diff options
Diffstat (limited to 'java/src/hdf/hdf5lib')
18 files changed, 526 insertions, 142 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 960c872..63547df 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -512,8 +512,8 @@ public class H5 implements java.io.Serializable { * * @param file_export_name * The file name to export data into. - * @param file_name - * The name of the HDF5 file containing the dataset. + * @param file_id + * The identifier of the HDF5 file containing the dataset. * @param object_path * The full path of the dataset to be exported. * @param binary_order @@ -525,10 +525,31 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native void H5export_dataset(String file_export_name, String file_name, + public synchronized static native void H5export_dataset(String file_export_name, long file_id, String object_path, int binary_order) throws HDF5LibraryException; /** + * H5export_attribute is a utility function to save data in a file. + * + * @param file_export_name + * The file name to export data into. + * @param dataset_id + * The identifier of the dataset containing the attribute. + * @param attribute_name + * The attribute to be exported. + * @param binary_order + * 99 - export data as text. + * 1 - export data as binary Native Order. + * 2 - export data as binary Little Endian. + * 3 - export data as binary Big Endian. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native void H5export_attribute(String file_export_name, long dataset_id, + String attribute_name, int binary_order) throws HDF5LibraryException; + + /** * H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled. * * @return true if hdf5 library implements threadsafe @@ -10705,7 +10726,18 @@ public class H5 implements java.io.Serializable { * @exception IllegalArgumentException * - an input array is invalid. **/ - public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) + public static long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + long id = _H5Ropen_object(ref_ptr, rapl_id, oapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Ropen_object add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** @@ -10733,7 +10765,18 @@ public class H5 implements java.io.Serializable { * @exception IllegalArgumentException * - an input array is invalid. **/ - public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) + public static long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + long id = _H5Ropen_region(ref_ptr, rapl_id, oapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Ropen_region add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** @@ -10761,7 +10804,18 @@ public class H5 implements java.io.Serializable { * @exception IllegalArgumentException * - an input array is invalid. **/ - public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) + public static long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + long id = _H5Ropen_attr(ref_ptr, rapl_id, aapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Ropen_attr add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // Get type // diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java index 334abee..4125907 100644 --- a/java/src/hdf/hdf5lib/HDF5Constants.java +++ b/java/src/hdf/hdf5lib/HDF5Constants.java @@ -55,15 +55,15 @@ public class HDF5Constants { public static final int H5_INDEX_CRT_ORDER = H5_INDEX_CRT_ORDER(); /** indices on links, number of indices defined */ public static final int H5_INDEX_N = H5_INDEX_N(); - /** */ + /** Common iteration orders, Unknown order */ public static final int H5_ITER_UNKNOWN = H5_ITER_UNKNOWN(); - /** */ + /** Common iteration orders, Increasing order */ public static final int H5_ITER_INC = H5_ITER_INC(); - /** */ + /** Common iteration orders, Decreasing order */ public static final int H5_ITER_DEC = H5_ITER_DEC(); - /** */ + /** Common iteration orders, No particular order, whatever is fastest */ public static final int H5_ITER_NATIVE = H5_ITER_NATIVE(); - /** */ + /** Common iteration orders, Number of iteration orders */ public static final int H5_ITER_N = H5_ITER_N(); /** */ public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION(); diff --git a/java/src/hdf/hdf5lib/HDF5GroupInfo.java b/java/src/hdf/hdf5lib/HDF5GroupInfo.java index e08f991..4c31af7 100644 --- a/java/src/hdf/hdf5lib/HDF5GroupInfo.java +++ b/java/src/hdf/hdf5lib/HDF5GroupInfo.java @@ -90,32 +90,44 @@ public class HDF5GroupInfo { linklen = 0; } - /** fileno accessors */ + /** fileno accessors + * @return the file number if successful + */ public long[] getFileno() { return fileno; } - /** accessors */ + /** accessors + * @return the object number if successful + */ public long[] getObjno() { return objno; } - /** accessors */ + /** accessors + * @return type of group if successful + */ public int getType() { return type; } - /** accessors */ + /** accessors + * @return the number of links in the group if successful + */ public int getNlink() { return nlink; } - /** accessors */ + /** accessors + * @return the modified time value if successful + */ public long getMtime() { return mtime; } - /** accessors */ + /** accessors + * @return a length of link name if successful + */ public int getLinklen() { return