/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/hdf5/ |
H A D | HDF5LibraryUnitTest.java | 39 final HDF5File reader = new HDF5File(TEST_PON); in testOpenReadOnly() 53 final HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testCreateHDF5File() 60 final HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testIsPresent() 78 final HDF5File file2 = new HDF5File(testFile, HDF5File.OpenMode.READ_ONLY); in testIsPresent() 90 final HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testCreateGroup() 102 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeDouble() 118 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeNaNDouble() 134 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeDoubleArray() 151 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testReMakeDoubleArray() 174 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeDoubleMatrix() [all …]
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/packages/external/muq2/modules/Utilities/src/HDF5/ |
H A D | HDF5File.cpp | 8 HDF5File::HDF5File(std::string const& filename_){ in HDF5File() function in HDF5File 17 HDF5File::~HDF5File() { in ~HDF5File() 25 bool HDF5File::DoesFileExist(const std::string& name) const { in DoesFileExist() 30 void HDF5File::Open(std::string const& filename_) { in Open() 58 void HDF5File::Close() { in Close() 76 void HDF5File::Copy(std::string const& dstName, std::shared_ptr<HDF5File> srcFile, std::string cons… in Copy() 167 void HDF5File::CreateGroup(std::string const& name) { in CreateGroup() 224 void HDF5File::FlushFile() { in FlushFile() 234 const std::shared_ptr<HDF5File> hdf5file; 259 void HDF5File::MergeFile(std::shared_ptr<HDF5File> const& otherFile) { in MergeFile() [all …]
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/dports/graphics/vigra/vigra-8acd73a/include/vigra/ |
H A D | random_forest_hdf5_impex.hxx | 60 VIGRA_EXPORT void options_import_HDF5(HDF5File &, RandomForestOptions &, 66 VIGRA_EXPORT void dt_import_HDF5(HDF5File &, detail::DecisionTree &, 73 void rf_import_HDF5_to_map(HDF5File & h5context, X & param, in rf_import_HDF5_to_map() 119 void rf_export_map_to_HDF5(HDF5File & h5context, const X & param) in rf_export_map_to_HDF5() 154 inline std::string get_cwd(HDF5File & h5context) in get_cwd() 177 HDF5File & h5context, in rf_export_HDF5() 223 HDF5File h5context(filename , HDF5File::Open); in rf_export_HDF5() 250 HDF5File h5context(fileHandle, pathname); in rf_export_HDF5() 269 HDF5File & h5context, in rf_import_HDF5() 327 HDF5File h5context(filename, HDF5File::OpenReadOnly); in rf_import_HDF5() [all …]
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H A D | multi_array_chunked_hdf5.hxx | 226 HDF5File::OpenMode mode = HDF5File::ReadOnly, in ChunkedArrayHDF5() 251 init(HDF5File::ReadOnly); in ChunkedArrayHDF5() 253 init(HDF5File::ReadWrite); in ChunkedArrayHDF5() 256 void init(HDF5File::OpenMode mode) in init() 260 if(mode == HDF5File::Replace) in init() 262 mode = HDF5File::New; in init() 264 else if(mode == HDF5File::Default) in init() 267 mode = HDF5File::ReadOnly; in init() 269 mode = HDF5File::New; in init() 272 if(mode == HDF5File::ReadOnly) in init() [all …]
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H A D | hdf5impex.hxx | 974 class HDF5File class 1047 HDF5File() in HDF5File() function in vigra::HDF5File 1055 explicit HDF5File(bool track_creation_times) in HDF5File() function in vigra::HDF5File 1126 HDF5File(HDF5File const & other) in HDF5File() function in vigra::HDF5File 1137 ~HDF5File() in ~HDF5File() 1150 HDF5File & operator=(HDF5File const & other) in operator =() 2761 HDF5File::createDataset(std::string datasetName, in createDataset() 2838 void HDF5File::write_(std::string &datasetName, in write_() 3118 void HDF5File::read_(std::string datasetName, in read_() 3404 HDF5File file(info.getFilePath(), HDF5File::OpenReadOnly); in doxygen_overloaded_function() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/hdf5/ |
