diff --git a/libs/native/jhdf5/amd64-Linux/libjhdf5.so b/libs/native/jhdf5/amd64-Linux/libjhdf5.so
index 02d5d5029e9e7425f35dffcde0bffdbc2de17d18..93ee237affba09ee6670d25d9ec16c18972dd98d 100755
Binary files a/libs/native/jhdf5/amd64-Linux/libjhdf5.so and b/libs/native/jhdf5/amd64-Linux/libjhdf5.so differ
diff --git a/source/c/compile_linux_amd64.sh b/source/c/compile_linux_amd64.sh
index d675f02022e8ad48a07af8cc548c5818d3f333e7..ad22b5839c89be694d311560cb299b088653e783 100755
--- a/source/c/compile_linux_amd64.sh
+++ b/source/c/compile_linux_amd64.sh
@@ -8,7 +8,7 @@ fi
rm -fR build/jni
rm -f build/libjhdf5.so
-cp -a jni build/
+cp -a build/hdf5-$VERSION/java/src/jni build/
cp -a *.c build/jni/
cd build
cp hdf5-$VERSION/src/H5win32defs.h jni/
diff --git a/source/c/h5lHelperImp.c b/source/c/h5lHelperImp.c
index 35d5f17022d45015659bb879e323a8784fdc4ede..6986d4eaf00cb4ab9081781a2781d7cc8a313534 100644
--- a/source/c/h5lHelperImp.c
+++ b/source/c/h5lHelperImp.c
@@ -17,6 +17,7 @@
#include "hdf5.h"
#include "H5Ppublic.h"
#include "h5jni.h"
+#include "h5util.h"
#include <jni.h>
#include <stdlib.h>
@@ -75,14 +76,12 @@ Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lexists
(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong access_id)
{
htri_t bval = JNI_FALSE;
- const char *lName;
+ const char *lName = NULL;
- PIN_JAVA_STRING(name, lName);
+ PIN_JAVA_STRING(ENVONLY, name, lName, NULL, "H5Lexists: name not pinned");
if (lName != NULL) {
bval = H5Lexists((hid_t)loc_id, lName, (hid_t)access_id);
- UNPIN_JAVA_STRING(name, lName);
-
if (bval > 0)
bval = JNI_TRUE;
else if (bval < 0)
@@ -92,10 +91,14 @@ Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lexists
bval = JNI_FALSE;
} else
{
- h5libraryError(env);
+ H5_LIBRARY_ERROR(ENVONLY);
}
}
}
+
+done:
+ if (lName != NULL)
+ UNPIN_JAVA_STRING(ENVONLY, name, lName);
return (jboolean)bval;
} /* end Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lexists */
@@ -108,37 +111,32 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
(JNIEnv *env, jclass clss, jlong loc_id, jstring object_name,
jobjectArray linkName)
{
- jint type;
- herr_t status;
+ jint type = FAIL;
+ herr_t status = FAIL;
long minor_err_num;
- char *oName;
+ const char *oName = NULL;
char *linkval_buf;
const char *filename;
const char *obj_path;
- jboolean isCopy;
jstring str;
H5L_info_t link_info;
- H5O_info_t obj_info;
+ H5O_info1_t obj_info;
- PIN_JAVA_STRING(object_name, oName);
+ PIN_JAVA_STRING(ENVONLY, object_name, oName, NULL, "H5Lget_link_info: name not pinned");
type = H5Lget_info( (hid_t) loc_id, oName, &link_info, H5P_DEFAULT );
if (type < 0)
{
- UNPIN_JAVA_STRING(object_name, oName);
- h5libraryError(env);
- return -1;
+ H5_LIBRARY_ERROR(ENVONLY);
} else {
str = NULL;
if (link_info.type == H5L_TYPE_HARD)
{
status = H5Oget_info_by_name1(loc_id, oName, &obj_info, H5P_DEFAULT);
- UNPIN_JAVA_STRING(object_name, oName);
if (status < 0 )
{
- h5libraryError(env);
- return -1;
+ H5_LIBRARY_ERROR(ENVONLY);
} else {
type = obj_info.type;
}
@@ -155,8 +153,7 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
}
if (H5Lget_val(loc_id, oName, linkval_buf, link_info.u.val_size, H5P_DEFAULT) < 0)
{
- h5libraryError(env);
- return -1;
+ H5_LIBRARY_ERROR(ENVONLY);
}
if (link_info.type == H5L_TYPE_EXTERNAL)
{
@@ -174,6 +171,10 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
}
}
}
+
+done:
+ if (oName != NULL)
+ UNPIN_JAVA_STRING(ENVONLY, object_name, oName);
return (jint)type;
}
@@ -183,9 +184,9 @@ typedef struct link_info_all
JNIEnv *env;
char **name;
int *type;
- char **linkname;
- char **linkfname;
- void **buf;
+ const char **linkname;
+ const char **linkfname;
+ char **buf;
int count;
} link_info_all_t;
@@ -207,7 +208,7 @@ herr_t link_names_all(hid_t loc_id, const char *name, const H5L_info_t *link_inf
return 0;
}
-herr_t H5Lget_link_names_all( JNIEnv *env, hid_t loc_id, char *group_name, char **names )
+herr_t H5Lget_link_names_all( JNIEnv *env, hid_t loc_id, const char *group_name, char **names )
{
link_info_all_t info;
info.env = env;
@@ -228,37 +229,32 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
(JNIEnv *env, jclass clss, jlong loc_id, jstring group_name,
jobjectArray oname, jint n)
{
- herr_t status;
- char *gName=NULL;
- char **oName=NULL;
- char **lName=NULL;
+ herr_t status = FAIL;
+ const char *gName = NULL;
+ char **oName = NULL;
+ char **lName = NULL;
jstring str;
jboolean isCopy;
int i;
if (oname == NULL) {
- h5nullArgument( env, "_H5Lget_link_names_all: oname is NULL");
- return -1;
+ H5_NULL_ARGUMENT_ERROR(ENVONLY, "_H5Lget_link_names_all: oname is NULL");
}
- PIN_JAVA_STRING(group_name, gName);
+ PIN_JAVA_STRING(ENVONLY, group_name, gName, NULL, "H5Lget_link_names_all: group_name not pinned");
- oName = malloc(n * sizeof (*oName));
+ oName = HDmalloc(n * sizeof (*oName));
if (oName == NULL) {
- UNPIN_JAVA_STRING(group_name, gName);
- h5outOfMemory(env, "_H5Lget_link_names_all: malloc failed");
- return -1;
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "_H5Lget_link_names_all: failed to allocate oName buffer");
}
for (i=0; i<n; i++) {
oName[i] = NULL;
} /* for (i=0; i<n; i++)*/
- status = H5Lget_link_names_all(env, (hid_t) loc_id, gName, oName);
-
- UNPIN_JAVA_STRING(group_name, gName);
+ status = H5Lget_link_names_all(env, (hid_t) loc_id, gName, oName);
if (status < 0) {
h5str_array_free(oName, n);
- h5libraryError(env);
+ H5_LIBRARY_ERROR(ENVONLY);
} else {
for (i=0; i<n; i++) {
if (*(oName+i)) {
@@ -268,6 +264,10 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
} /* for (i=0; i<n; i++)*/
h5str_array_free(oName, n);
}
+
+done:
+ if (gName != NULL)
+ UNPIN_JAVA_STRING(ENVONLY, group_name, gName);
return (jint)status;
@@ -277,11 +277,11 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
herr_t link_info_all(hid_t loc_id, const char *name, const H5L_info_t *link_info, void *opdata)
{
link_info_all_t* info = (link_info_all_t*)opdata;
- H5O_info_t obj_info;
+ H5O_info1_t obj_info;
char *linkval_buf;
const char *filename;
const char *obj_path;
- *(info->name+info->count) = (char *) malloc(strlen(name)+1);
+ *(info->name+info->count) = (char *) HDmalloc(strlen(name)+1);
if (*(info->name+info->count) == NULL)
{
h5outOfMemory(info->env, "H5Lget_link_info_all: malloc failed");
@@ -306,7 +306,7 @@ herr_t link_info_all(hid_t loc_id, const char *name, const H5L_info_t *link_info
*(info->type+info->count) = H5O_TYPE_NTYPES + link_info->type;
if (info->linkname != NULL)
{
- linkval_buf = (char*) malloc(link_info->u.val_size);
+ linkval_buf = (char*) HDmalloc(link_info->u.val_size);
if (linkval_buf == NULL)
{
h5outOfMemory(info->env, "H5Lget_link_info_all: malloc failed");
@@ -337,7 +337,7 @@ herr_t link_info_all(hid_t loc_id, const char *name, const H5L_info_t *link_info
return 0;
}
-herr_t H5Lget_link_info_all( JNIEnv *env, hid_t loc_id, char *group_name, char **names, int *linktypes, char **linknames, char **linkfnames, void **buf )
+herr_t H5Lget_link_info_all( JNIEnv *env, hid_t loc_id, const char *group_name, char **names, int *linktypes, const char **linknames, const char **linkfnames, char **buf )
{
link_info_all_t info;
info.env = env;
@@ -362,18 +362,17 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
(JNIEnv *env, jclass clss, jlong loc_id, jstring group_name,
jobjectArray oname, jintArray otype, jobjectArray lname, jobjectArray lfname, jint n)
{
- herr_t status;
- char *gName=NULL;
- char **oName=NULL;
- char **lName=NULL;
- char **lfName=NULL;
- void **buf=NULL;
- jboolean isCopy;
+ herr_t status = FAIL;
+ const char *gName = NULL;
+ char **oName = NULL;
+ char **lName = NULL;
+ char **lfName = NULL;
+ char **buf = NULL;
jstring str;
jint *tarr;
int i;
- PIN_JAVA_STRING(group_name, gName);
+ PIN_JAVA_STRING(ENVONLY, group_name, gName, NULL, "H5Lget_link_info_all: group_name not pinned");
if (oname == NULL) {
h5nullArgument( env, "H5Lget_link_info_all: oname is NULL");
@@ -390,19 +389,17 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
return -1;
}
- tarr = (*env)->GetIntArrayElements(env,otype,&isCopy);
+ tarr = (*env)->GetIntArrayElements(env,otype, NULL);
if (tarr == NULL) {
(*env)->ReleaseStringUTFChars(env,group_name,gName);
h5JNIFatalError( env, "H5Lget_link_info_all: type not pinned");
return -1;
}
- oName = malloc(n * sizeof (*oName));
+ oName = HDmalloc(n * sizeof (*oName));
if (oName == NULL) {
- UNPIN_JAVA_STRING(group_name, gName);
(*env)->ReleaseIntArrayElements(env,otype,tarr,0);
- h5outOfMemory(env, "H5Lget_link_info_all: malloc failed");
- return -1;
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Lget_link_info_all: malloc failed");
}
for (i=0; i<n; i++)
{
@@ -412,30 +409,24 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
{
lName = malloc(n * sizeof (*lName));
if (lName == NULL) {
- UNPIN_JAVA_STRING(group_name, gName);
(*env)->ReleaseIntArrayElements(env,otype,tarr,0);
h5str_array_free(oName, n);
- h5outOfMemory(env, "H5Lget_link_info_all: malloc failed");
- return -1;
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Lget_link_info_all: malloc failed");
}
lfName = malloc(n * sizeof (*lfName));
if (lfName == NULL) {
- UNPIN_JAVA_STRING(group_name, gName);
(*env)->ReleaseIntArrayElements(env,otype,tarr,0);
h5str_array_free(oName, n);
free(lName);
- h5outOfMemory(env, "H5Lget_link_info_all: malloc failed");
- return -1;
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Lget_link_info_all: malloc failed");
}
buf = malloc(n * sizeof (*buf));
if (buf == NULL) {
- UNPIN_JAVA_STRING(group_name, gName);
(*env)->ReleaseIntArrayElements(env,otype,tarr,0);
h5str_array_free(oName, n);
free(lName);
free(lfName);