linklen; } diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java index 385d71b..21e2b02 100644 --- a/java/src/hdf/hdf5lib/HDFArray.java +++ b/java/src/hdf/hdf5lib/HDFArray.java @@ -46,10 +46,10 @@ public class HDFArray { * * @param anArray * The array object. - * @exception hdf.hdf5lib.exceptions.HDF5Exception - * object is not an array. + * @exception hdf.hdf5lib.exceptions.HDF5JavaException + * object is not an array. */ - public HDFArray(Object anArray) throws HDF5Exception + public HDFArray(Object anArray) throws HDF5JavaException { if (anArray == null) { HDF5JavaException ex = new HDF5JavaException("HDFArray: array is null?: "); @@ -76,16 +76,14 @@ public class HDFArray { * @return A one-D array of bytes, filled with zeroes. The bytes are sufficient to hold the data of the Array passed * to the constructor. * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * Allocation failed. + * Allocation failed. */ - public byte[] emptyBytes() - throws HDF5JavaException + public byte[] emptyBytes() throws HDF5JavaException { byte[] b = null; - if ((ArrayDescriptor.dims == 1) - && (ArrayDescriptor.NT == 'B')) { + if ((ArrayDescriptor.dims == 1) && (ArrayDescriptor.NT == 'B')) { b = (byte[]) _theArray; } else { @@ -103,10 +101,9 @@ public class HDFArray { * * @return A one-D array of bytes, constructed from the Array passed to the constructor. * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * the object not an array or other internal error. + * the object not an array or other internal error. */ - public byte[] byteify() - throws HDF5JavaException + public byte[] byteify() throws HDF5JavaException { if (_barray != null) { return _barray; @@ -224,8 +221,6 @@ public class HDFArray { if (ArrayDescriptor.NT == 'J') { arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); - arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'I') { arow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], @@ -552,8 +547,7 @@ public class HDFArray { + "?")); } } - if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - - 1]) { + if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) { throw new java.lang.InternalError( new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i]) + "?")); @@ -580,7 +574,7 @@ public class HDFArray { Integer[] out = new Integer[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Integer(in[i]); + out[i] = Integer.valueOf(in[i]); } return out; } @@ -592,7 +586,7 @@ public class HDFArray { Integer[] out = new Integer[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Integer(in[i]); + out[i] = Integer.valueOf(in[i]); } return out; } @@ -615,7 +609,7 @@ public class HDFArray { Short[] out = new Short[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Short(in[i]); + out[i] = Short.valueOf(in[i]); } return out; } @@ -627,7 +621,7 @@ public class HDFArray { Short[] out = new Short[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Short(in[i]); + out[i] = Short.valueOf(in[i]); } return out; } @@ -649,7 +643,7 @@ public class HDFArray { Byte[] out = new Byte[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Byte(bin[i]); + out[i] = Byte.valueOf(bin[i]); } return out; } @@ -659,7 +653,7 @@ public class HDFArray { Byte[] out = new Byte[len]; for (int i = 0; i < len; i++) { - out[i] = new Byte(bin[i]); + out[i] = Byte.valueOf(bin[i]); } return out; } @@ -682,7 +676,7 @@ public class HDFArray { Float[] out = new Float[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Float(in[i]); + out[i] = Float.valueOf(in[i]); } return out; } @@ -694,7 +688,7 @@ public class HDFArray { Float[] out = new Float[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Float(in[i]); + out[i] = Float.valueOf(in[i]); } return out; } @@ -717,7 +711,7 @@ public class HDFArray { Double[] out = new Double[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Double(in[i]); + out[i] = Double.valueOf(in[i]); } return out; } @@ -729,7 +723,7 @@ public class HDFArray { Double[] out = new Double[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Double(in[i]); + out[i] = Double.valueOf(in[i]); } return out; } @@ -752,7 +746,7 @@ public class HDFArray { Long[] out = new Long[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Long(in[i]); + out[i] = Long.valueOf(in[i]); } return out; } @@ -764,7 +758,7 @@ public class HDFArray { Long[] out = new Long[nelems]; for (int i = 0; i < nelems; i++) { - out[i] = new Long(in[i]); + out[i] = Long.valueOf(in[i]); } return out; } @@ -790,12 +784,12 @@ class ArrayDescriptor { static int dims = 0; static String className; - public ArrayDescriptor(Object anArray) throws HDF5Exception + public ArrayDescriptor(Object anArray) throws HDF5JavaException { Class tc = anArray.getClass(); if (tc.isArray() == false) { /* exception: not an array */ - HDF5Exception ex = new HDF5JavaException("ArrayDescriptor: not an array?: "); + HDF5JavaException ex = new HDF5JavaException("ArrayDescriptor: not an array?: "); throw (ex); } @@ -827,12 +821,10 @@ class ArrayDescriptor { else if (NT == 'S') { NTsize = 2; } - else if ((NT == 'I') - || (NT == 'F')) { + else if ((NT == 'I') || (NT == 'F')) { NTsize = 4; } - else if ((NT == 'J') - || (NT == 'D')) { + else if ((NT == 'J') || (NT == 'D')) { NTsize = 8; } else if (css.startsWith("Ljava.lang.Byte")) { @@ -925,8 +917,8 @@ class