diff options
Diffstat (limited to 'java/src/hdf/hdf5lib')
-rw-r--r-- | java/src/hdf/hdf5lib/CMakeLists.txt | 22 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 55 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/HDFArray.java | 52 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/HDFNativeData.java | 30 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/callbacks/package-info.java | 27 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/exceptions/package-info.java | 31 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/package-info.java | 174 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java | 15 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java | 15 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/structs/package-info.java | 17 |
10 files changed, 349 insertions, 89 deletions
diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt index 5651031..a26e117 100644 --- a/java/src/hdf/hdf5lib/CMakeLists.txt +++ b/java/src/hdf/hdf5lib/CMakeLists.txt @@ -40,6 +40,11 @@ set (HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES callbacks/Callbacks.java ) +set (HDF5_JAVADOC_HDF_HDF5_CALLBACKS_SOURCES + ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES} + callbacks/package-info.java +) + set (HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES exceptions/HDF5Exception.java exceptions/HDF5IdException.java @@ -67,6 +72,11 @@ set (HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES exceptions/HDF5SymbolTableException.java ) +set (HDF5_JAVADOC_HDF_HDF5_EXCEPTIONS_SOURCES + ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES} + exceptions/package-info.java +) + set (HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES structs/H5_ih_info_t.java structs/H5A_info_t.java @@ -83,6 +93,11 @@ set (HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES structs/H5O_token_t.java ) +set (HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES + ${HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES} + structs/package-info.java +) + set (HDF5_JAVA_HDF_HDF5_SOURCES HDFArray.java HDF5Constants.java @@ -91,6 +106,11 @@ set (HDF5_JAVA_HDF_HDF5_SOURCES H5.java ) +set (HDF5_JAVADOC_HDF_HDF5_SOURCES + ${HDF5_JAVA_HDF_HDF5_SOURCES} + package-info.java +) + set (CMAKE_JNI_TARGET TRUE) file (WRITE ${PROJECT_BINARY_DIR}/Manifest.txt @@ -114,7 +134,7 @@ add_dependencies (${HDF5_JAVA_HDF5_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_TARGET}) set_target_properties (${HDF5_JAVA_HDF5_LIB_TARGET} PROPERTIES FOLDER libraries/java) create_javadoc(hdf5_java_doc - FILES ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVA_HDF_HDF5_SOURCES} + FILES ${HDF5_JAVADOC_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_SOURCES} OVERVIEW ${HDF5_JAVA_HDF5_SRC_DIR}/overview.html CLASSPATH ${CMAKE_JAVA_INCLUDE_PATH} WINDOWTITLE "HDF5 Java" diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 63547df..4129f50 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -64,8 +64,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps a single * HDF5 entry point, generally with the arguments and return codes analogous to the C interface. * <p> - * For details of the HDF5 library, see the HDF5 Documentation at: <a - * href="http://hdfgroup.org/HDF5/">http://hdfgroup.org/HDF5/</a> + * For details of the HDF5 library, see the HDF5 Documentation at: + * <a href="http://hdfgroup.org/HDF5/">http://hdfgroup.org/HDF5/</a> * <hr> * <p> * <b>Mapping of arguments for Java</b> @@ -162,8 +162,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * <p> * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, multidimensional * arrays are definitely <i>not</i> layed out contiguously in memory. It would be infeasible to declare a separate - * routine for every combination of number type and dimensionality. For that reason, the <a - * href="./hdf.hdf5lib.HDFArray.html"><b>HDFArray</b></a> class is used to discover the type, shape, and size of the + * routine for every combination of number type and dimensionality. For that reason, the + * <a href="./hdf.hdf5lib.HDFArray.html"><b>HDFArray</b></a> class is used to discover the type, shape, and size of the * data array at run time, and to convert to and from a contiguous array of bytes in synchronized static native C order. * <p> * The upshot is that any Java array of numbers (either primitive or sub-classes of type <b>Number</b>) can be passed as @@ -187,8 +187,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * <b><i>H5F_ACC_RDWR</i></b> and <b><i>H5P_DEFAULT</i></b>. * <p> * The HDF-5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and "hsize_t". - * These values are determined at run time by the HDF-5 C library. To support these parameters, the Java class <a - * href="./hdf.hdf5lib.HDF5CDataTypes.html"> <b>HDF5CDataTypes</b></a> looks up the values when initiated. The values + * These values are determined at run time by the HDF-5 C library. To support these parameters, the Java class + * <a href="./hdf.hdf5lib.HDF5CDataTypes.html"> <b>HDF5CDataTypes</b></a> looks up the values when initiated. The values * can be accessed as public variables of the Java class, such as: * * <pre> @@ -204,8 +204,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural * for Java programming. * <p> - * The exceptions of the JHI5 are organized as sub-classes of the class <a - * href="./hdf.hdf5lib.exceptions.HDF5Exception.html"> <b>HDF5Exception</b></a>. There are two subclasses of + * The exceptions of the