- h5outOfMemory(env, "H5Lget_link_info_all: malloc failed");
- return -1;
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Lget_link_info_all: malloc failed");
}
for (i=0; i<n; i++) {
lName[i] = NULL;
@@ -443,9 +434,8 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
buf[i] = NULL;
} /* for (i=0; i<n; i++)*/
}
- status = H5Lget_link_info_all( env, (hid_t) loc_id, gName, oName, (int *)tarr, lName, lfName, buf );
+ status = H5Lget_link_info_all( env, (hid_t) loc_id, gName, oName, (int *)tarr, (const char **)lName, (const char **)lfName, buf );
- UNPIN_JAVA_STRING(group_name, gName);
if (status < 0) {
(*env)->ReleaseIntArrayElements(env,otype,tarr,JNI_ABORT);
h5str_array_free(oName, n);
@@ -455,7 +445,7 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
h5str_array_free(lfName, n);
h5str_array_free(buf, n);
}
- h5libraryError(env);
+ H5_LIBRARY_ERROR(ENVONLY);
} else {
(*env)->ReleaseIntArrayElements(env,otype,tarr,0);
@@ -486,6 +476,10 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_HDFHelper__1H5Lget_1li
}
h5str_array_free(oName, n);
}
+
+done:
+ if (gName != NULL)
+ UNPIN_JAVA_STRING(ENVONLY, group_name, gName);
return (jint)status;
diff --git a/source/c/version.sh b/source/c/version.sh
index cd88f74e43466772f49d15c5601c37aa9c686f47..5621bc4eac058c6c6bc44e04f2a344769712100a 100755
--- a/source/c/version.sh
+++ b/source/c/version.sh
@@ -1,2 +1,2 @@
-VERSION=1.10.5
+VERSION=1.12.0
POSTFIX=
diff --git a/source/java/ch/systemsx/cisd/hdf5/HDF5.java b/source/java/ch/systemsx/cisd/hdf5/HDF5.java
index 7c5d57f5ab077c7e966a9fab600a9c1937859ea1..abba0527860a145976089b538cca43e5c67309e0 100644
--- a/source/java/ch/systemsx/cisd/hdf5/HDF5.java
+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5.java
@@ -279,9 +279,7 @@ class HDF5
public long openObject(long fileId, String path, ICleanUpRegistry registry)
{
checkMaxLength(path);
- final long objectId =
- isReference(path) ? H5Oopen_by_addr(fileId, Long.parseLong(path.substring(1)))
- : H5Oopen(fileId, path, H5P_DEFAULT);
+ final long objectId = H5Oopen(fileId, path, H5P_DEFAULT);
registry.registerCleanUp(new Runnable()
{
@Override
@@ -372,8 +370,7 @@ class HDF5
public long openGroup(long fileId, String path, ICleanUpRegistry registry)
{
checkMaxLength(path);
- final long groupId = isReference(path) ? H5Oopen_by_addr(fileId, Long.parseLong(path.substring(1)))
- : H5Gopen(fileId, path, H5P_DEFAULT);
+ final long groupId = H5Gopen(fileId, path, H5P_DEFAULT);
registry.registerCleanUp(new Runnable()
{
@Override
@@ -932,8 +929,7 @@ class HDF5
public long openDataSet(long fileId, String path, ICleanUpRegistry registry)
{
checkMaxLength(path);
- final long dataSetId = isReference(path) ? H5Oopen_by_addr(fileId, Long.parseLong(path.substring(1)))
- : H5Dopen(fileId, path, H5P_DEFAULT);
+ final long dataSetId = H5Dopen(fileId, path, H5P_DEFAULT);
if (registry != null)
{
registry.registerCleanUp(new Runnable()
@@ -948,6 +944,7 @@ class HDF5
return dataSetId;
}
+ // TODO: remove!
boolean isReference(String path)
{
return autoDereference && (path.charAt(0) == '\0');
@@ -1778,8 +1775,7 @@ class HDF5
public long openDataType(long fileId, String name, ICleanUpRegistry registry)
{
checkMaxLength(name);
- final long dataTypeId = isReference(name) ? H5Oopen_by_addr(fileId, Long.parseLong(name.substring(1)))
- : H5Topen(fileId, name, H5P_DEFAULT);
+ final long dataTypeId = H5Topen(fileId, name, H5P_DEFAULT);
registry.registerCleanUp(new Runnable()
{
@Override
diff --git a/source/java/ch/systemsx/cisd/hdf5/HDF5ObjectInformation.java b/source/java/ch/systemsx/cisd/hdf5/HDF5ObjectInformation.java
index 8f5b98449909197e6a155e044a93de7e739d7c80..3c1d2215fa011687b0eec9a143e50ec98b39e93f 100644
--- a/source/java/ch/systemsx/cisd/hdf5/HDF5ObjectInformation.java
+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5ObjectInformation.java
@@ -16,7 +16,10 @@
package ch.systemsx.cisd.hdf5;
+import java.util.Arrays;
+
import hdf.hdf5lib.structs.H5O_info_t;
+import hdf.hdf5lib.structs.H5O_token_t;
/**
* Information about an object in an HDF5 file.
@@ -28,7 +31,7 @@ public final class HDF5ObjectInformation extends HDF5CommonInformation
private final long fileNumber;
- private final long address;
+ private final H5O_token_t token;
private final int referenceCount;
@@ -40,7 +43,7 @@ public final class HDF5ObjectInformation extends HDF5CommonInformation
{
super(path, objectType);
this.fileNumber = info.fileno;
- this.address = info.addr;
+ this.token = info.token;
this.referenceCount = info.rc;
this.creationTime = info.ctime;
this.numberOfAttributes = info.num_attrs;
@@ -59,9 +62,9 @@ public final class HDF5ObjectInformation extends HDF5CommonInformation
* Returns the address of the object in the file. If the address of two links is the same, then
* they point to the same object. Can be used to spot hard or soft links.
*/
- public long getAddress()
+ public H5O_token_t getToken()
{
- return address;
+ return token;
}
/**
@@ -96,7 +99,7 @@ public final class HDF5ObjectInformation extends HDF5CommonInformation
final int prime = 31;
int result = 1;
result = prime * result + ((path == null) ? 0 : path.hashCode());
- result = prime * result + ((int) address);
+ result = prime * result + Arrays.hashCode(token.data);
return result;
}
@@ -126,7 +129,7 @@ public final class HDF5ObjectInformation extends HDF5CommonInformation
{
return false;
}
- if (other.address != address)
+ if (other.token.equals(token) == false)
{
return false;
}
diff --git a/source/java/ch/systemsx/cisd/hdf5/hdf5lib/HDFHelper.java b/source/java/ch/systemsx/cisd/hdf5/hdf5lib/HDFHelper.java
index b04c43b55d78d19c710332d1b66a2d6feb124185..d3ed9299f0a8596c9d7e0712e2abeec2947499d6 100644
--- a/source/java/ch/systemsx/cisd/hdf5/hdf5lib/HDFHelper.java
+++ b/source/java/ch/systemsx/cisd/hdf5/hdf5lib/HDFHelper.java
@@ -101,7 +101,7 @@ public class HDFHelper
}
}
- return new H5O_info_t(-1, -1, -1, -1, -1, -1, -1, -1, -1, null, null, null);
+ return new H5O_info_t(-1, null, -1, -1, -1, -1, -1, -1, -1);
}
/**
diff --git a/source/java/hdf/CMakeLists.txt b/source/java/hdf/CMakeLists.txt
index 161ddf1bef326ef333f22b4dadede1f268f1b8b6..5660158d25348832e7aae6e29ec3d3e79e0b8335 100644
--- a/source/java/hdf/CMakeLists.txt
+++ b/source/java/hdf/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.10)
+cmake_minimum_required (VERSION 3.12)
project (HDF5_JAVA_HDF C)
add_subdirectory (hdf5lib)
diff --git a/source/java/hdf/hdf5lib/CMakeLists.txt b/source/java/hdf/hdf5lib/CMakeLists.txt
index c171ea89cdea828b410ee1e27fe11a52992a99c7..f3d9b8de8054378ceb02c73e6de47ce74e9fea68 100644
--- a/source/java/hdf/hdf5lib/CMakeLists.txt
+++ b/source/java/hdf/hdf5lib/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.10)
+cmake_minimum_required (VERSION 3.12)
project (HDF5_JAVA_HDF_HDF5 Java)
set (CMAKE_VERBOSE_MAKEFILE 1)
@@ -18,10 +18,10 @@ set (HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES
callbacks/H5D_iterate_t.java
callbacks/H5E_walk_cb.java
callbacks/H5E_walk_t.java
- callbacks/H5L_iterate_cb.java
callbacks/H5L_iterate_t.java
- callbacks/H5O_iterate_cb.java
+ callbacks/H5L_iterate_opdata_t.java
callbacks/H5O_iterate_t.java
+ callbacks/H5O_iterate_opdata_t.java
callbacks/H5P_cls_close_func_cb.java
callbacks/H5P_cls_close_func_t.java
callbacks/H5P_cls_copy_func_cb.java
@@ -73,10 +73,14 @@ set (HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES
structs/H5AC_cache_config_t.java
structs/H5E_error2_t.java
structs/H5F_info2_t.java
+ structs/H5FD_ros3_fapl_t.java
+ structs/H5FD_hdfs_fapl_t.java
structs/H5G_info_t.java
structs/H5L_info_t.java
structs/H5O_hdr_info_t.java
structs/H5O_info_t.java
+ structs/H5O_native_info_t.java
+ structs/H5O_token_t.java
)
set (HDF5_JAVA_HDF_HDF5_SOURCES
diff --git a/source/java/hdf/hdf5lib/H5.java b/source/java/hdf/hdf5lib/H5.java
index eaa8de81aad51e2fec7605b1543783a973b633c7..1f1dd848fd5f90f669e0a434e5f0e8c4b4a10ffc 100644
--- a/source/java/hdf/hdf5lib/H5.java
+++ b/source/java/hdf/hdf5lib/H5.java
@@ -23,9 +23,9 @@ import hdf.hdf5lib.callbacks.H5D_iterate_cb;
import hdf.hdf5lib.callbacks.H5D_iterate_t;
import hdf.hdf5lib.callbacks.H5E_walk_cb;
import hdf.hdf5lib.callbacks.H5E_walk_t;
-import hdf.hdf5lib.callbacks.H5L_iterate_cb;
+import hdf.hdf5lib.callbacks.H5L_iterate_opdata_t;
import hdf.hdf5lib.callbacks.H5L_iterate_t;
-import hdf.hdf5lib.callbacks.H5O_iterate_cb;
+import hdf.hdf5lib.callbacks.H5O_iterate_opdata_t;
import hdf.hdf5lib.callbacks.H5O_iterate_t;
import hdf.hdf5lib.callbacks.H5P_iterate_cb;
import hdf.hdf5lib.callbacks.H5P_iterate_t;
@@ -34,10 +34,14 @@ import hdf.hdf5lib.exceptions.HDF5JavaException;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import hdf.hdf5lib.structs.H5AC_cache_config_t;
import hdf.hdf5lib.structs.H5A_info_t;
+import hdf.hdf5lib.structs.H5FD_hdfs_fapl_t;
+import hdf.hdf5lib.structs.H5FD_ros3_fapl_t;
import hdf.hdf5lib.structs.H5F_info2_t;
import hdf.hdf5lib.structs.H5G_info_t;
import hdf.hdf5lib.structs.H5L_info_t;
import hdf.hdf5lib.structs.H5O_info_t;
+import hdf.hdf5lib.structs.H5O_native_info_t;
+import hdf.hdf5lib.structs.H5O_token_t;
/**
* This class is the Java interface for the HDF5 library.
@@ -55,8 +59,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF
* Reference Manual.
*
- * <center>
- * <table border=2 cellpadding=2>
+ * <table border=1>
* <caption><b>HDF-5 C types to Java types</b> </caption>
* <tr>
* <td><b>HDF-5</b></td>
@@ -92,8 +95,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* <td>Special -- see HDFArray</td>
* </tr>
* </table>
- * </center>
- * <center> <b>General Rules for Passing Arguments and Results</b> </center>
+ * <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.