ArrayDescriptor { System.out.println("Type: " + theType); System.out.println("Class: " + theClass); System.out.println("NT: " + NT + " NTsize: " + NTsize); - System.out - .println("Array has " + dims + " dimensions (" + totalSize + " bytes, " + totalElements + " elements)"); + System.out.println("Array has " + dims + " dimensions (" + totalSize + + " bytes, " + totalElements + " elements)"); int i; for (i = 0; i <= dims; i++) { Class tc = objs[i].getClass(); diff --git a/java/src/hdf/hdf5lib/HDFNativeData.java b/java/src/hdf/hdf5lib/HDFNativeData.java index 5b29050..85378db 100644 --- a/java/src/hdf/hdf5lib/HDFNativeData.java +++ b/java/src/hdf/hdf5lib/HDFNativeData.java @@ -153,8 +153,7 @@ public class HDFNativeData { * The input array of bytes * @return an array of 'len' float */ - public synchronized static native float[] byteToFloat(int start, int len, - byte[] data); + public synchronized static native float[] byteToFloat(int start, int len, byte[] data); /** * Convert 4 bytes from an array of bytes into a single float @@ -437,41 +436,38 @@ public class HDFNativeData { * - Error unsupported type. */ public synchronized static Object byteToNumber(byte[] barray, Object obj) - throws HDF5Exception { + throws HDF5Exception + { Class theClass = obj.getClass(); String type = theClass.getName(); Object retobj = null; if (type.equals("java.lang.Integer")) { int[] i = hdf.hdf5lib.HDFNativeData.byteToInt(0, 1, barray); - retobj = new Integer(i[0]); + retobj = Integer.valueOf(i[0]); } else if (type.equals("java.lang.Byte")) { - retobj = new Byte(barray[0]); + retobj = Byte.valueOf(barray[0]); } else if (type.equals("java.lang.Short")) { - short[] f = hdf.hdf5lib.HDFNativeData - .byteToShort(0, 1, barray); - retobj = new Short(f[0]); + short[] f = hdf.hdf5lib.HDFNativeData.byteToShort(0, 1, barray); + retobj = Short.valueOf(f[0]); } else if (type.equals("java.lang.Float")) { - float[] f = hdf.hdf5lib.HDFNativeData - .byteToFloat(0, 1, barray); - retobj = new Float(f[0]); + float[] f = hdf.hdf5lib.HDFNativeData.byteToFloat(0, 1, barray); + retobj = Float.valueOf(f[0]); } else if (type.equals("java.lang.Long")) { long[] f = hdf.hdf5lib.HDFNativeData.byteToLong(0, 1, barray); - retobj = new Long(f[0]); + retobj = Long.valueOf(f[0]); } else if (type.equals("java.lang.Double")) { - double[] f = hdf.hdf5lib.HDFNativeData.byteToDouble(0, 1, - barray); - retobj = new Double(f[0]); + double[] f = hdf.hdf5lib.HDFNativeData.byteToDouble(0, 1, barray); + retobj = Double.valueOf(f[0]); } else { /* exception: unsupported type */ - HDF5Exception ex = new HDF5JavaException( - "byteToNumber: setfield bad type: " + obj + " " + type); + HDF5Exception ex = new HDF5JavaException("byteToNumber: setfield bad type: " + obj + " " + type); throw (ex); } return (retobj); diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java index e3e774c..532355e 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java @@ -30,7 +30,9 @@ import hdf.hdf5lib.HDF5Constants; @SuppressWarnings("serial") public class HDF5LibraryException extends HDF5Exception { + /** major error number of the first error on the HDF5 library error stack. */ private final long majorErrorNumber; + /** minor error number of the first error on the HDF5 library error stack. */ private final long minorErrorNumber; /** diff --git a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java index 9f04211..cf84532 100644 --- a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java +++ b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java @@ -20,41 +20,270 @@ import java.io.Serializable; */ public class H5AC_cache_config_t implements Serializable{ private static final long serialVersionUID = -6748085696476149972L; - // general configuration fields: + // general configuration fields + /** + * version: Integer field containing the version number of this version + * of the H5AC_cache_config_t structure. Any instance of + * H5AC_cache_config_t passed to the cache must have a known + * version number, or an error will be flagged. + */ public int version; + /** + * rpt_fcn_enabled: Boolean field used to enable and disable the default + * reporting function. This function is invoked every time the + * automatic cache resize code is run, and reports on its activities. + * + * This is a debugging function, and should normally be turned off. + */ public boolean rpt_fcn_enabled; + /** + * open_trace_file: Boolean field indicating whether the trace_file_name + * field should be used to open a trace file for the cache. + * + * *** DEPRECATED *** Use H5Fstart/stop logging functions instead + */ public boolean open_trace_file; + /** + * close_trace_file: Boolean field indicating whether the current trace + * file (if any) should be closed. + * + * *** DEPRECATED *** Use H5Fstart/stop logging functions instead + */ public boolean close_trace_file; + /** + * trace_file_name: Full path of the trace file to be opened if the + * open_trace_file field is TRUE. + * + * *** DEPRECATED *** Use H5Fstart/stop logging functions instead + */ public String trace_file_name; + /** + * evictions_enabled: Boolean field used to either report the current + * evictions enabled status of the cache, or to set the cache's + * evictions enabled status. + */ public