JHI5 are organized as sub-classes of the class + * <a href="./hdf.hdf5lib.exceptions.HDF5Exception.html"> <b>HDF5Exception</b></a>. There are two subclasses of * <b>HDF5Exception</b>, <a href="./hdf.hdf5lib.exceptions.HDF5LibraryException.html"> <b>HDF5LibraryException</b></a> * and <a href="./hdf.hdf5lib.exceptions.HDF5JavaException.html"> <b>HDF5JavaException</b></a>. The sub-classes of the * former represent errors from the HDF-5 C library, while sub-classes of the latter represent errors in the JHI5 @@ -216,7 +216,7 @@ import hdf.hdf5lib.structs.H5O_token_t; * exception handlers to print out the HDF-5 error stack. * <hr> * - * @version HDF5 1.13.0 <BR> + * @version HDF5 1.13.1 <BR> * <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR> * <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR> * <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR> @@ -239,7 +239,7 @@ public class H5 implements java.io.Serializable { * * Make sure to update the versions number when a different library is used. */ - public final static int LIB_VERSION[] = { 1, 13, 0 }; + public final static int LIB_VERSION[] = { 1, 13, 1 }; /** * add system property to load library by path @@ -12776,8 +12776,11 @@ public class H5 implements java.io.Serializable { * IN: Field name of the field index to retrieve. * * @return if field is defined, the index; else negative. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. **/ - public synchronized static native int H5Tget_member_index(long type_id, String field_name); + public synchronized static native int H5Tget_member_index(long type_id, String field_name) throws HDF5LibraryException; /** * H5Tget_member_name retrieves the name of a field of a compound datatype or an element of an enumeration datatype. @@ -12788,8 +12791,11 @@ public class H5 implements java.io.Serializable { * IN: Field index (0-based) of the field name to retrieve. * * @return a valid pointer to the name if successful; otherwise null. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. **/ - public synchronized static native String H5Tget_member_name(long type_id, int field_idx); + public synchronized static native String H5Tget_member_name(long type_id, int field_idx) throws HDF5LibraryException; /** * H5Tget_member_offset returns the byte offset of the specified member of the compound datatype. This is the byte @@ -12801,11 +12807,8 @@ public class H5 implements java.io.Serializable { * IN: Field index (0-based) of the field type to retrieve. * * @return the offset of the member. - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Tget_member_offset(long type_id, int membno) throws HDF5LibraryException; + public synchronized static native long H5Tget_member_offset(long type_id, int membno); /** * H5Tget_member_type returns the datatype of the specified member. @@ -13460,7 +13463,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id); + public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id) throws HDF5LibraryException; /** * H5VLregister_connector_by_value registers a new VOL connector as a member of the virtual object layer class. * @@ -13475,7 +13478,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id); + public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id) throws HDF5LibraryException; /** * H5VLis_connector_registered_by_name tests whether a VOL class has been registered. * @@ -13487,7 +13490,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native boolean H5VLis_connector_registered_by_name(String name); + public synchronized static native boolean H5VLis_connector_registered_by_name(String name) throws HDF5LibraryException; /** * H5VLis_connector_registered_by_value tests whether a VOL class has been registered. * @@ -13499,7 +13502,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value); + public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value) throws HDF5LibraryException; /** * H5VLget_connector_id retrieves the ID for a registered VOL connector for a given object. * @@ -13511,7 +13514,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5VLget_connector_id(long object_id); + public synchronized static native long H5VLget_connector_id(long object_id) throws HDF5LibraryException; /** * H5VLget_connector_id_by_name retrieves the ID for a registered VOL connector. * @@ -13523,7 +13526,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5VLget_connector_id_by_name(String name); + public synchronized static native long H5VLget_connector_id_by_name(String name) throws HDF5LibraryException; /** * H5VLget_connector_id_by_value retrieves the ID for a registered VOL connector. * @@ -13535,7 +13538,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5VLget_connector_id_by_value(int connector_value); + public synchronized static native long H5VLget_connector_id_by_value(int connector_value) throws HDF5LibraryException; /** * H5VLget_connector_name returns the connector name for the VOL associated with the * object or file ID. @@ -13548,7 +13551,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native String H5VLget_connector_name(long object_id); + public synchronized static native String H5VLget_connector_name(long object_id) throws HDF5LibraryException; /** * H5VLclose closes a VOL connector ID. * @@ -13558,7 +13561,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native void H5VLclose(long connector_id); + public synchronized static native void H5VLclose(long connector_id) throws HDF5LibraryException; /** * H5VLunregister_connector removes a VOL connector ID from the library. * @@ -13568,7 +13571,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native void H5VLunregister_connector(long connector_id); + public synchronized static native void H5VLunregister_connector(long connector_id) throws HDF5LibraryException; // /////// unimplemented //////// // hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id); diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java index bb9357e..