@@ -128,7 +130,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* <p>
* All the routines where this convention is used will have specific documentation of the details, given below.
* <p>
- * <a NAME="ARRAYS"> <b>Arrays</b> </a>
+ * <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,
@@ -161,7 +163,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or int[][][], or
* Double[][].
* <p>
- * <a NAME="CONSTANTS"> <b>HDF-5 Constants</b></a>
+ * <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
@@ -181,7 +183,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* 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>
- * <a NAME="ERRORS"> <b>Error handling and Exceptions</b></a>
+ * <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 omitted from the
* JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural
@@ -199,7 +201,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* exception handlers to print out the HDF-5 error stack.
* <hr>
*
- * @version HDF5 1.10.3 <BR>
+ * @version HDF5 1.12.0 <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>
@@ -220,12 +222,19 @@ 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, 10, 3 };
+ public final static int LIB_VERSION[] = { 1, 12, 0 };
- private static boolean isLibraryLoaded = false;
+ public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib";
+ // add system property to load library by name from library path, via
+ // System.loadLibrary()
+ public final static String H5_LIBRARY_NAME_PROPERTY_KEY = "hdf.hdf5lib.H5.loadLibraryName";
+ private static String s_libraryName;
+ private static boolean isLibraryLoaded = false;
private static int openFileCount = 0;
-
+
+ private final static boolean IS_CRITICAL_PINNING = true;
+
static {
loadH5Lib();
}
@@ -419,9 +428,9 @@ public class H5 implements java.io.Serializable {
private synchronized static native boolean H5is_library_threadsafe();
// /////// unimplemented ////////
- // H5_DLL herr_t H5free_memory(void *mem);
- // H5_DLL void *H5allocate_memory(size_t size, hbool_t clear);
- // H5_DLL void *H5resize_memory(void *mem, size_t size);
+ // herr_t H5free_memory(void *mem);
+ // void *H5allocate_memory(size_t size, hbool_t clear);
+ // void *H5resize_memory(void *mem, size_t size);
// ////////////////////////////////////////////////////////////
// //
@@ -759,7 +768,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public static long H5Aget_space(long attr_id) throws HDF5LibraryException {
+ public static long H5Aget_space(long attr_id) throws HDF5LibraryException
+ {
long id = _H5Aget_space(attr_id);
return id;
}
@@ -790,7 +800,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public static long H5Aget_type(long attr_id) throws HDF5LibraryException {
+ public static long H5Aget_type(long attr_id) throws HDF5LibraryException
+ {
long id = _H5Aget_type(attr_id);
return id;
}
@@ -815,8 +826,9 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - Name is null.
**/
- public static long H5Aopen(long obj_id, String attr_name, long aapl_id) throws HDF5LibraryException,
- NullPointerException {
+ public static long H5Aopen(long obj_id, String attr_name, long aapl_id)
+ throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen(obj_id, attr_name, aapl_id);
return id;
}
@@ -851,7 +863,8 @@ public class H5 implements java.io.Serializable {
* - Name is null.
**/
public static long H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long aapl_id,
- long lapl_id) throws HDF5LibraryException, NullPointerException {
+ long lapl_id) throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
return id;
}
@@ -881,7 +894,8 @@ public class H5 implements java.io.Serializable {
* - obj_name is null.
**/
public static long H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, long lapl_id)
- throws HDF5LibraryException, NullPointerException {
+ throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id);
return id;
}
@@ -897,8 +911,10 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of an attribute to read.
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
- * @param buf
- * IN: Buffer for data to be read.
+ * @param obj
+ * Buffer to store data read from the file.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
@@ -907,9 +923,19 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - data buffer is null.
**/
- public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] buf)
+ public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ return H5Aread(attr_id, mem_type_id, obj, true);
+ }
+
/**
* H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with
* mem_type_id. The entire attribute is read into data object from the file.
@@ -920,31 +946,135 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Object for data to be read.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
+ * @exception HDF5Exception
+ * - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data buffer is null. See public synchronized static native int H5Aread( )
**/
- public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception,
- NullPointerException {
- HDFArray theArray = new HDFArray(obj);
- byte[] buf = theArray.emptyBytes();
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ int status = -1;
+ boolean is1D = false;
- // This will raise an exception if there is an error
- int status = H5Aread(attr_id, mem_type_id, buf);
+ Class dataClass = obj.getClass();
+ if (!dataClass.isArray()) {
+ throw (new HDF5JavaException("H5Aread: data is not an array"));
+ }
- // No exception: status really ought to be OK
- if (status >= 0) {
- obj = theArray.arrayify(buf);
+ String cname = dataClass.getName();
+ is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
+ char dname = cname.charAt(cname.lastIndexOf("[") + 1);
+
+ if (is1D && (dname == 'B')) {
+ status = H5Aread(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'S')) {
+ status = H5Aread_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'I')) {
+ status = H5Aread_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'J')) {
+ status = H5Aread_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'F')) {
+ status = H5Aread_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'D')) {
+ status = H5Aread_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
+ }
+ else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
+ (is1D && (dataClass.getComponentType() == String.class))) ||
+ H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+ status = H5Aread_reg_ref(attr_id, mem_type_id, (String[]) obj);
+ }
+ else if (is1D && (dataClass.getComponentType() == String.class)) {
+ status = H5Aread_string(attr_id, mem_type_id, (String[]) obj);
+ }
+ else {
+ // Create a data buffer to hold the data into a Java Array
+ HDFArray theArray = new HDFArray(obj);
+ byte[] buf = theArray.emptyBytes();
+
+ // This will raise an exception if there is an error
+ status = H5Aread(attr_id, mem_type_id, buf, isCriticalPinning);
+
+ // No exception: status really ought to be OK
+ if (status >= 0) {
+ obj = theArray.arrayify(buf);
+ }
+
+ // clean up these: assign 'null' as hint to gc()
+ buf = null;
+ theArray = null;
}
return status;
}
- public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, String[] buf)
+ public synchronized static native int H5Aread_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_double(long attr_id, long mem_type_id, double[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_double(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_float(long attr_id, long mem_type_id, float[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_float(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_int(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_long(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_short(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf)
@@ -1005,7 +1135,9 @@ public class H5 implements java.io.Serializable {
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
* @param buf
- * IN: Data to be written.
+ * IN: Buffer with data to be written to the file.
+ * @param isCriticalPinning
+ * IN: request lock on data reference.
*
* @return a non-negative value if successful
*
@@ -1014,9 +1146,21 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - data is null.
**/
- public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
+ public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite(attr_id, mem_type_id, obj, true);
+ }
+
/**
* H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with
* mem_type_id. The entire attribute is written from data object to the file.
@@ -1027,28 +1171,139 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Data object to be written.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
+ * @exception HDF5Exception
+ * - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
- * - data object is null. See public synchronized static native int H5Awrite(int attr_id, int
- * mem_type_id, byte[] buf);
+ * - data object is null
**/
- public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj)
- throws HDF5Exception, NullPointerException
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
{
- HDFArray theArray = new HDFArray(obj);
- byte[] buf = theArray.byteify();
+ int status = -1;
+ boolean is1D = false;
- int retVal = H5Awrite(attr_id, mem_type_id, buf);
- buf = null;
- theArray = null;
- return retVal;
+ Class dataClass = obj.getClass();
+ if (!dataClass.isArray()) {
+ throw (new HDF5JavaException("H5Dwrite: data is not an array"));
+ }
+
+ String cname = dataClass.getName();
+ is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
+ char dname = cname.charAt(cname.lastIndexOf("[") + 1);
+
+ if (is1D && (dname == 'B')) {
+ status = H5Awrite(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'S')) {
+ status = H5Awrite_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'I')) {
+ status = H5Awrite_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'J')) {
+ status = H5Awrite_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'F')) {
+ status = H5Awrite_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'D')) {
+ status = H5Awrite_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dataClass.getComponentType() == String.class)) {
+ status = H5Awrite_string(attr_id, mem_type_id, (String[]) obj);
+ }
+ else {
+ HDFArray theArray = new HDFArray(obj);
+ byte[] buf = theArray.byteify();
+
+ status = H5Awrite(attr_id, mem_type_id, buf);
+ buf = null;
+ theArray = null;
+ }
+
+ return status;
+ }
+
+ public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_double(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_float(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_int(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_long(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_short(attr_id, mem_type_id, buf, true);
}
- public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, String[] buf)
+ public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ /**
+ * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from
+ * the application memory buffer buf into the file.
+ *
+ * ---- contributed by Rosetta Biosoftware
+ *
+ * @param attr_id
+ * Identifier of the attribute read from.
+ * @param mem_type_id
+ * Identifier of the memory datatype.
+ * @param buf
+ * Buffer with data to be written to the file.
+ *
+ * @return a non-negative value if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+
+ public synchronized static native int H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
/**
@@ -1463,8 +1718,8 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException,
- NullPointerException {
+ public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Dopen2(loc_id, name, dapl_id);
return id;
}
@@ -1508,12 +1763,14 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true);
}
@@ -1547,11 +1804,12 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException,
- NullPointerException {
+ NullPointerException
+ {
int status = -1;
boolean is1D = false;
- Class<? extends Object> dataClass = obj.getClass();
+ Class dataClass = obj.getClass();
if (!dataClass.isArray()) {
throw (new HDF5JavaException("H5Dread: data is not an array"));
}
@@ -1573,7 +1831,8 @@ public class H5 implements java.io.Serializable {
isCriticalPinning);
}
else if (is1D && (dname == 'J')) {
- status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj);
+ status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj,
+ isCriticalPinning);
}
else if (is1D && (dname == 'F')) {
status = H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj,
@@ -1583,7 +1842,9 @@ public class H5 implements java.io.Serializable {
status = H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
(double[]) obj, isCriticalPinning);
}
- else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && (is1D && (dataClass.getComponentType() == String.class))) || H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+ else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
+ (is1D && (dataClass.getComponentType() == String.class))) ||
+ H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
status = H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
(String[]) obj);
}
@@ -1617,7 +1878,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1626,7 +1888,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1635,7 +1898,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1644,22 +1908,21 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
- public synchronized static native int H5Dread_reg_ref_data(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
-
public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1728,7 +1991,10 @@ public class H5 implements java.io.Serializable {
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
+ *
+ * @deprecated As of HDF5 1.12.0 in favor of H5Treclaim
**/
+ @Deprecated
public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException;
@@ -1763,12 +2029,14 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true);
}
@@ -1802,11 +2070,12 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException,
- NullPointerException {
+ NullPointerException
+ {
int status = -1;
boolean is1D = false;
- Class<? extends Object> dataClass = obj.getClass();
+ Class dataClass = obj.getClass();
if (!dataClass.isArray()) {
throw (new HDF5JavaException("H5Dwrite: data is not an array"));
}
@@ -1864,7 +2133,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1873,7 +2143,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1882,7 +2153,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1891,7 +2163,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1900,7 +2173,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1966,10 +2240,10 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Drefresh(long dset_id) throws HDF5LibraryException;
// /////// unimplemented ////////
- // H5_DLL herr_t H5Ddebug(hid_t dset_id);
- // H5_DLL herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
- // H5_DLL herr_t H5Dformat_convert(hid_t dset_id);
- // H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
+ // herr_t H5Ddebug(hid_t dset_id);
+ // herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
+ // herr_t H5Dformat_convert(hid_t dset_id);
+ // herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
// herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
// size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data);
@@ -2315,7 +2589,7 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public static synchronized int H5Fclose(long file_id) throws HDF5LibraryException {
+ public static int H5Fclose(long file_id) throws HDF5LibraryException {
if (file_id < 0)
return 0; // throw new HDF5LibraryException("Negative ID");;
--openFileCount;
@@ -2342,7 +2616,7 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public static synchronized long H5Fopen(String name, int flags, long access_id) throws HDF5LibraryException,
+ public static long H5Fopen(String name, int flags, long access_id) throws HDF5LibraryException,
NullPointerException {
long id = _H5Fopen(name, flags, access_id);
++openFileCount;
@@ -2362,7 +2636,7 @@ public class H5 implements java.io.Serializable {
* - Error from the HDF-5 Library.