boolean evictions_enabled; + /** + * set_initial_size: Boolean flag indicating whether the size of the + * initial size of the cache is to be set to the value given in + * the initial_size field. If set_initial_size is FALSE, the + * initial_size field is ignored. + */ public boolean set_initial_size; + /** + * initial_size: If enabled, this field contain the size the cache is + * to be set to upon receipt of this structure. Needless to say, + * initial_size must lie in the closed interval [min_size, max_size]. + */ public long initial_size; + /** + * min_clean_fraction: double in the range 0 to 1 indicating the fraction + * of the cache that is to be kept clean. This field is only used + * in parallel mode. Typical values are 0.1 to 0.5. + */ public double min_clean_fraction; + /** + * max_size: Maximum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * [MIN_MAX_CACHE_SIZE, MAX_MAX_CACHE_SIZE]. Also, max_size must + * be greater than or equal to min_size. + */ public long max_size; + /** + * min_size: Minimum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * [H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE]. Also, min_size + * must be less than or equal to max_size. + */ public long min_size; + /** + * epoch_length: Number of accesses on the cache over which to collect + * hit rate stats before running the automatic cache resize code, + * if it is enabled. + */ public long epoch_length; - // size increase control fields: - public int incr_mode; // H5C_cache_incr_mode + // size increase control fields + /** + * incr_mode: Instance of the H5C_cache_incr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * increased. At present there are two possible values. + */ + public int incr_mode; + /** + * lower_hr_threshold: Lower hit rate threshold. If the increment mode + * (incr_mode) is H5C_incr__threshold and the hit rate drops below the + * value supplied in this field in an epoch, increment the cache size by + * size_increment. Note that cache size may not be incremented above + * max_size, and that the increment may be further restricted by the + * max_increment field if it is enabled. + */ public double lower_hr_threshold; + /** + * increment: Double containing the multiplier used to derive the new + * cache size from the old if a cache size increment is triggered. + * The increment must be greater than 1.0, and should not exceed 2.0. + */ public double increment; + /** + * apply_max_increment: Boolean flag indicating whether the max_increment + * field should be used to limit the maximum cache size increment. + */ public boolean apply_max_increment; + /** + * max_increment: If enabled by the apply_max_increment field described + * above, this field contains the maximum number of bytes by which the + * cache size can be increased in a single re-size. + */ public long max_increment; - public int flash_incr_mode; // H5C_cache_flash_incr_mode + /** + * flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated + * type whose value indicates whether and by which algorithm we should + * make flash increases in the size of the cache to accommodate insertion + * of large entries and large increases in the size of a single entry. + */ + public int flash_incr_mode; + /** + * flash_multiple: Double containing the multiple described above in the + * H5C_flash_incr__add_space section of the discussion of the + * flash_incr_mode section. This field is ignored unless flash_incr_mode + * is H5C_flash_incr__add_space. + */ public double flash_multiple; + /** + * flash_threshold: Double containing the factor by which current max cache + * size is multiplied to obtain the size threshold for the add_space flash + * increment algorithm. The field is ignored unless flash_incr_mode is + * H5C_flash_incr__add_space. + */ public double flash_threshold; - // size decrease control fields: - public int decr_mode; // H5C_cache_decr_mode + // size decrease control fields + /** + * decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * decreased. At present there are four possibilities. + */ + public int decr_mode; + /** + * upper_hr_threshold: Upper hit rate threshold. The use of this field + * varies according to the current decr_mode. + */ public double upper_hr_threshold; + /** + * decrement: This field is only used when the decr_mode is + * H5C_decr__threshold. + */ public double decrement; + /** + * apply_max_decrement: Boolean flag used to determine whether decrements + * in cache size are to be limited by the max_decrement field. + */ public boolean apply_max_decrement; + /** + * max_decrement: Maximum number of bytes by which the cache size can be + * decreased in a single re-size. Note that decrements may also be + * restricted by the min_size of the cache, and (in age out modes) by + * the empty_reserve field. + */ public long max_decrement; + /** + * epochs_before_eviction: Integer field used in H5C_decr__age_out and + * H5C_decr__age_out_with_threshold decrement modes. + */ public int epochs_before_eviction; + /** + * apply_empty_reserve: Boolean field controlling whether the empty_reserve + * field is to be used in computing the new cache size when the + * decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold. + */ public boolean