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); } 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/callbacks/package-info.java b/java/src/hdf/hdf5lib/callbacks/package-info.java new file mode 100644 index 0000000..0833162 --- /dev/null +++ b/java/src/hdf/hdf5lib/callbacks/package-info.java @@ -0,0 +1,27 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * 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. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/** All callback definitions must derive from the Callbacks interface. Any + * derived interfaces must define a single public method named "callback". + * You are responsible for deregistering your callback (if necessary) + * in its {@link Object#finalize} method. If native code attempts to call + * a callback which has been GC'd, you will likely crash the VM. If + * there is no method to deregister the callback (e.g. <code>atexit</code> + * in the C library), you must ensure that you always keep a live reference + * to the callback object.<p> + * A callback should generally never throw an exception, since it doesn't + * necessarily have an encompassing Java environment to catch it. Any + * exceptions thrown will be passed to the default callback exception + * handler. + */ +package hdf.hdf5lib.callbacks; diff --git a/java/src/hdf/hdf5lib/exceptions/package-info.java b/java/src/hdf/hdf5lib/exceptions/package-info.java new file mode 100644 index 0000000..8640ccb --- /dev/null +++ b/java/src/hdf/hdf5lib/exceptions/package-info.java @@ -0,0 +1,31 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * 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. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/** + * <p> + * The package exceptions contains error classes for the Java HDF5 Interface. + * <p> + * There are two sub-classes of exceptions defined: + * <ol> + * <li> + * HDF5LibraryException -- errors raised the HDF5 library code + * <li> + * HDF5JavaException -- errors raised the HDF5 Java wrapper code + * </ol> + * <p> + * The HDF5LibraryException is the base class for the classes that represent specific error conditions. + * In particular, HDF5LibraryException has a sub-class for each major + * error code returned by the HDF5 library. + * + */ +package hdf.hdf5lib.exceptions;
\ No newline at end of file diff --git a/java/src/hdf/hdf5lib/package-info.java b/java/src/hdf/hdf5lib/package-info.java new file mode 100644 index 0000000..838a266 --- /dev/null +++ b/java/src/hdf/hdf5lib/package-info.java @@ -0,0 +1,174 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * 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. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + + +/** + * This package is the Java interface for the HDF5 library. + * <p> + * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps a single + * HDF5 entry point, generally with the arguments and return codes analogous to the C interface. + * <p> + * For details of the HDF5 library, see the HDF5 Documentation at: + * <a href="http://hdfgroup.org/HDF5/">http://hdfgroup.org/HDF5/</a> + * <hr> + * <p> + * <b>Mapping of arguments for Java</b> + * + * <p> + * In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF + * Reference Manual. + * + * <table border=1> + * <caption><b>HDF-5 C types to Java types</b> </caption> + * <tr> + * <td><b>HDF-5</b></td> + * <td><b>Java</b></td> + * </tr> + * <tr> + * <td>H5T_NATIVE_INT</td> + * <td>int, Integer</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_SHORT</td> + * <td>short, Short</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_FLOAT</td> + * <td>float, Float</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_DOUBLE</td> + * <td>double, Double</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_CHAR</td> + * <td>byte, Byte</td> + * </tr> + * <tr> + * <td>H5T_C_S1</td> + * <td>java.lang.String</td> + * </tr> + * <tr> + * <td>void * <BR> + * (i.e., pointer to `Any')</td> + * <td>Special -- see HDFArray</td> + * </tr> + * </table> + * <b>General Rules for Passing Arguments and Results</b> + * <p> + * In general, arguments passed <b>IN</b> to Java are the analogous basic types, as above. The exception is for arrays, + * which are discussed below. + * <p> + * The <i>return value</i> of Java methods is also the analogous type, as above. A major exception to that rule is that + * all HDF functions that return SUCCEED/FAIL are declared <i>boolean</i> in the Java version, rather than <i>int</i> as + * in the C. Functions that return a value or else FAIL are declared the equivalent to the C function. However, in most + * cases the Java method will raise an exception instead of returning an error code. + * See <a href="#ERRORS">Errors and Exceptions</a> below. + * <p> + * Java does not support pass by reference of arguments, so arguments that are returned through <b>OUT</b> parameters + * must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in arrays. + * <p> + * For instance, a function