* @return a new file identifier if successful
**/
- public static synchronized long H5Freopen(long file_id) throws HDF5LibraryException {
+ public static long H5Freopen(long file_id) throws HDF5LibraryException {
long id = _H5Freopen(file_id);
++openFileCount;
return id;
@@ -2509,6 +2783,19 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native int H5Fget_intent(long file_id) throws HDF5LibraryException;
+ /**
+ * H5Fget_fileno retrieves the "file number" for an open file.
+ *
+ * @param file_id
+ * IN: File identifier for a currently-open HDF5 file
+ *
+ * @return the unique file number for the file.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native long H5Fget_fileno(long file_id) throws HDF5LibraryException;
+
/**
* H5Fget_mdc_hit_rate queries the metadata cache of the target file to obtain its hit rate (cache hits / (cache
* hits + cache misses)) since the last time hit rate statistics were reset.
@@ -2617,9 +2904,29 @@ public class H5 implements java.io.Serializable {
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
+ *
+ * @deprecated As of HDF5 1.10.5 in favor of H5Fis_accessible.
**/
+ @Deprecated
public synchronized static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException;
+ /**
+ * H5Fis_accessible determines if the file can be opened with the given fapl.
+ *
+ * @param name
+ * IN: File name to check.
+ * @param file_id
+ * IN: File identifier for a currently-open HDF5 file
+ *
+ * @return true if file is accessible, false if not.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public synchronized static native boolean H5Fis_accessible(String name, long file_id) throws HDF5LibraryException, NullPointerException;
+
/**
* H5Fmount mounts the file specified by child_id onto the group specified by loc_id and name using the mount
* properties plist_id.
@@ -2750,21 +3057,66 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Fget_mdc_logging_status(long file_id, boolean[] mdc_logging_status)
throws HDF5LibraryException, NullPointerException;
+ /**
+ * H5Fget_dset_no_attrs_hint gets the file-level setting to create minimized dataset object headers.
+ *
+ * @param file_id
+ * IN: Identifier of the target file.
+ *
+ * @return true if the file-level is set to create minimized dataset object headers, false if not.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native boolean H5Fget_dset_no_attrs_hint(long file_id)
+ throws HDF5LibraryException;
+
+
+ /**
+ * H5Fset_dset_no_attrs_hint sets the file-level setting to create minimized dataset object headers.
+ *
+ * @param file_id
+ * IN: Identifier of the target file.
+ * @param minimize
+ * the minimize hint setting
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native void H5Fset_dset_no_attrs_hint(long file_id, boolean minimize)
+ throws HDF5LibraryException;
+
+
+ /**
+ * H5Fset_libver_bounds sets a different low and high bounds while a file is open.
+ *
+ * @param file_id
+ * IN: Identifier of the target file.
+ * @param low
+ * IN: The earliest version of the library that will be used for writing objects
+ * @param high
+ * IN: The latest version of the library that will be used for writing objects.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native void H5Fset_libver_bounds(long file_id, int low, int high)
+ throws HDF5LibraryException;
+
// /////// unimplemented ////////
- // H5_DLL herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
- // H5_DLL herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
+ // herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
+ // herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
// ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len);
// herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info);
// ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/);
- // H5_DLL herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high);
- // H5_DLL herr_t H5Fformat_convert(hid_t fid);
- // H5_DLL herr_t H5Freset_page_buffering_stats(hid_t file_id);
- // H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
+ // herr_t H5Fformat_convert(hid_t fid);
+ // herr_t H5Freset_page_buffering_stats(hid_t file_id);
+ // herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
// unsigned hits[2], unsigned misses[2], unsigned evictions[2], unsigned bypasses[2]);
- // H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size);
+ // herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size);
// #ifdef H5_HAVE_PARALLEL
- // H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag);
- // H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
+ // herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag);
+ // herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
// #endif /* H5_HAVE_PARALLEL */
// /**
@@ -2824,25 +3176,25 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// /////// unimplemented ////////
- // H5_DLL hid_t H5FDregister(const H5FD_class_t *cls);
- // H5_DLL herr_t H5FDunregister(hid_t driver_id);
- // H5_DLL H5FD_t *H5FDopen(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr);
- // H5_DLL herr_t H5FDclose(H5FD_t *file);
- // H5_DLL int H5FDcmp(const H5FD_t *f1, const H5FD_t *f2);
- // H5_DLL int H5FDquery(const H5FD_t *f, unsigned long *flags);
- // H5_DLL haddr_t H5FDalloc(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size);
- // H5_DLL herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size);
- // H5_DLL haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type);
- // H5_DLL herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa);
- // H5_DLL haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type);
- // H5_DLL herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle);
- // H5_DLL herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/);
- // H5_DLL herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf);
- // H5_DLL herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
- // H5_DLL herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
- // H5_DLL herr_t H5FDlock(H5FD_t *file, hbool_t rw);
- // H5_DLL herr_t H5FDunlock(H5FD_t *file);
- // H5_DLL herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/);
+ // hid_t H5FDregister(const H5FD_class_t *cls);
+ // herr_t H5FDunregister(hid_t driver_id);
+ // H5FD_t *H5FDopen(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr);
+ // herr_t H5FDclose(H5FD_t *file);
+ // int H5FDcmp(const H5FD_t *f1, const H5FD_t *f2);
+ // int H5FDquery(const H5FD_t *f, unsigned long *flags);
+ // haddr_t H5FDalloc(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size);
+ // herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size);
+ // haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type);
+ // herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa);
+ // haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type);
+ // herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle);
+ // herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/);
+ // herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf);
+ // herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
+ // herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
+ // herr_t H5FDlock(H5FD_t *file, hbool_t rw);
+ // herr_t H5FDunlock(H5FD_t *file);
+ // herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/);
// ////////////////////////////////////////////////////////////
// //
@@ -3019,8 +3371,8 @@ public class H5 implements java.io.Serializable {
* OUT: Names of all objects under the group, name.
* @param objTypes
* OUT: Types of all objects under the group, name.
- * @param objRef
- * OUT: Reference number of all objects under the group, name.
+ * @param tokens
+ * OUT: Object token of all objects under the group, name.
*
* @return the number of items found
*
@@ -3030,26 +3382,26 @@ public class H5 implements java.io.Serializable {
* - name is null.
*/
public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes,
- long[] objRef) throws HDF5LibraryException, NullPointerException {
+ H5O_token_t[] tokens) throws HDF5LibraryException, NullPointerException {
if (objNames == null) {
throw new NullPointerException("H5Gget_obj_info_all(): name array is null");
}
- return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, objRef, HDF5Constants.H5_INDEX_NAME);
+ return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, tokens, HDF5Constants.H5_INDEX_NAME);
}
public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype,
- int[] ltype, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException {
- return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, ref, indx_type, -1);
+ int[] ltype, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException {
+ return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, tokens, indx_type, -1);
}
public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype,
- int[] ltype, long[] fno, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException {
- return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, -1);
+ int[] ltype, long[] fno, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException {
+ return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, indx_type, -1);
}
public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype,
- int[] ltype, long[] fno, long[] ref, int indx_type, int indx_order) throws HDF5LibraryException,
+ int[] ltype, long[] fno, H5O_token_t[] tokens, int indx_type, int indx_order) throws HDF5LibraryException,
NullPointerException {
if (oname == null) {
throw new NullPointerException("H5Gget_obj_info_full(): name array is null");
@@ -3071,7 +3423,7 @@ public class H5 implements java.io.Serializable {
ltype = new int[otype.length];
if (fno == null)
- fno = new long[ref.length];
+ fno = new long[tokens.length];
if (indx_type < 0)
indx_type = HDF5Constants.H5_INDEX_NAME;
@@ -3079,13 +3431,13 @@ public class H5 implements java.io.Serializable {
if (indx_order < 0)
indx_order = HDF5Constants.H5_ITER_INC;
- int status = H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type,
+ int status = H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, oname.length, indx_type,
indx_order);
return status;
}
private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype,
- int[] ltype, long[] fno, long[] ref, int n, int indx_type, int indx_order) throws HDF5LibraryException,
+ int[] ltype, long[] fno, H5O_token_t[] tokens, int n, int indx_type, int indx_order) throws HDF5LibraryException,
NullPointerException;
/**
@@ -3140,8 +3492,8 @@ public class H5 implements java.io.Serializable {
* OUT: Types of all objects under the group, name.
* @param lnkTypes
* OUT: Types of all links under the group, name.
- * @param objRef
- * OUT: Reference number of all objects under the group, name.
+ * @param objToken
+ * OUT: Object token of all objects under the group, name.
* @param objMax
* IN: Maximum number of all objects under the group, name.
*
@@ -3153,7 +3505,7 @@ public class H5 implements java.io.Serializable {
* - name is null.
*/
public synchronized static int H5Gget_obj_info_max(long loc_id, String[] objNames, int[] objTypes, int[] lnkTypes,
- long[] objRef, long objMax) throws HDF5LibraryException, NullPointerException {
+ H5O_token_t[] objToken, long objMax) throws HDF5LibraryException, NullPointerException {
if (objNames == null) {
throw new NullPointerException("H5Gget_obj_info_max(): name array is null");
}
@@ -3178,11 +3530,11 @@ public class H5 implements java.io.Serializable {
throw new HDF5LibraryException("H5Gget_obj_info_max(): name and type array sizes are different");
}
- return H5Gget_obj_info_max(loc_id, objNames, objTypes, lnkTypes, objRef, objMax, objNames.length);
+ return H5Gget_obj_info_max(loc_id, objNames, objTypes, lnkTypes, objToken, objMax, objNames.length);
}
private synchronized static native int H5Gget_obj_info_max(long loc_id, String[] oname, int[] otype, int[] ltype,
- long[] ref, long amax, int n) throws HDF5LibraryException, NullPointerException;
+ H5O_token_t[] tokens, long amax, int n) throws HDF5LibraryException, NullPointerException;
/**
* H5Gn_members report the number of objects in a Group. The 'objects' include everything that will be visited by
@@ -3294,7 +3646,7 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// //
- // H5I: HDF5 1.8 Identifier Interface API Functions //
+ // H5I: HDF5 Identifier Interface API Functions //
// //
// ////////////////////////////////////////////////////////////
@@ -3450,12 +3802,20 @@ public class H5 implements java.io.Serializable {
// hid_t H5Iregister(H5I_type_t type, const void *object);
+ // typedef herr_t (*H5I_free_t)(void *);
// H5I_type_t H5Iregister_type(size_t hash_size, unsigned reserved, H5I_free_t free_func);
// void *H5Iremove_verify(hid_t id, H5I_type_t id_type);
+ // Type of the function to compare objects & keys
+ // typedef int (*H5I_search_func_t)(void *obj, hid_t id, void *key);
// void *H5Isearch(H5I_type_t type, H5I_search_func_t func, void *key);
+ // Type of the H5Iiterate callback function
+ // typedef herr_t (*H5I_iterate_func_t)(hid_t id, void *udata);
+ // herr_t H5Iiterate(H5I_type_t type, H5I_iterate_func_t op, void *op_data);
+
+
// //////////////////////////////////////////////////////////////////
// H5L: Link Interface Functions //
// //////////////////////////////////////////////////////////////////
@@ -3766,8 +4126,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public synchronized static native int H5Literate(long grp_id, int idx_type, int order, long idx, H5L_iterate_cb op,
- H5L_iterate_t op_data) throws HDF5LibraryException;
+ public synchronized static native int H5Literate(long grp_id, int idx_type, int order, long idx, H5L_iterate_t op,
+ H5L_iterate_opdata_t op_data) throws HDF5LibraryException;
/**
* H5Literate_by_name iterates through links in a group.
@@ -3798,7 +4158,7 @@ public class H5 implements java.io.Serializable {
* - group_name is null.