apply_empty_reserve; + /** + * empty_reserve: To avoid a constant racheting down of cache size by small + * amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold + * modes, this field allows one to require that any cache size + * reductions leave the specified fraction of unused space in the cache. + */ public double empty_reserve; - // parallel configuration fields: + // parallel configuration fields + /** + * dirty_bytes_threshold: Threshold of dirty byte creation used to + * synchronize updates between caches. + */ public long dirty_bytes_threshold; + /** + * metadata_write_strategy: Integer field containing a code indicating the + * desired metadata write strategy. + */ public int metadata_write_strategy; + /** H5AC_cache_config_t is a public structure intended for use in public APIs. + * At least in its initial incarnation, it is basically a copy of struct + * H5C_auto_size_ctl_t, minus the report_fcn field, and plus the + * dirty_bytes_threshold field. + * + * @param version: Integer field containing the version number of this version + * @param rpt_fcn_enabled: Boolean field used to enable and disable the default reporting function. + * @param open_trace_file: Boolean field indicating whether the trace_file_name + * field should be used to open a trace file for the cache. + * @param close_trace_file: Boolean field indicating whether the current trace + * file (if any) should be closed. + * @param trace_file_name: Full path of the trace file to be opened if the + * open_trace_file field is TRUE. + * @param evictions_enabled: Boolean field used to either report or set the current + * evictions enabled status of the cache. + * @param set_initial_size: Boolean flag indicating whether the size of the + * initial size of the cache is to be set to the value given in + * the initial_size field. + * @param initial_size: If enabled, this field contain the size the cache is + * to be set to upon receipt of this structure. + * @param min_clean_fraction: double in the range 0 to 1 indicating the fraction + * of the cache that is to be kept clean. + * @param max_size: Maximum size to which the cache can be adjusted. + * @param min_size: Minimum size to which the cache can be adjusted. + * @param epoch_length: Number of accesses on the cache over which to collect + * hit rate stats before running the automatic cache resize code. + * @param incr_mode: Instance of the H5C_cache_incr_mode enumerated type. + * @param lower_hr_threshold: Lower hit rate threshold. + * @param increment: Double containing the multiplier used to derive the new + * cache size from the old if a cache size increment is triggered. + * @param apply_max_increment: Boolean flag indicating whether the max_increment + * field should be used to limit the maximum cache size increment. + * @param max_increment: If enabled by the apply_max_increment field described + * above, this field contains the maximum number of bytes by which the + * cache size can be increased in a single re-size. + * @param flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated + * type whose value indicates whether and by which algorithm we should + * make flash increases in the size of the cache to accommodate insertion + * of large entries and large increases in the size of a single entry. + * @param flash_multiple: Double containing the multiple described above in the + * H5C_flash_incr__add_space section of the discussion of the + * flash_incr_mode section. + * @param flash_threshold: Double containing the factor by which current max cache + * size is multiplied to obtain the size threshold for the add_space flash + * increment algorithm. + * @param decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * decreased. + * @param upper_hr_threshold: Upper hit rate threshold. The use of this field + * varies according to the current decr_mode. + * @param decrement: This field is only used when the decr_mode is + * H5C_decr__threshold. + * @param apply_max_decrement: Boolean flag used to determine whether decrements + * in cache size are to be limited by the max_decrement field. + * @param max_decrement: Maximum number of bytes by which the cache size can be + * decreased in a single re-size. + * @param epochs_before_eviction: Integer field used in H5C_decr__age_out and + * H5C_decr__age_out_with_threshold decrement modes. + * @param apply_empty_reserve: Boolean field controlling whether the empty_reserve + * field is to be used in computing the new cache size when the + * decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold. + * @param empty_reserve: To avoid a constant racheting down of cache size by small + * amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold + * modes. + * @param dirty_bytes_threshold: Threshold of dirty byte creation used to + * synchronize updates between caches. + * @param metadata_write_strategy: Integer field containing a code indicating the + * desired metadata write strategy. + */ public H5AC_cache_config_t (int version, boolean rpt_fcn_enabled, boolean open_trace_file, boolean close_trace_file, String trace_file_name, boolean evictions_enabled, boolean set_initial_size, long initial_size, double min_clean_fraction, long max_size, diff --git a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java