H A D | hdf5file.c | 27 typedef struct HDF5File HDF5File; typedef 28 #define KFILE_IMPL HDF5File 43 struct HDF5File struct 62 rc_t CC HDF5FileDestroy ( HDF5File *self ) in HDF5FileDestroy() argument 91 rc_t CC HDF5FileRandomAccess ( const HDF5File *self ) in HDF5FileRandomAccess() 116 rc_t CC HDF5FileSetSize ( HDF5File *self, uint64_t size ) in HDF5FileSetSize() 294 rc_t CC HDF5FileWrite ( HDF5File *self, uint64_t pos, in HDF5FileWrite() 307 uint32_t CC HDF5FileType ( const HDF5File *self ) in HDF5FileType() 339 HDF5File *f; in HDF5FileMake() 369 HDF5File * hdf5_self; in MakeHDF5ArrayFile() [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/hdf5/ |
H A D | hdf5file.c | 27 typedef struct HDF5File HDF5File; typedef 28 #define KFILE_IMPL HDF5File 43 struct HDF5File struct 62 rc_t CC HDF5FileDestroy ( HDF5File *self ) in HDF5FileDestroy() argument 91 rc_t CC HDF5FileRandomAccess ( const HDF5File *self ) in HDF5FileRandomAccess() 116 rc_t CC HDF5FileSetSize ( HDF5File *self, uint64_t size ) in HDF5FileSetSize() 294 rc_t CC HDF5FileWrite ( HDF5File *self, uint64_t pos, in HDF5FileWrite() 307 uint32_t CC HDF5FileType ( const HDF5File *self ) in HDF5FileType() 339 HDF5File *f; in HDF5FileMake() 369 HDF5File * hdf5_self; in MakeHDF5ArrayFile() [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/utils/ |
H A D | HDF5UtilsUnitTest.java | 7 import org.broadinstitute.hdf5.HDF5File; 43 try (final HDF5File hdf5File = new HDF5File(tempOutputHD5, HDF5File.OpenMode.CREATE)) { in testCreateLargeMatrix() 47 …try (final HDF5File hdf5FileForReading = new HDF5File(tempOutputHD5, HDF5File.OpenMode.READ_ONLY))… in testCreateLargeMatrix()
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/dports/graphics/vigra/vigra-8acd73a/vigranumpy/src/core/ |
H A D | multi_array_chunked.cxx | 691 if(mode == HDF5File::Default) in construct_ChunkedArrayHDF5() 694 mode = HDF5File::New; in construct_ChunkedArrayHDF5() 695 else if(HDF5File(filename, HDF5File::ReadOnly).existsDataset(datasetName)) in construct_ChunkedArrayHDF5() 696 mode = HDF5File::ReadOnly; in construct_ChunkedArrayHDF5() 698 mode = HDF5File::Replace; in construct_ChunkedArrayHDF5() 701 if(mode == HDF5File::Replace) in construct_ChunkedArrayHDF5() 703 mode = HDF5File::New; in construct_ChunkedArrayHDF5() 707 filemode = HDF5File::New; in construct_ChunkedArrayHDF5() 709 HDF5File file(filename, filemode); in construct_ChunkedArrayHDF5() 727 HDF5File file(handle); in construct_ChunkedArrayHDF5id() [all …]
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H A D | random_forest_3.cxx | 158 HDF5File h5ctx(filename); in pythonImportFromHDF5() 168 HDF5File h5ctx(filename, HDF5File::ReadWrite ); in pythonExportHDF5()
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/dports/audio/csound/csound-6.15.0/Opcodes/hdf5/ |
H A D | HDF5IO.h | 76 typedef struct HDF5File struct 82 } HDF5File; argument 85 HDF5File *HDF5IO_newHDF5File(CSOUND *csound, AUXCH *hdf5FileMemory, 88 void HDF5IO_deleteHDF5File(CSOUND *csound, HDF5File *hdf5File); 96 HDF5File *hdf5File; 126 HDF5File *hdf5File;
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/ |
H A D | HDF5SimpleCountCollection.java | 10 import org.broadinstitute.hdf5.HDF5File; 55 private final HDF5File file; 66 HDF5SimpleCountCollection(final HDF5File file) { in HDF5SimpleCountCollection() 113 try (final HDF5File file = new HDF5File(outFile, HDF5File.OpenMode.CREATE)) { in write()
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H A D | SimpleCountCollection.java | 4 import org.broadinstitute.hdf5.HDF5File; 98 ? readHDF5(new HDF5File(file)) in readAndSubset() 115 private static SimpleCountCollection readHDF5(final HDF5File file) { in readHDF5()
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/dports/graphics/vigra/vigra-8acd73a/src/impex/ |
H A D | hdf5_rf_impex.cxx | 70 void options_import_HDF5(HDF5File & h5context, in options_import_HDF5() 79 void options_export_HDF5(HDF5File & h5context, RandomForestOptions const & opt, in options_export_HDF5() 87 void dt_import_HDF5(HDF5File & h5context, detail::DecisionTree & tree, in dt_import_HDF5() 104 void dt_export_HDF5(HDF5File & h5context, in dt_export_HDF5()
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/dports/graphics/vigra/vigra-8acd73a/test/hdf5impex/ |