**/
public synchronized static native int H5Literate_by_name(long grp_id, String group_name, int idx_type, int order,
- long idx, H5L_iterate_cb op, H5L_iterate_t op_data, long lapl_id) throws HDF5LibraryException,
+ long idx, H5L_iterate_t op, H5L_iterate_opdata_t op_data, long lapl_id) throws HDF5LibraryException,
NullPointerException;
/**
@@ -3845,8 +4205,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public synchronized static native int H5Lvisit(long grp_id, int idx_type, int order, H5L_iterate_cb op,
- H5L_iterate_t op_data) throws HDF5LibraryException;
+ public synchronized static native int H5Lvisit(long grp_id, int idx_type, int order, H5L_iterate_t op,
+ H5L_iterate_opdata_t op_data) throws HDF5LibraryException;
/**
* H5Lvisit_by_name recursively visits all links starting from a specified group.
@@ -3875,7 +4235,7 @@ public class H5 implements java.io.Serializable {
* - group_name is null.
**/
public synchronized static native int H5Lvisit_by_name(long loc_id, String group_name, int idx_type, int order,
- H5L_iterate_cb op, H5L_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException;
+ H5L_iterate_t op, H5L_iterate_opdata_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException;
/**
@@ -4088,6 +4448,52 @@ public class H5 implements java.io.Serializable {
public synchronized static native H5O_info_t H5Oget_info(long loc_id, int fields) throws HDF5LibraryException,
NullPointerException;
+ /**
+ * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name.
+ *
+ * @param loc_id
+ * IN: File or group identifier specifying location of group in which object is located
+ * @param name
+ * IN: Relative name of group
+ * @param lapl_id
+ * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as
+ * H5P_DEFAULT.)
+ *
+ * @return object information
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public static H5O_info_t H5Oget_info_by_name(long loc_id, String name, long lapl_id)
+ throws HDF5LibraryException, NullPointerException {
+ return H5Oget_info_by_name(loc_id, name, HDF5Constants.H5O_INFO_ALL, lapl_id);
+ }
+
+ /**
+ * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name.
+ *
+ * @param loc_id
+ * IN: File or group identifier specifying location of group in which object is located
+ * @param name
+ * IN: Relative name of group
+ * @param fields
+ * IN: Object fields to select
+ * @param lapl_id
+ * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as
+ * H5P_DEFAULT.)
+ *
+ * @return object information
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public synchronized static native H5O_info_t H5Oget_info_by_name(long loc_id, String name, int fields, long lapl_id)
+ throws HDF5LibraryException, NullPointerException;
+
/**
* H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position.
*
@@ -4147,7 +4553,47 @@ public class H5 implements java.io.Serializable {
int order, long n, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException;
/**
- * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name.
+ * H5Oget_native_info retrieves the native HDF5-specific metadata for an HDF5 object specified by an identifier.
+ * Native HDF5-specific metadata includes things like object header information and object storage layout information.
+ *
+ * @param loc_id
+ * IN: Identifier for target object
+ *
+ * @return object information
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public static H5O_native_info_t H5Oget_native_info(long loc_id) throws HDF5LibraryException,
+ NullPointerException {
+ return H5Oget_native_info(loc_id, HDF5Constants.H5O_NATIVE_INFO_ALL);
+ }
+
+ /**
+ * H5Oget_native_info retrieves the native HDF5-specific metadata for an HDF5 object specified by an identifier.
+ * Native HDF5-specific metadata includes things like object header information and object storage layout information.
+ *
+ * @param loc_id
+ * IN: Identifier for target object
+ * @param fields
+ * IN: Object fields to select
+ *
+ * @return object information
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public synchronized static native H5O_native_info_t H5Oget_native_info(long loc_id, int fields) throws HDF5LibraryException,
+ NullPointerException;
+
+ /**
+ * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object
+ * by location and relative name. Native HDF5-specific metadata includes things like object header information and
+ * object storage layout information.
*
* @param loc_id
* IN: File or group identifier specifying location of group in which object is located
@@ -4164,13 +4610,15 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public static H5O_info_t H5Oget_info_by_name(long loc_id, String name, long lapl_id)
+ public static H5O_native_info_t H5Oget_native_info_by_name(long loc_id, String name, long lapl_id)
throws HDF5LibraryException, NullPointerException {
- return H5Oget_info_by_name(loc_id, name, HDF5Constants.H5O_INFO_ALL, lapl_id);
+ return H5Oget_native_info_by_name(loc_id, name, HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id);
}
/**
- * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name.
+ * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object
+ * by location and relative name. Native HDF5-specific metadata includes things like object header information and
+ * object storage layout information.
*
* @param loc_id
* IN: File or group identifier specifying location of group in which object is located
@@ -4189,9 +4637,71 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public synchronized static native H5O_info_t H5Oget_info_by_name(long loc_id, String name, int fields, long lapl_id)
+ public synchronized static native H5O_native_info_t H5Oget_native_info_by_name(long loc_id, String name, int fields, long lapl_id)
throws HDF5LibraryException, NullPointerException;
+ /**
+ * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object
+ * by an index position. Native HDF5-specific metadata includes things like object header information and
+ * object storage layout information.
+ *
+ * @param loc_id
+ * IN: File or group identifier
+ * @param group_name
+ * IN: Name of group, relative to loc_id, in which object is located
+ * @param idx_type
+ * IN: Type of index by which objects are ordered
+ * @param order
+ * IN: Order of iteration within index
+ * @param n
+ * IN: Object to open
+ * @param lapl_id
+ * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as
+ * H5P_DEFAULT.)
+ *
+ * @return object information
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public static H5O_native_info_t H5Oget_native_info_by_idx(long loc_id, String group_name, int idx_type,
+ int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException {
+ return H5Oget_native_info_by_idx(loc_id, group_name, idx_type, order, n, HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id);
+ }
+
+ /**
+ * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object
+ * by an index position. Native HDF5-specific metadata includes things like object header information and
+ * object storage layout information.
+ *
+ * @param loc_id
+ * IN: File or group identifier
+ * @param group_name
+ * IN: Name of group, relative to loc_id, in which object is located
+ * @param idx_type
+ * IN: Type of index by which objects are ordered
+ * @param order
+ * IN: Order of iteration within index
+ * @param n
+ * IN: Object to open
+ * @param fields
+ * IN: Object fields to select
+ * @param lapl_id
+ * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as
+ * H5P_DEFAULT.)
+ *
+ * @return object information
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public synchronized static native H5O_native_info_t H5Oget_native_info_by_idx(long loc_id, String group_name, int idx_type,
+ int order, long n, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException;
+
/**
* H5Olink creates a new hard link to an object in an HDF5 file.
*
@@ -4261,7 +4771,7 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public static int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data)
+ public static int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_t op, H5O_iterate_opdata_t op_data)
throws HDF5LibraryException, NullPointerException {
return H5Ovisit(obj_id, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL);
}
@@ -4290,8 +4800,8 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public synchronized static native int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_cb op,
- H5O_iterate_t op_data, int fields) throws HDF5LibraryException, NullPointerException;
+ public synchronized static native int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_t op,
+ H5O_iterate_opdata_t op_data, int fields) throws HDF5LibraryException, NullPointerException;
/**
* H5Ovisit_by_name recursively visits all objects starting from a specified object.
@@ -4320,7 +4830,7 @@ public class H5 implements java.io.Serializable {
* - name is null.
**/
public static int H5Ovisit_by_name(long loc_id, String obj_name, int idx_type, int order,
- H5O_iterate_cb op, H5O_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException {
+ H5O_iterate_t op, H5O_iterate_opdata_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException {
return H5Ovisit_by_name(loc_id, obj_name, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL, lapl_id);
}
@@ -4353,7 +4863,7 @@ public class H5 implements java.io.Serializable {
* - name is null.
**/
public synchronized static native int H5Ovisit_by_name(long loc_id, String obj_name, int idx_type, int order,
- H5O_iterate_cb op, H5O_iterate_t op_data, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException;
+ H5O_iterate_t op, H5O_iterate_opdata_t op_data, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException;
/**
@@ -4395,21 +4905,22 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Oincr_refcount(long object_id) throws HDF5LibraryException;
/**
- * H5Oopen_by_addr opens a group, dataset, or named datatype using its address within an HDF5 file.
+ * H5Oopen_by_token opens a group, dataset, or named datatype using its object token within an HDF5 file.
*
* @param loc_id IN: File or group identifier
- * @param addr IN: Object's address in the file
+ * @param token IN: Object's token in the file
*
* @return an object identifier for the opened object
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
- public static long H5Oopen_by_addr(long loc_id, long addr) throws HDF5LibraryException {
- long id = _H5Oopen_by_addr(loc_id, addr);
+ public static long H5Oopen_by_token(long loc_id, H5O_token_t token) throws HDF5LibraryException {
+ long id = _H5Oopen_by_token(loc_id, token);
+
return id;
}
- private synchronized static native long _H5Oopen_by_addr(long loc_id, long addr)
+ private synchronized static native long _H5Oopen_by_token(long loc_id, H5O_token_t token)
throws HDF5LibraryException, NullPointerException;
/**
@@ -4464,10 +4975,15 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException;
+ public synchronized static native void H5Odisable_mdc_flushes(long object_id);
+ public synchronized static native void H5Oenable_mdc_flushes(long object_id);
+ public synchronized static native boolean H5Oare_mdc_flushes_disabled(long object_id);
+
// /////// unimplemented ////////
- // H5_DLL herr_t H5Odisable_mdc_flushes(hid_t object_id);
- // H5_DLL herr_t H5Oenable_mdc_flushes(hid_t object_id);
- // H5_DLL herr_t H5Oare_mdc_flushes_disabled(hid_t object_id, hbool_t *are_disabled);
+ // herr_t H5Otoken_cmp(hid_t loc_id, const H5O_token_t *token1, const H5O_token_t *token2,
+ // int *cmp_value);
+ // herr_t H5Otoken_to_str(hid_t loc_id, const H5O_token_t *token, char **token_str);
+ // herr_t H5Otoken_from_str(hid_t loc_id, const char *token_str, H5O_token_t *token);
// ////////////////////////////////////////////////////////////
// //
@@ -4736,6 +5252,27 @@ public class H5 implements java.io.Serializable {
private synchronized static native long _H5Pcopy(long plist) throws HDF5LibraryException;
+ // Define property list class callback function pointer types
+ // typedef herr_t (*H5P_cls_create_func_t)(hid_t prop_id, void *create_data);
+ // typedef herr_t (*H5P_cls_copy_func_t)(hid_t new_prop_id, hid_t old_prop_id, void *copy_data);
+ // typedef herr_t (*H5P_cls_close_func_t)(hid_t prop_id, void *close_data);
+
+ // Define property list callback function pointer types
+ // typedef herr_t (*H5P_prp_cb1_t)(const char *name, size_t size, void *value);
+ // typedef herr_t (*H5P_prp_cb2_t)(hid_t prop_id, const char *name, size_t size, void *value);
+ // typedef H5P_prp_cb1_t H5P_prp_create_func_t;
+ // typedef H5P_prp_cb2_t H5P_prp_set_func_t;
+ // typedef H5P_prp_cb2_t H5P_prp_get_func_t;
+ // typedef herr_t (*H5P_prp_encode_func_t)(const void *value, void **buf, size_t *size);
+ // typedef herr_t (*H5P_prp_decode_func_t)(const void **buf, void *value);
+ // typedef H5P_prp_cb2_t H5P_prp_delete_func_t;
+ // typedef H5P_prp_cb1_t H5P_prp_copy_func_t;
+ // typedef int (*H5P_prp_compare_func_t)(const void *value1, const void *value2, size_t size);
+ // typedef H5P_prp_cb1_t H5P_prp_close_func_t;
+
+ // Define property list iteration function type
+ // typedef herr_t (*H5P_iterate_t)(hid_t id, const char *name, void *iter_data);
+
public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException {
long id = _H5Pcreate_class_nocb(parent_class, name);
return id;
@@ -5894,6 +6431,11 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close)
throws HDF5LibraryException;
+ // ///// unimplemented /////
+ // herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info);
+ // herr_t H5Pget_vol_id(hid_t plist_id, hid_t *vol_id);
+ // herr_t H5Pget_vol_info(hid_t plist_id, void **vol_info);
+
// Dataset creation property list (DCPL) routines //
/**
@@ -6349,8 +6891,6 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException,
NullPointerException;
- // /////// Dataset creation property list (DCPL) routines ///////
-
/**
* H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
*
@@ -6379,6 +6919,38 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException;
+ /**
+ * H5Pget_dset_no_attrs_hint accesses the flag for whether or not datasets created by the given dcpl
+ * will be created with a "minimized" object header.