index e074156..5981fc7 100644 --- a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java +++ b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java @@ -20,14 +20,20 @@ import java.io.Serializable; */ public class H5E_error2_t implements Serializable{ private static final long serialVersionUID = 279144359041667613L; - - public long cls_id; //class ID - public long maj_num; //major error ID - public long min_num; //minor error number - public int line; //line in file where error occurs - public String func_name; //function in which error occurred - public String file_name; //file in which error occurred - public String desc; //optional supplied description + /** class ID */ + public long cls_id; + /** major error ID */ + public long maj_num; + /** minor error number */ + public long min_num; + /** line in file where error occurs */ + public int line; + /** function in which error occurred */ + public String func_name; + /** file in which error occurred */ + public String file_name; + /** optional supplied description */ + public String desc; H5E_error2_t(long cls_id, long maj_num, long min_num, int line, String func_name, String file_name, String desc) { this.cls_id = cls_id; diff --git a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java index 26690ec..95a9254 100644 --- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java +++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java @@ -1,15 +1,14 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Read-Only HDFS Virtual File Driver (VFD) * - * Copyright (c) 2018, The HDF Group. * + * Copyright by The HDF Group. * * * * All rights reserved. * * * - * NOTICE: * - * All information contained herein is, and remains, the property of The HDF * - * Group. The intellectual and technical concepts contained herein are * - * proprietary to The HDF Group. Dissemination of this information or * - * reproduction of this material is strictly forbidden unless prior written * - * permission is obtained from The HDF Group. * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.structs; @@ -26,15 +25,31 @@ import java.io.Serializable; public class H5FD_hdfs_fapl_t implements Serializable { private static final long serialVersionUID = 2072473407027648309L; + /** Version number of the H5FD_hdfs_fapl_t structure. */ private int version; + /** Name of "Name Node" to access as the HDFS server. */ private String namenode_name; + /** Port number to use to connect with Name Node. */ private int namenode_port; + /** Username to use when accessing file. */ private String user_name; + /** Path to the location of the Kerberos authentication cache. */ private String kerberos_ticket_cache; + /** Size (in bytes) of the file read stream buffer. */ private int stream_buffer_size; - /* + /** * Create a fapl_t structure with the specified components. + * @param namenode_name + * Name of "Name Node" to access as the HDFS server. + * @param namenode_port + * Port number to use to connect with Name Node. + * @param user_name + * Username to use when accessing file. + * @param kerberos_ticket_cache + * Path to the location of the Kerberos authentication cache. + * @param stream_buffer_size + * Size (in bytes) of the file read stream buffer. */ public H5FD_hdfs_fapl_t( String namenode_name, diff --git a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java index 735cc7e..ad02979 100644 --- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java +++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java @@ -1,15 +1,14 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Read-Only S3 Virtual File Driver (VFD) * - * Copyright (c) 2017-2018, The HDF Group. * + * Copyright by The HDF Group. * * * * All rights reserved. * * * - * NOTICE: * - * All information contained herein is, and remains, the property of The HDF * - * Group. The intellectual and technical concepts contained herein are * - * proprietary to The HDF Group. Dissemination of this information or * - * reproduction of this material is strictly forbidden unless prior written * - * permission is obtained from The HDF Group. * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.structs; @@ -46,10 +45,15 @@ import java.io.Serializable; public class H5FD_ros3_fapl_t implements Serializable { private static final long serialVersionUID = 8985533001471224030L; + /** Version number of the H5FD_ros3_fapl_t structure */ private int version; + /** Flag TRUE or FALSE whether or not requests are to be authenticated with the AWS4 algorithm. */ private boolean authenticate; + /** region "aws region" for authenticating request */ private String aws_region; + /** id "secret id" or "access id" for authenticating request */ private String secret_id; + /** key "secret key" or "access key" for authenticating request */ private String secret_key; /** diff --git a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java index bb87201..f951bb4 100644 --- a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java +++ b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java @@ -20,16 +20,37 @@ import java.io.Serializable; */ public class H5F_info2_t implements Serializable{ private static final long serialVersionUID = 4691681162544054518L; - public int