H A D | test.cxx | 407 HDF5File file (file_name, HDF5File::New); in testHDF5FileDataAccess() 420 HDF5File file_copy(file); in testHDF5FileDataAccess() 427 HDF5File file_copy2; in testHDF5FileDataAccess() 689 HDF5File file (file_name, HDF5File::New); in testHDF5FileAttributes() 888 HDF5File file (file_name, HDF5File::New); in testHDF5FileBlockAccess() 968 HDF5File file (file_name, HDF5File::New); in testHDF5FileChunks() 1049 HDF5File file (file_name, HDF5File::New); in testHDF5FileCompression() 1122 HDF5File file (file_name, HDF5File::New); in testHDF5FileBrowsing() 1182 HDF5File file; in testHDF5FileTutorial() 1249 HDF5File file_open ("tutorial_HDF5File.h5", HDF5File::Open); in testHDF5FileTutorial() [all …]
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/packages/external/muq2/MUQ/Utilities/HDF5/ |
H A D | Attributes.h | 23 Attribute(std::shared_ptr<HDF5File> file_, in Attribute() 75 std::shared_ptr<HDF5File> file; 89 AttributeList(std::shared_ptr<HDF5File> file_, in AttributeList() 99 std::shared_ptr<HDF5File> file;
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H A D | H5Object.h | 25 H5Object AddChildren(std::shared_ptr<HDF5File> file, 55 …friend H5Object muq::Utilities::AddChildren(std::shared_ptr<HDF5File> file, std::string const& pat… 61 H5Object(std::shared_ptr<HDF5File> file_, in H5Object() 205 std::shared_ptr<HDF5File> file;
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H A D | HDF5File.h | 23 class HDF5File : public std::enable_shared_from_this<HDF5File> { 33 HDF5File(std::string const& filename_); 36 virtual ~HDF5File(); 56 …void Copy(std::string const& destName, std::shared_ptr<HDF5File> srcFile, std::string const& srcNa… 613 void MergeFile(std::shared_ptr<HDF5File> const& otherFile);
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H A D | BlockDataset.h | 26 std::shared_ptr<HDF5File> file_, in BlockDataset() 94 std::shared_ptr<HDF5File> file;
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/dports/biology/py-loompy/loompy-3.0.6/loompy/ |
H A D | utils.py | 4 from h5py import File as HDF5File unknown 18 def get_loom_spec_version(f: HDF5File) -> str: argument 26 def compare_loom_spec_version(f: HDF5File, v: str) -> int: argument
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/dports/graphics/vigra/vigra-8acd73a/test/random_forest_3/ |
H A D | test.cxx | 222 HDF5File hfile("data/rf.h5", HDF5File::ReadOnly); in test_import() 251 HDF5File infile("data/rf.h5", HDF5File::ReadOnly); in test_export() 255 HDF5File outfile("data/rf_out.h5", HDF5File::New); in test_export()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/utils/ |
H A D | HDF5Utils.java | 5 import org.broadinstitute.hdf5.HDF5File; 60 public static List<SimpleInterval> readIntervals(final HDF5File file, in readIntervals() 78 public static <T extends SimpleInterval> void writeIntervals(final HDF5File file, in writeIntervals() 99 public static double[][] readChunkedDoubleMatrix(final HDF5File file, in readChunkedDoubleMatrix() 146 public static void writeChunkedDoubleMatrix(final HDF5File file, in writeChunkedDoubleMatrix()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/denoising/ |
H A D | HDF5SVDReadCountPanelOfNormals.java | 16 import org.broadinstitute.hdf5.HDF5File; 120 private final HDF5File file; 131 private HDF5SVDReadCountPanelOfNormals(final HDF5File file) { in HDF5SVDReadCountPanelOfNormals() 224 public static HDF5SVDReadCountPanelOfNormals read(final HDF5File file) { in read() 256 try (final HDF5File file = new HDF5File(outFile, HDF5File.OpenMode.CREATE)) { in create()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/ |
H A D | DenoiseReadCounts.java | 7 import org.broadinstitute.hdf5.HDF5File; 184 …try (final HDF5File hdf5PanelOfNormalsFile = new HDF5File(inputPanelOfNormalsFile)) { //HDF5File … in doWork()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/ |
H A D | HDF5SimpleCountCollectionUnitTest.java | 5 import org.broadinstitute.hdf5.HDF5File; 32 … final HDF5SimpleCountCollection rcc = new HDF5SimpleCountCollection(new HDF5File(outputFile)); in basicTest()
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