+ *
+ * @param dcpl_id
+ * IN: Dataset creation property list
+ *
+ * @return true if the given dcpl is set to create minimized dataset object headers, false if not.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native boolean H5Pget_dset_no_attrs_hint(long dcpl_id)
+ throws HDF5LibraryException;
+
+
+ /**
+ * H5Pset_dset_no_attrs_hint sets the dcpl to minimize (or explicitly to not minimized) dataset object
+ * headers upon creation.
+ *
+ * @param dcpl_id
+ * IN: Dataset creation property list
+ *
+ * @param minimize
+ * the minimize hint setting
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native void H5Pset_dset_no_attrs_hint(long dcpl_id, boolean minimize)
+ throws HDF5LibraryException;
+
// /////// Dataset access property list (DAPL) routines ///////
/**
@@ -7071,42 +7643,14 @@ public class H5 implements java.io.Serializable {
* @param ocp_plist_id
* IN: Object copy property list identifier
* @param copy_options
- * IN: Copy option(s) to be set
- *
- * @exception HDF5LibraryException
- * - Error from the HDF-5 Library.
- *
- **/
- public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options)
- throws HDF5LibraryException;
-
- // /////// Other/Older property list routines ///////
-
- /**
- * H5Pget_version retrieves the version information of various objects for a file creation property list.
- *
- * @param plist
- * IN: Identifier of the file creation property list.
- * @param version_info
- * OUT: version information.
- *
- * <pre>
- * version_info[0] = boot // boot block version number
- * version_info[1] = freelist // global freelist version
- * version_info[2] = stab // symbol tabl version number
- * version_info[3] = shhdr // shared object header version
- * </pre>
- * @return a non-negative value, with the values of version_info initialized, if successful
+ * IN: Copy option(s) to be set
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
- * @exception NullPointerException
- * - version_info is null.
- * @exception IllegalArgumentException
- * - version_info is illegal.
+ *
**/
- public synchronized static native int H5Pget_version(long plist, int[] version_info) throws HDF5LibraryException,
- NullPointerException, IllegalArgumentException;
+ public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options)
+ throws HDF5LibraryException;
// /////// file drivers property list routines ///////
@@ -7160,6 +7704,10 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Pset_fapl_family(long fapl_id, long memb_size, long memb_fapl_id)
throws HDF5LibraryException, NullPointerException;
+ public synchronized static native int H5Pset_fapl_hdfs(long fapl_id, H5FD_hdfs_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native H5FD_hdfs_fapl_t H5Pget_fapl_hdfs(long fapl_id) throws HDF5LibraryException, NullPointerException;
+
/**
* H5Pget_fapl_multi Sets up use of the multi I/O driver.
*
@@ -7244,6 +7792,10 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Pset_fapl_windows(long fapl_id) throws HDF5LibraryException, NullPointerException;
+ public synchronized static native int H5Pset_fapl_ros3(long fapl_id, H5FD_ros3_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id) throws HDF5LibraryException, NullPointerException;
+
// /////// unimplemented ////////
// Generic property list routines //
@@ -7267,13 +7819,13 @@ public class H5 implements java.io.Serializable {
// herr_t H5Pget_core_write_tracking(hid_t fapl_id, hbool_t *is_enabled, size_t *page_size);
// #ifdef H5_HAVE_PARALLEL
// herr_t H5Pset_all_coll_metadata_ops(hid_t accpl_id, hbool_t is_collective);
- // H5_DLL herr_t H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective);
+ // herr_t H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective);
// herr_t H5Pset_coll_metadata_write(hid_t fapl_id, hbool_t is_collective);
// herr_t H5Pget_coll_metadata_write(hid_t fapl_id, hbool_t *is_collective);
// #endif /* H5_HAVE_PARALLEL */
- // H5_DLL herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr);
- // H5_DLL herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/);
- // H5_DLL herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per);
+ // herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr);
+ // herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/);
+ // herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per);
// herr_t H5Pget_page_buffer_size(hid_t fapl_id, size_t *buf_size, unsigned *min_meta_perc, unsigned *min_raw_perc);
// herr_t H5Pset_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t func, void *user_data);
// herr_t H5Pget_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t *func, void **user_data);
@@ -7296,9 +7848,9 @@ public class H5 implements java.io.Serializable {
// herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data)
// herr_t H5Pset_type_conv_cb( hid_t plist, H5T_conv_except_func_t func, void *op_data)
// #ifdef H5_HAVE_PARALLEL
- // H5_DLL herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode);
- // H5_DLL herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode);
- // H5_DLL herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause);
+ // herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode);
+ // herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode);
+ // herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause);
// #endif /* H5_HAVE_PARALLEL */
// Link creation property list (LCPL) routines //
@@ -7444,6 +7996,331 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native int H5PLsize() throws HDF5LibraryException;
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5R: HDF5 1.12 Reference API Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // Constructors //
+
+ /**
+ * H5Rcreate_object creates a reference pointing to the object named name located at loc id.
+ *
+ * @param loc_id
+ * IN: Location identifier used to locate the object being pointed to.
+ * @param name
+ * IN: Name of object at location loc_id.
+ * @param access_id
+ * IN: Object access identifier to the object being pointed to.
+ *
+ * @return the reference (byte[]) if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcreate_object(long loc_id, String name, long access_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rcreate_region creates the reference, pointing to the region represented by
+ * space id within the object named name located at loc id.
+ *
+ * @param loc_id
+ * IN: Location identifier used to locate the object being pointed to.
+ * @param name
+ * IN: Name of object at location loc_id.
+ * @param space_id
+ * IN: Identifies the dataset region that a dataset region reference points to.
+ * @param access_id
+ * IN: Object access identifier to the object being pointed to.
+ *
+ * @return the reference (byte[]) if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcreate_region(long loc_id, String name, long space_id, long access_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rcreate_attr creates the reference, pointing to the attribute named attr name
+ * and attached to the object named name located at loc id.
+ *
+ * @param loc_id
+ * IN: Location identifier used to locate the object being pointed to.
+ * @param name
+ * IN: Name of object at location loc_id.
+ * @param attr_name
+ * IN: Name of the attribute within the object.
+ * @param access_id
+ * IN: Object access identifier to the object being pointed to.
+ *
+ * @return the reference (byte[]) if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name, long access_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rdestroy destroys a reference and releases resources.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native void H5Rdestroy(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Info //
+
+ /**
+ * H5Rget_type retrieves the type of a reference.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return a valid reference type if successful; otherwise returns H5R UNKNOWN.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native int H5Rget_type(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Requal determines whether two references point to the same object, region or attribute.
+ *
+ * @param ref1_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param ref2_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return true if equal, else false
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native boolean H5Requal(byte[] ref1_ptr, byte[] ref2_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rcopy creates a copy of an existing reference.
+ *
+ * @param src_ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return a valid copy of the reference (byte[]) if successful.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Dereference //
+
+ /**
+ * H5Ropen_object opens that object and returns an identifier.
+ * The object opened with this function should be closed when it is no longer needed
+ * so that resource leaks will not develop. Use the appropriate close function such
+ * as H5Oclose or H5Dclose for datasets.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ * @param oapl_id
+ * IN: An object access property list identifier for the reference. The access property
+ * property list must be of the same type as the object being referenced,
+ * that is a group or dataset property list.
+ *
+ * @return a valid identifier if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Ropen region creates a copy of the dataspace of the dataset pointed to by a region reference,
+ * ref ptr, and defines a selection matching the selection pointed to by ref ptr within the dataspace copy.
+ * Use H5Sclose to release the dataspace identifier returned by this function when the identifier is no longer needed.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ * @param oapl_id
+ * IN: An object access property list identifier for the reference. The access property
+ * property list must be of the same type as the object being referenced,
+ * that is a group or dataset property list.
+ *
+ * @return a valid dataspace identifier if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Ropen_attr opens the attribute attached to the object and returns an identifier.
+ * The attribute opened with this function should be closed with H5Aclose when it is no longer needed
+ * so that resource leaks will not develop.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ * @param aapl_id
+ * IN: An attribute access property list identifier for the reference. The access property
+ * property list must be of the same type as the object being referenced,
+ * that is a group or dataset property list.
+ *
+ * @return a valid attribute identifier if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Get type //
+
+ /**
+ * H5Rget obj type3 retrieves the type of the referenced object pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ *
+ * @return Returns the object type
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Get name //
+
+ /**
+ * H5Rget_file_name retrieves the file name for the object, region or attribute reference pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return Returns the file name of the reference
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native String H5Rget_file_name(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rget_obj_name retrieves the object name for the object, region or attribute reference pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ *
+ * @return Returns the object name of the reference
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native String H5Rget_obj_name(byte[] ref_ptr, long rapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rget_attr_name retrieves the attribute name for the object, region or attribute reference pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return Returns the attribute name of the reference
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native String H5Rget_attr_name(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
// ////////////////////////////////////////////////////////////
// //
// H5R: HDF5 1.8 Reference API Functions //
@@ -8213,16 +9090,17 @@ public class H5 implements java.io.Serializable {
// /////// unimplemented ////////
// #ifdef NEW_HYPERSLAB_API
- // H5_DLL hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
+ // hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
// const hsize_t start[],
// const hsize_t _stride[],
// const hsize_t count[],
// const hsize_t _block[]);
- // H5_DLL herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
+ // herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
// hid_t space2_id);
- // H5_DLL hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
+ // hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
// hid_t space2_id);
// #endif /* NEW_HYPERSLAB_API */
+ // herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id);
@@ -9585,6 +10463,26 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native int H5Tpack(long type_id) throws HDF5LibraryException;
+ /**
+ * H5Treclaim reclaims buffer used for VL data.
+ *
+ * @param type_id
+ * Identifier of the datatype.
+ * @param space_id
+ * Identifier of the dataspace.
+ * @param xfer_plist_id
+ * Identifier of a transfer property list for this I/O operation.
+ * @param buf
+ * Buffer with data to be reclaimed.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - buf is null.
+ **/
+ public synchronized static native void H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
/**
* H5Tvlen_create creates a new variable-length (VL) dataype.