super_version; // Superblock version # - public long super_size; // Superblock size - public long super_ext_size; // Superblock extension size - public int free_version; // Version # of file free space management - public long free_meta_size; // Free space manager metadata size - public long free_tot_space; // Amount of free space in the file - public int sohm_version; // Version # of shared object header info - public long sohm_hdr_size; // Shared object header message header size - public H5_ih_info_t sohm_msgs_info; // Shared object header message index & heap size + /** Superblock version number */ + public int super_version; + /** Superblock size */ + public long super_size; + /** Superblock extension size */ + public long super_ext_size; + /** Version number of file free space management */ + public int free_version; + /** Free space manager metadata size */ + public long free_meta_size; + /** Amount of free space in the file */ + public long free_tot_space; + /** Version number of shared object header info */ + public int sohm_version; + /** Shared object header message header size */ + public long sohm_hdr_size; + /** Shared object header message index and heap size */ + public H5_ih_info_t sohm_msgs_info; + /** + * Constructor fot current "global" information about file + * @param super_version: Superblock version number + * @param super_size: Superblock size + * @param super_ext_size: Superblock extension size + * @param free_version: Version number of file free space management + * @param free_meta_size: Free space manager metadata size + * @param free_tot_space: Amount of free space in the file + * @param sohm_version: Version number of shared object header info + * @param sohm_hdr_size: Shared object header message header size + * @param sohm_msgs_info: Shared object header message index and heap size + */ public H5F_info2_t (int super_version, long super_size, long super_ext_size, int free_version, long free_meta_size, long free_tot_space, int sohm_version, long sohm_hdr_size, H5_ih_info_t sohm_msgs_info) diff --git a/java/src/hdf/hdf5lib/structs/H5G_info_t.java b/java/src/hdf/hdf5lib/structs/H5G_info_t.java index 6d4f405..e79f859 100644 --- a/java/src/hdf/hdf5lib/structs/H5G_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5G_info_t.java @@ -20,8 +20,12 @@ import java.io.Serializable; */ public class H5G_info_t implements Serializable{ private static final long serialVersionUID = -3746463015312132912L; - public int storage_type; // Type of storage for links in group - public long nlinks; // Number of links in group - public long max_corder; // Current max. creation order value for group - public boolean mounted; // Whether group has a file mounted on it + /** Type of storage for links in group */ + public int storage_type; + /** Number of links in group */ + public long nlinks; + /** Current max. creation order value for group */ + public long max_corder; + /** Whether group has a file mounted on it */ + public boolean mounted; } diff --git a/java/src/hdf/hdf5lib/structs/H5L_info_t.java b/java/src/hdf/hdf5lib/structs/H5L_info_t.java index eaf0da5..a3011c0 100644 --- a/java/src/hdf/hdf5lib/structs/H5L_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5L_info_t.java @@ -22,14 +22,20 @@ import hdf.hdf5lib.HDF5Constants; */ public class H5L_info_t implements Serializable { private static final long serialVersionUID = -4754320605310155033L; + /** Type of link */ public int type; + /** Indicate if creation order is valid */ public boolean corder_valid; + /** Creation order */ public long corder; + /** Character set of link name */ public int cset; + /** Character set of link name */ public H5O_token_t token; + /** Size of a soft link or user-defined link value */ public long val_size; - // Constructor for using object token portion of C union + /** Constructor for using object token portion of C union */ H5L_info_t (int type, boolean corder_valid, long corder, int cset, H5O_token_t token) { @@ -41,7 +47,7 @@ public class H5L_info_t implements Serializable { this.val_size = -1; } - // Constructor for using val_size portion of C union + /** Constructor for using val_size portion of C union */ H5L_info_t (int type, boolean corder_valid, long corder, int cset, long val_size) { diff --git a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java index 9a1749d..2475dd9 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java @@ -20,16 +20,26 @@ import java.io.Serializable; */ public class H5O_hdr_info_t implements Serializable { private static final long serialVersionUID = 7883826382952577189L; - public int version; /* Version number of header format in file */ - public int nmesgs; /* Number of object header messages */ - public int nchunks; /* Number of object header chunks */ - public int flags; /* Object header status flags */ - public long space_total; /* Total space for storing object header in file */ - public long space_meta; /* Space within header for object header metadata information */ - public long space_mesg; /* Space within header for actual message information */ - public long space_free; /* Free space within object header */ - public long mesg_present; /* Flags to indicate presence of message type in header */ - public long mesg_shared; /* Flags