data")); 59 59 check_file_access(knni_data); 60 60 check_file_access(knni_result); -
trunk/test/regression_test.cc
r1247 r1251 202 202 suite.err() << " testing regression::Polynomial" << std::endl; 203 203 { 204 std::ifstream s( "data/regression_gauss.data");204 std::ifstream s(test::filename("data/regression_gauss.data").c_str()); 205 205 utility::Matrix data(s); 206 206 utility::Vector x(data.rows()); -
trunk/test/score_test.cc
r1248 r1251 73 73 } 74 74 75 std::ifstream is( "data/rank_data.txt");75 std::ifstream is(test::filename("data/rank_data.txt").c_str()); 76 76 utility::Matrix data(is); 77 77 is.close(); 78 78 79 is.open( "data/rank_target.txt");79 is.open(test::filename("data/rank_target.txt").c_str()); 80 80 classifier::Target target2(is); 81 81 is.close(); -
trunk/test/subset_generator_test.cc
r1248 r1251 67 67 { 68 68 bool ok=true; 69 std::ifstream is( "data/nm_target_bin.txt");69 std::ifstream is(test::filename("data/nm_target_bin.txt").c_str()); 70 70 suite.err() << "loading target " << std::endl; 71 71 classifier::Target target(is); … … 73 73 suite.err() << "number of targets: " << target.size() << std::endl; 74 74 suite.err() << "number of classes: " << target.nof_classes() << std::endl; 75 is.open( "data/nm_data_centralized.txt");75 is.open(test::filename("data/nm_data_centralized.txt").c_str()); 76 76 suite.err() << "loading data " << std::endl; 77 77 utility::Matrix m(is); -
trunk/test/svd_test.cc
r1248 r1251 60 60 Areconstruct*=S; 61 61 Areconstruct*=Vtranspose; 62 if (!suite.equal_range(A.begin(), A.end(), Areconstruct.begin(), 1000 )) {62 if (!suite.equal_range(A.begin(), A.end(), Areconstruct.begin(), 10000)) { 63 63 suite.err() << "test_svd: FAILED, algorithm " << algo << std::endl; 64 64 suite.err() << "reconstruction error" << std::endl; -
trunk/test/svm_test.cc
r1248 r1251 105 105 106 106 107 std::ifstream is( "data/nm_data_centralized.txt");107 std::ifstream is(test::filename("data/nm_data_centralized.txt").c_str()); 108 108 utility::Matrix data_core(is); 109 109 is.close(); … … 115 115 116 116 117 is.open( "data/nm_target_bin.txt");117 is.open(test::filename("data/nm_target_bin.txt").c_str()); 118 118 classifier::Target target(is); 119 119 is.close(); 120 120 121 is.open( "data/nm_alpha_linear_matlab.txt");121 is.open(test::filename("data/nm_alpha_linear_matlab.txt").c_str()); 122 122 theplu::yat::utility::Vector alpha_matlab(is); 123 123 is.close(); -
trunk/test/target_test.cc
r1248 r1251 106 106 suite.err() << "Error: target.binary(20) not true" << std::endl; 107 107 } 108 std::ifstream is( "data/rank_target.txt");108 std::ifstream is(test::filename("data/rank_target.txt").c_str()); 109 109 classifier::Target target2(is); 110 110 is.close(); -
trunk/test/vector_test.cc
r1248 r1251 193 193 try { 194 194 suite.err() << "stream" << std::endl; 195 std::string data1( "data/vector1.data");196 std::string data2( "data/vector2.data");197 std::string data3( "data/vector3.data");198 std::string data4( "data/vector4.data");195 std::string data1(test::filename("data/vector1.data")); 196 std::string data2(test::filename("data/vector2.data")); 197 std::string data3(test::filename("data/vector3.data")); 198 std::string data4(test::filename("data/vector4.data")); 199 199 check_file_access(data1); 200 200 check_file_access(data2); … … 235 235 // Checking that unexpected characters in a stream gives error. 236 236 try { 237 std::string data5( "data/vector5.data");237 std::string data5(test::filename("data/vector5.data")); 238 238 check_file_access(data5); 239 239 std::ifstream data_stream5(data5.c_str()); … … 244 244 } 245 245 try { 246 std::string data( "data/vector6.data");246 std::string data(test::filename("data/vector6.data")); 247 247 check_file_access(data); 248 248 std::ifstream data_stream(data.c_str()); … … 256 256 this_ok=false; 257 257 try { 258 std::string data( "data/vector7.data");258 std::string data(test::filename("data/vector7.data")); 259 259 check_file_access(data); 260 260 std::ifstream data_stream(data.c_str()); … … 269 269 // Test sort algorithms 270 270 { 271 std::string data3( "data/vector3.data");271 std::string data3(test::filename("data/vector3.data")); 272 272 std::ifstream data_stream3(data3.c_str()); 273 273 utility::Vector vec3(data_stream3); -
trunk/yat/classifier/KNN_ReciprocalDistance.cc
r1112 r1251 8 8 9 9 #include <vector> 10 11 #include <iostream> 10 12 11 13 namespace theplu {
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