*
@@ -9641,6 +10539,28 @@ public class H5 implements java.io.Serializable {
// H5T_conv_t func)
// throws HDF5LibraryException, NullPointerException;
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5VL: VOL Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ /// VOL Connector Functionality
+ public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id);
+ public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id);
+ public synchronized static native boolean H5VLis_connector_registered_by_name(String name);
+ public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value);
+ public synchronized static native long H5VLget_connector_id(long object_id);
+ public synchronized static native long H5VLget_connector_id_by_name(String name);
+ public synchronized static native long H5VLget_connector_id_by_value(int connector_value);
+ public synchronized static native String H5VLget_connector_name(long object_id);
+ public synchronized static native void H5VLclose(long connector_id);
+ public synchronized static native void H5VLunregister_connector(long connector_id);
+
+ // /////// unimplemented ////////
+ // hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id);
+
+
// ////////////////////////////////////////////////////////////
// //
// H5Z: Filter Interface Functions //
@@ -9653,9 +10573,9 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException;
-}
+ // /////// unimplemented ////////
-// /////// unimplemented ////////
+ // herr_t H5Zregister(const void *cls);
-// herr_t H5Zregister(const void *cls);
+}
diff --git a/source/java/hdf/hdf5lib/HDF5Constants.java b/source/java/hdf/hdf5lib/HDF5Constants.java
index 7eddac095dcb9c0b00b6fcf98b5aab69bd7f96cc..b3901836e2886e33bdab478866f032c0f3d67692 100644
--- a/source/java/hdf/hdf5lib/HDF5Constants.java
+++ b/source/java/hdf/hdf5lib/HDF5Constants.java
@@ -14,6 +14,8 @@
package hdf.hdf5lib;
+import hdf.hdf5lib.structs.H5O_token_t;
+
/**
* /** This class contains C constants and enumerated types of HDF5 library. The
* values of these constants are obtained from the library by calling J2C(int
@@ -121,6 +123,7 @@ public class HDF5Constants {
public static final long H5E_CANTDEC = H5E_CANTDEC();
public static final long H5E_CANTDECODE = H5E_CANTDECODE();
public static final long H5E_CANTDELETE = H5E_CANTDELETE();
+ public static final long H5E_CANTDELETEFILE = H5E_CANTDELETEFILE();
public static final long H5E_CANTENCODE = H5E_CANTENCODE();
public static final long H5E_CANTFLUSH = H5E_CANTFLUSH();
public static final long H5E_CANTFREE = H5E_CANTFREE();
@@ -190,10 +193,16 @@ public class HDF5Constants {
public static final long H5E_UNSUPPORTED = H5E_UNSUPPORTED();
public static final long H5E_VERSION = H5E_VERSION();
public static final long H5E_VFL = H5E_VFL();
+ public static final long H5E_VOL = H5E_VOL();
public static final long H5E_WALK_DOWNWARD = H5E_WALK_DOWNWARD();
public static final long H5E_WALK_UPWARD = H5E_WALK_UPWARD();
public static final long H5E_WRITEERROR = H5E_WRITEERROR();
+ private static final int H5ES_STATUS_IN_PROGRESS = H5ES_STATUS_IN_PROGRESS();
+ private static final int H5ES_STATUS_SUCCEED = H5ES_STATUS_SUCCEED();
+ private static final int H5ES_STATUS_FAIL = H5ES_STATUS_FAIL();
+ private static final int H5ES_STATUS_CANCELED = H5ES_STATUS_CANCELED();
+
public static final int H5F_ACC_CREAT = H5F_ACC_CREAT();
public static final int H5F_ACC_EXCL = H5F_ACC_EXCL();
public static final int H5F_ACC_RDONLY = H5F_ACC_RDONLY();
@@ -210,6 +219,7 @@ public class HDF5Constants {
public static final int H5F_LIBVER_EARLIEST = H5F_LIBVER_EARLIEST();
public static final int H5F_LIBVER_V18 = H5F_LIBVER_V18();
public static final int H5F_LIBVER_V110 = H5F_LIBVER_V110();
+ public static final int H5F_LIBVER_V112 = H5F_LIBVER_V112();
public static final int H5F_LIBVER_NBOUNDS = H5F_LIBVER_NBOUNDS();
public static final int H5F_LIBVER_LATEST = H5F_LIBVER_LATEST();
public static final int H5F_OBJ_ALL = H5F_OBJ_ALL();
@@ -238,6 +248,8 @@ public class HDF5Constants {
public static final long H5FD_SEC2 = H5FD_SEC2();
public static final long H5FD_STDIO = H5FD_STDIO();
public static final long H5FD_WINDOWS = H5FD_WINDOWS();
+ public static final long H5FD_ROS3 = H5FD_ROS3();
+ public static final long H5FD_HDFS = H5FD_HDFS();
public static final int H5FD_LOG_LOC_READ = H5FD_LOG_LOC_READ();
public static final int H5FD_LOG_LOC_WRITE = H5FD_LOG_LOC_WRITE();
public static final int H5FD_LOG_LOC_SEEK = H5FD_LOG_LOC_SEEK();
@@ -314,9 +326,9 @@ public class HDF5Constants {
public static final int H5I_GROUP = H5I_GROUP();
public static final int H5I_INVALID_HID = H5I_INVALID_HID();
public static final int H5I_NTYPES = H5I_NTYPES();
- public static final int H5I_REFERENCE = H5I_REFERENCE();
public static final int H5I_UNINIT = H5I_UNINIT();
public static final int H5I_VFL = H5I_VFL();
+ public static final int H5I_VOL = H5I_VOL();
public static final int H5L_TYPE_ERROR = H5L_TYPE_ERROR();
public static final int H5L_TYPE_HARD = H5L_TYPE_HARD();
@@ -333,9 +345,10 @@ public class HDF5Constants {
public static final int H5O_INFO_BASIC = H5O_INFO_BASIC();
public static final int H5O_INFO_TIME = H5O_INFO_TIME();
public static final int H5O_INFO_NUM_ATTRS = H5O_INFO_NUM_ATTRS();
- public static final int H5O_INFO_HDR = H5O_INFO_HDR();
- public static final int H5O_INFO_META_SIZE = H5O_INFO_META_SIZE();
public static final int H5O_INFO_ALL = H5O_INFO_ALL();
+ public static final int H5O_NATIVE_INFO_HDR = H5O_NATIVE_INFO_HDR();
+ public static final int H5O_NATIVE_INFO_META_SIZE = H5O_NATIVE_INFO_META_SIZE();
+ public static final int H5O_NATIVE_INFO_ALL = H5O_NATIVE_INFO_ALL();
public static final int H5O_SHMESG_NONE_FLAG = H5O_SHMESG_NONE_FLAG();
public static final int H5O_SHMESG_SDSPACE_FLAG = H5O_SHMESG_SDSPACE_FLAG();
public static final int H5O_SHMESG_DTYPE_FLAG = H5O_SHMESG_DTYPE_FLAG();
@@ -348,6 +361,8 @@ public class HDF5Constants {
public static final int H5O_TYPE_DATASET = H5O_TYPE_DATASET();
public static final int H5O_TYPE_NAMED_DATATYPE = H5O_TYPE_NAMED_DATATYPE();
public static final int H5O_TYPE_NTYPES = H5O_TYPE_NTYPES();
+ public static final int H5O_MAX_TOKEN_SIZE = H5O_MAX_TOKEN_SIZE();
+ public static final H5O_token_t H5O_TOKEN_UNDEF = H5O_TOKEN_UNDEF();
public static final long H5P_ROOT = H5P_ROOT();
public static final long H5P_OBJECT_CREATE = H5P_OBJECT_CREATE();
@@ -367,6 +382,7 @@ public class HDF5Constants {
public static final long H5P_OBJECT_COPY = H5P_OBJECT_COPY();
public static final long H5P_LINK_CREATE = H5P_LINK_CREATE();
public static final long H5P_LINK_ACCESS = H5P_LINK_ACCESS();
+ public static final long H5P_VOL_INITIALIZE = H5P_VOL_INITIALIZE();
public static final long H5P_FILE_CREATE_DEFAULT = H5P_FILE_CREATE_DEFAULT();
public static final long H5P_FILE_ACCESS_DEFAULT = H5P_FILE_ACCESS_DEFAULT();
public static final long H5P_DATASET_CREATE_DEFAULT = H5P_DATASET_CREATE_DEFAULT();
@@ -382,20 +398,31 @@ public class HDF5Constants {
public static final long H5P_OBJECT_COPY_DEFAULT = H5P_OBJECT_COPY_DEFAULT();
public static final long H5P_LINK_CREATE_DEFAULT = H5P_LINK_CREATE_DEFAULT();
public static final long H5P_LINK_ACCESS_DEFAULT = H5P_LINK_ACCESS_DEFAULT();
+ public static final long H5P_VOL_INITIALIZE_DEFAULT = H5P_VOL_INITIALIZE_DEFAULT();
public static final int H5P_CRT_ORDER_TRACKED = H5P_CRT_ORDER_TRACKED();
public static final int H5P_CRT_ORDER_INDEXED = H5P_CRT_ORDER_INDEXED();
public static final long H5P_DEFAULT = H5P_DEFAULT();
public static final int H5PL_TYPE_ERROR = H5PL_TYPE_ERROR();
public static final int H5PL_TYPE_FILTER = H5PL_TYPE_FILTER();
+ public static final int H5PL_TYPE_VOL = H5PL_TYPE_VOL();
+ public static final int H5PL_TYPE_NONE = H5PL_TYPE_NONE();
public static final int H5PL_FILTER_PLUGIN = H5PL_FILTER_PLUGIN();
+ public static final int H5PL_VOL_PLUGIN = H5PL_VOL_PLUGIN();
public static final int H5PL_ALL_PLUGIN = H5PL_ALL_PLUGIN();
+ public static final int H5R_ATTR = H5R_ATTR();
public static final int H5R_BADTYPE = H5R_BADTYPE();
public static final int H5R_DATASET_REGION = H5R_DATASET_REGION();
+ public static final int H5R_DATASET_REGION1 = H5R_DATASET_REGION1();
+ public static final int H5R_DATASET_REGION2 = H5R_DATASET_REGION2();
public static final int H5R_MAXTYPE = H5R_MAXTYPE();
+ public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
public static final int H5R_OBJECT = H5R_OBJECT();
+ public static final int H5R_OBJECT1 = H5R_OBJECT1();
+ public static final int H5R_OBJECT2 = H5R_OBJECT2();
+
public static final int H5S_ALL = H5S_ALL();
public static final int H5S_MAX_RANK = H5S_MAX_RANK();
public static final int H5S_NO_CLASS = H5S_NO_CLASS();
@@ -590,6 +617,7 @@ public class HDF5Constants {
public static final long H5T_STD_I8LE = H5T_STD_I8LE();
public static final long H5T_STD_REF_DSETREG = H5T_STD_REF_DSETREG();
public static final long H5T_STD_REF_OBJ = H5T_STD_REF_OBJ();
+ public static final long H5T_STD_REF = H5T_STD_REF();
public static final long H5T_STD_U16BE = H5T_STD_U16BE();
public static final long H5T_STD_U16LE = H5T_STD_U16LE();
public static final long H5T_STD_U32BE = H5T_STD_U32BE();
@@ -624,6 +652,18 @@ public class HDF5Constants {
public static final long H5T_VARIABLE = H5T_VARIABLE();
public static final int H5T_VLEN = H5T_VLEN();
public static final int H5T_VL_T = H5T_VL_T();
+
+ public static final int H5VL_CAP_FLAG_NONE = H5VL_CAP_FLAG_NONE();
+ public static final int H5VL_CAP_FLAG_THREADSAFE = H5VL_CAP_FLAG_THREADSAFE();
+ public static final long H5VL_NATIVE = H5VL_NATIVE();
+ public static final String H5VL_NATIVE_NAME = H5VL_NATIVE_NAME();
+ public static final int H5VL_NATIVE_VALUE = H5VL_NATIVE_VALUE();
+ public static final int H5VL_NATIVE_VERSION = H5VL_NATIVE_VERSION();
+ public static final int H5_VOL_INVALID = H5_VOL_INVALID();
+ public static final int H5_VOL_NATIVE = H5_VOL_NATIVE();
+ public static final int H5_VOL_RESERVED = H5_VOL_RESERVED();
+ public static final int H5_VOL_MAX = H5_VOL_MAX();
+
public static final int H5Z_CB_CONT = H5Z_CB_CONT();
public static final int H5Z_CB_ERROR = H5Z_CB_ERROR();
public static final int H5Z_CB_FAIL = H5Z_CB_FAIL();
@@ -839,6 +879,8 @@ public class HDF5Constants {
private static native final long H5E_CANTDELETE();
+ private static native final long H5E_CANTDELETEFILE();
+
private static native final long H5E_CANTENCODE();
private static native final long H5E_CANTFLUSH();
@@ -980,12 +1022,22 @@ public class HDF5Constants {
private static native final long H5E_VFL();
+ private static native final long H5E_VOL();
+
private static native final long H5E_WALK_DOWNWARD();
private static native final long H5E_WALK_UPWARD();
private static native final long H5E_WRITEERROR();
+ private static native final int H5ES_STATUS_IN_PROGRESS();
+
+ private static native final int H5ES_STATUS_SUCCEED();
+
+ private static native final int H5ES_STATUS_FAIL();
+
+ private static native final int H5ES_STATUS_CANCELED();
+
private static native final int H5F_ACC_CREAT();
private static native final int H5F_ACC_EXCL();
@@ -1018,6 +1070,8 @@ public class HDF5Constants {
private static native final int H5F_LIBVER_V110();
+ private static native final int H5F_LIBVER_V112();
+
private static native final int H5F_LIBVER_NBOUNDS();