that returns two integers is declared: + * + * <pre> + * h_err_t HDF5dummy( int *a1, int *a2) + * </pre> + * + * For the Java interface, this would be declared: + * + * <pre> + * public synchronized static native void HDF5dummy(int args[]); + * </pre> + * + * where <i>a1</i> is <i>args[0]</i> and <i>a2</i> is <i>args[1]</i>, and would be invoked: + * + * <pre> + * H5.HDF5dummy(a); + * </pre> + * + * <p> + * All the routines where this convention is used will have specific documentation of the details, given below. + * <p> + * <b>Arrays</b> + * <p> + * HDF5 needs to read and write multi-dimensional arrays of any number type (and records). The HDF5 API describes the + * layout of the source and destination, and the data for the array passed as a block of bytes, for instance, + * + * <pre> + * herr_t H5Dread(long fid, long filetype, long memtype, long memspace, void *data); + * </pre> + * + * <p> + * where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of bytes that is the + * data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype of the array on + * disk (source) and in memory (destination). + * <p> + * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, multidimensional + * arrays are definitely <i>not</i> layed out contiguously in memory. It would be infeasible to declare a separate + * routine for every combination of number type and dimensionality. For that reason, the + * <a href="./hdf.hdf5lib.HDFArray.html"><b>HDFArray</b></a> class is used to discover the type, shape, and size of the + * data array at run time, and to convert to and from a contiguous array of bytes in synchronized static native C order. + * <p> + * The upshot is that any Java array of numbers (either primitive or sub-classes of type <b>Number</b>) can be passed as + * an ``Object'', and the Java API will translate to and from the appropriate packed array of bytes needed by the C + * library. So the function above would be declared: + * + * <pre> + * public synchronized static native int H5Dread(long fid, long filetype, long memtype, long memspace, Object data); + * </pre> + * OPEN_IDS.addElement(id); + + * and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or int[][][], or + * Double[][]. + * <p> + * <b>HDF-5 Constants</b> + * <p> + * The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs + * via the class <a href="./hdf.hdf5lib.HDF5Constants.html"> <b>HDF5Constants</b></a>. For example, the parameters for + * the h5open() call include two numeric values, <b><i>HDFConstants.H5F_ACC_RDWR</i></b> and + * <b><i>HDF5Constants.H5P_DEFAULT</i></b>. As would be expected, these numbers correspond to the C constants + * <b><i>H5F_ACC_RDWR</i></b> and <b><i>H5P_DEFAULT</i></b>. + * <p> + * The HDF-5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and "hsize_t". + * These values are determined at run time by the HDF-5 C library. To support these parameters, the Java class + * <a href="./hdf.hdf5lib.HDF5CDataTypes.html"> <b>HDF5CDataTypes</b></a> looks up the values when initiated. The values + * can be accessed as public variables of the Java class, such as: + * + * <pre> + * long data_type = HDF5CDataTypes.JH5T_NATIVE_INT; + * </pre> + * + * The Java application uses both types of constants the same way, the only difference is that the + * <b><i>HDF5CDataTypes</i></b> may have different values on different platforms. + * <p> + * <b>Error handling and Exceptions</b> + * <p> + * The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is available from the + * JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural + * for Java programming. + * <p> + * The exceptions of the JHI5 are organized as sub-classes of the class + * <a href="./hdf.hdf5lib.exceptions.HDF5Exception.html"> <b>HDF5Exception</b></a>. There are two subclasses of + * <b>HDF5Exception</b>, <a href="./hdf.hdf5lib.exceptions.HDF5LibraryException.html"> <b>HDF5LibraryException</b></a> + * and <a href="./hdf.hdf5lib.exceptions.HDF5JavaException.html"> <b>HDF5JavaException</b></a>. The sub-classes of the + * former represent errors from the HDF-5 C library, while sub-classes of the latter represent errors in the JHI5 + * wrapper and support code. + * <p> + * The super-class <b><i>HDF5LibraryException</i></b> implements the method '<b><i>printStackTrace()</i></b>', which + * prints out the HDF-5 error stack, as described in the HDF-5 C API <i><b>H5Eprint()</b>.</i> This may be used by Java + * exception handlers to print out the HDF-5 error stack. + * <hr> + * + * <b>See also: <a href="http://hdfgroup.org/HDF5/"> http://hdfgroup.org/HDF5"</a></b> + **/ +package hdf.hdf5lib;
\ No newline at end of file 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 5da4abd..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; 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 39f5424..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; diff --git a/java/src/hdf/hdf5lib/structs/package-info.java b/java/src/hdf/hdf5lib/structs/package-info.java new file mode 100644 index 0000000..8a9d97d --- /dev/null +++ b/java/src/hdf/hdf5lib/structs/package-info.java @@ -0,0 +1,17 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * 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. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/** All structure definitions define java equivalents of the C structures needed + * by the C API calls. See the C API for information about the structures. + */ +package hdf.hdf5lib.structs; |