to indicate message type is shared in header */ + /** Version number of header format in file */ + public int version; + /** Number of object header messages */ + public int nmesgs; + /** Number of object header chunks */ + public int nchunks; + /** Object header status flags */ + public int flags; + /** Total space for storing object header in file */ + public long space_total; + /** Space within header for object header metadata information */ + public long space_meta; + /** Space within header for actual message information */ + public long space_mesg; + /** Free space within object header */ + public long space_free; + /** Flags to indicate presence of message type in header */ + public long mesg_present; + /** Flags to indicate message type is shared in header */ + public long mesg_shared; H5O_hdr_info_t (int version, int nmesgs, int nchunks, int flags, long space_total, long space_meta, long space_mesg, long space_free, diff --git a/java/src/hdf/hdf5lib/structs/H5O_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_info_t.java index cc94247..d2208d2 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_info_t.java @@ -20,16 +20,37 @@ import java.io.Serializable; */ public class H5O_info_t implements Serializable { private static final long serialVersionUID = 4691681163544054518L; - public long fileno; /* File number that object is located in */ - public H5O_token_t token; /* Object token in file */ - public int type; /* Basic object type (group, dataset, etc.) */ - public int rc; /* Reference count of object */ - public long atime; /* Access time */ - public long mtime; /* Modification time */ - public long ctime; /* Change time */ - public long btime; /* Birth time */ - public long num_attrs; /* # of attributes attached to object */ + /** File number that object is located in */ + public long fileno; + /** Object token in file */ + public H5O_token_t token; + /** Basic object type (group, dataset, etc.) */ + public int type; + /** Reference count of object */ + public int rc; + /** Access time */ + public long atime; + /** Modification time */ + public long mtime; + /** Change time */ + public long ctime; + /** Birth time */ + public long btime; + /** Number of attributes attached to object */ + public long num_attrs; + /** Constructor for data model information struct for objects + * + * @param fileno: File number that object is located in + * @param token: Object token in file + * @param type: Basic object type + * @param rc: Reference count of object + * @param atime: Access time + * @param mtime: Modification time + * @param ctime: Change time + * @param btime: Birth time + * @param num_attrs: Number of attributes attached to object + */ public H5O_info_t (long fileno, H5O_token_t token, int type, int rc, long atime, long mtime, long ctime, long btime, long num_attrs) { diff --git a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java index ff801e8..70e5231 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java @@ -20,12 +20,14 @@ import java.io.Serializable; */ public class H5O_native_info_t implements Serializable { private static final long serialVersionUID = 7883826382952577189L; - - public H5O_hdr_info_t hdr_info; /* Object header information */ + /** Object header information */ + public H5O_hdr_info_t hdr_info; /* Extra metadata storage for obj & attributes */ - public H5_ih_info_t obj_info; /* v1/v2 B-tree & local/fractal heap for groups, B-tree for chunked datasets */ - public H5_ih_info_t attr_info; /* v2 B-tree & heap for attributes */ + /** v1/v2 B-tree and local/fractal heap for groups, B-tree for chunked datasets */ + public H5_ih_info_t obj_info; + /** v2 B-tree and heap for attributes */ + public H5_ih_info_t attr_info; H5O_native_info_t (H5O_hdr_info_t oheader_info, H5_ih_info_t obj_info, H5_ih_info_t attr_info) { diff --git a/java/src/hdf/hdf5lib/structs/H5O_token_t.java b/java/src/hdf/hdf5lib/structs/H5O_token_t.java index c7ac437..f0bb978 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_token_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_token_t.java @@ -23,12 +23,22 @@ import hdf.hdf5lib.HDF5Constants; */ public class H5O_token_t implements Serializable { private static final long serialVersionUID = -4754320605310155032L; + /** + * Tokens are unique and permanent identifiers that are + * used to reference HDF5 objects in a container. + * Use basic byte array to store the dat + */ public byte[] data; H5O_token_t (byte[] data) { this.data = data; } + /** + * Check if token data is undefined + * + * @return true if token data is undefined + */ public boolean isUndefined() { return this.equals(HDF5Constants.H5O_TOKEN_UNDEF); } diff --git a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java index eec50c2..0c6111b 100644 --- a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java @@ -20,9 +20,9 @@ import java.io.Serializable; */ public class H5_ih_info_t implements Serializable { private static final long serialVersionUID = -142238015615462707L; - /** */ - public long index_size; /* btree and/or list */ - /** */ + /** btree and/or list size of index */ + public long index_size; + /** btree and/or list size of hp */ public long heap_size; H5_ih_info_t (long index_size, long heap_size) |