private static native final int H5F_LIBVER_LATEST();
@@ -1072,6 +1126,10 @@ public class HDF5Constants {
private static native final long H5FD_WINDOWS();
+ private static native final long H5FD_ROS3();
+
+ private static native final long H5FD_HDFS();
+
private static native final int H5FD_LOG_LOC_READ();
private static native final int H5FD_LOG_LOC_WRITE();
@@ -1218,12 +1276,12 @@ public class HDF5Constants {
private static native final int H5I_NTYPES();
- private static native final int H5I_REFERENCE();
-
private static native final int H5I_UNINIT();
private static native final int H5I_VFL();
+ private static native final int H5I_VOL();
+
private static native final int H5L_TYPE_ERROR();
private static native final int H5L_TYPE_HARD();
@@ -1252,11 +1310,13 @@ public class HDF5Constants {
private static native final int H5O_INFO_NUM_ATTRS();
- private static native final int H5O_INFO_HDR();
+ private static native final int H5O_INFO_ALL();
- private static native final int H5O_INFO_META_SIZE();
+ private static native final int H5O_NATIVE_INFO_HDR();
- private static native final int H5O_INFO_ALL();
+ private static native final int H5O_NATIVE_INFO_META_SIZE();
+
+ private static native final int H5O_NATIVE_INFO_ALL();
private static native final int H5O_SHMESG_NONE_FLAG();
@@ -1282,6 +1342,10 @@ public class HDF5Constants {
private static native final int H5O_TYPE_NTYPES();
+ private static native final int H5O_MAX_TOKEN_SIZE();
+
+ private static native final H5O_token_t H5O_TOKEN_UNDEF();
+
private static native final long H5P_ROOT();
private static native final long H5P_OBJECT_CREATE();
@@ -1318,6 +1382,8 @@ public class HDF5Constants {
private static native final long H5P_LINK_ACCESS();
+ private static native final long H5P_VOL_INITIALIZE();
+
private static native final long H5P_FILE_CREATE_DEFAULT();
private static native final long H5P_FILE_ACCESS_DEFAULT();
@@ -1348,6 +1414,8 @@ public class HDF5Constants {
private static native final long H5P_LINK_ACCESS_DEFAULT();
+ private static native final long H5P_VOL_INITIALIZE_DEFAULT();
+
private static native final int H5P_CRT_ORDER_TRACKED();
private static native final int H5P_CRT_ORDER_INDEXED();
@@ -1358,20 +1426,38 @@ public class HDF5Constants {
private static native final int H5PL_TYPE_FILTER();
+ private static native final int H5PL_TYPE_VOL();
+
+ private static native final int H5PL_TYPE_NONE();
+
private static native final int H5PL_FILTER_PLUGIN();
private static native final int H5PL_ALL_PLUGIN();
+ private static native final int H5PL_VOL_PLUGIN();
+
+ private static native final int H5R_ATTR();
+
private static native final int H5R_BADTYPE();
private static native final int H5R_DATASET_REGION();
+ private static native final int H5R_DATASET_REGION1();
+
+ private static native final int H5R_DATASET_REGION2();
+
private static native final int H5R_MAXTYPE();
+ private static native final int H5R_REF_BUF_SIZE();
+
private static native final int H5R_OBJ_REF_BUF_SIZE();
private static native final int H5R_OBJECT();
+ private static native final int H5R_OBJECT1();
+
+ private static native final int H5R_OBJECT2();
+
private static native final int H5S_ALL();
private static native final int H5S_MAX_RANK();
@@ -1760,6 +1846,8 @@ public class HDF5Constants {
private static native final long H5T_STD_REF_OBJ();
+ private static native final long H5T_STD_REF();
+
private static native final long H5T_STD_U16BE();
private static native final long H5T_STD_U16LE();
@@ -1828,6 +1916,26 @@ public class HDF5Constants {
private static native final int H5T_VL_T();
+ private static native final int H5VL_CAP_FLAG_NONE();
+
+ private static native final int H5VL_CAP_FLAG_THREADSAFE();
+
+ private static native final long H5VL_NATIVE();
+
+ private static native final String H5VL_NATIVE_NAME();
+
+ private static native final int H5VL_NATIVE_VALUE();
+
+ private static native final int H5VL_NATIVE_VERSION();
+
+ private static native final int H5_VOL_INVALID();
+
+ private static native final int H5_VOL_NATIVE();
+
+ private static native final int H5_VOL_RESERVED();
+
+ private static native final int H5_VOL_MAX();
+
private static native final int H5Z_CB_CONT();
private static native final int H5Z_CB_ERROR();
diff --git a/source/java/hdf/hdf5lib/callbacks/H5L_iterate_cb.java b/source/java/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java
similarity index 80%
rename from source/java/hdf/hdf5lib/callbacks/H5L_iterate_cb.java
rename to source/java/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java
index ec71911d8d580c858a1f316d61d03b0491e6f412..ad9ad8c719ceef2e178b3010b7ed788800921c05 100644
--- a/source/java/hdf/hdf5lib/callbacks/H5L_iterate_cb.java
+++ b/source/java/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java
@@ -13,9 +13,6 @@
package hdf.hdf5lib.callbacks;
-import hdf.hdf5lib.structs.H5L_info_t;
+public interface H5L_iterate_opdata_t {
-//Information class for link callback(for H5Lvisit/H5Lvisit_by_name)
-public interface H5L_iterate_cb extends Callbacks {
- int callback(long group, String name, H5L_info_t info, H5L_iterate_t op_data);
}
diff --git a/source/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java b/source/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java
index 28ffb8aa6bf4e69df5ccf33adb57f35d3ab9d335..f92fbc4f4401e1188db87b49f485ece149ead563 100644
--- a/source/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java
+++ b/source/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java
@@ -13,8 +13,9 @@
package hdf.hdf5lib.callbacks;
-public interface H5L_iterate_t {
-/** public ArrayList iterdata = new ArrayList();
- * Any derived interfaces must define the single public variable as above.
- */
+import hdf.hdf5lib.structs.H5L_info_t;
+
+// Information class for link callback (for H5Lvisit/H5Lvisit_by_name).
+public interface H5L_iterate_t extends Callbacks {
+ int callback(long group, String name, H5L_info_t info, H5L_iterate_opdata_t op_data);
}
diff --git a/source/java/hdf/hdf5lib/callbacks/H5O_iterate_cb.java b/source/java/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java
similarity index 80%
rename from source/java/hdf/hdf5lib/callbacks/H5O_iterate_cb.java
rename to source/java/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java
index 89cf2062c87d9b9908bc150c7e5e25c37b02e7c4..e1c47b57ba3b4d56c648bd493b38a9d4b295d16d 100644
--- a/source/java/hdf/hdf5lib/callbacks/H5O_iterate_cb.java
+++ b/source/java/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java
@@ -13,9 +13,6 @@
package hdf.hdf5lib.callbacks;
-import hdf.hdf5lib.structs.H5O_info_t;
+public interface H5O_iterate_opdata_t {
-//Information class for link callback(for H5Ovisit/H5Ovisit_by_name)
-public interface H5O_iterate_cb extends Callbacks {
- int callback(long group, String name, H5O_info_t info, H5O_iterate_t op_data);
}
diff --git a/source/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java b/source/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java
index 1491b09b854a338e405e2873a6fc6fd3d44c63a5..9a55106b103ab0fe99f2a13a5dbeb81b09a34925 100644
--- a/source/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java
+++ b/source/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java
@@ -13,8 +13,9 @@
package hdf.hdf5lib.callbacks;
-public interface H5O_iterate_t {
-/** public ArrayList iterdata = new ArrayList();
- * Any derived interfaces must define the single public variable as above.
- */
+import hdf.hdf5lib.structs.H5O_info_t;
+
+// Information class for link callback(for H5Ovisit/H5Ovisit_by_name)
+public interface H5O_iterate_t extends Callbacks {
+ int callback(long group, String name, H5O_info_t info, H5O_iterate_opdata_t op_data);
}
diff --git a/source/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java b/source/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java
index 7756c2f3e72169e0456ed52b5ca14b6d5b46ef5c..f3a41d1d91c3e1430528377a807933f33a7b9531 100644
--- a/source/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java
+++ b/source/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java
@@ -40,7 +40,6 @@ public class HDF5LibraryException extends HDF5Exception {
private final String hdf5ErrorStackLastElementString;
private final long majorErrorNumber;
-
private final long minorErrorNumber;
/**
@@ -256,6 +255,9 @@ public class HDF5LibraryException extends HDF5Exception {
else if (err_code == HDF5Constants.H5E_MOUNT) {
return "file mount error";
}
+ else if (err_code == HDF5Constants.H5E_CANTDELETEFILE) {
+ return "Unable to delete file";
+ }
else if (err_code == HDF5Constants.H5E_SEEKERROR) {
return "seek failed";
}
@@ -347,7 +349,7 @@ public class HDF5LibraryException extends HDF5Exception {
return "unrecognized message";
}
else if (err_code == HDF5Constants.H5E_CANTDELETE) {
- return " Can't delete message";
+ return "Can't delete message";
}
else if (err_code == HDF5Constants.H5E_CANTOPENOBJ) {
return "Can't open object";
diff --git a/source/java/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/source/java/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
new file mode 100644
index 0000000000000000000000000000000000000000..9fcff2e80a0d81171c7ab8e6e720e4a649b45124
--- /dev/null
+++ b/source/java/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
@@ -0,0 +1,102 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Read-Only HDFS Virtual File Driver (VFD) *
+ * Copyright (c) 2018, 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package hdf.hdf5lib.structs;
+
+import java.io.Serializable;
+
+/*
+ * Java representation of the HDFS VFD file access property list (fapl)
+ * structure.
+ *
+ * Used for the access of files hosted on the Hadoop Distributed File System.
+ */
+
+public class H5FD_hdfs_fapl_t implements Serializable {
+ private static final long serialVersionUID = 2072473407027648309L;
+
+ private int version;
+ private String namenode_name;
+ private int namenode_port;
+ private String user_name;
+ private String kerberos_ticket_cache;
+ private int stream_buffer_size;
+
+ /*
+ * Create a fapl_t structure with the specified components.
+ */
+ public H5FD_hdfs_fapl_t(
+ String namenode_name,
+ int namenode_port,
+ String user_name,
+ String kerberos_ticket_cache,
+ int stream_buffer_size)
+ {
+ this.version = 1;
+ this.namenode_name = namenode_name;
+ this.namenode_port = namenode_port;
+ this.user_name = user_name;
+ this.kerberos_ticket_cache = kerberos_ticket_cache;
+ this.stream_buffer_size = stream_buffer_size;
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (o == null)
+ return false;
+ if (!(o instanceof H5FD_hdfs_fapl_t))
+ return false;
+
+ H5FD_hdfs_fapl_t other = (H5FD_hdfs_fapl_t)o;
+ if (this.version != other.version)
+ return false;
+ if (!this.namenode_name.equals(other.namenode_name))
+ return false;
+ if (this.namenode_port != other.namenode_port)
+ return false;
+ if (!this.user_name.equals(other.user_name))
+ return false;
+ if (!this.kerberos_ticket_cache.equals(other.kerberos_ticket_cache))
+ return false;
+ if (this.stream_buffer_size != other.stream_buffer_size)
+ return false;
+ return true;
+ }
+
+ @Override
+ public int hashCode() {
+ /* this is a _very bad_ hash algorithm for purposes of hashing! */
+ /* implemented to satisfy the "contract" regarding equality */
+ int k = (int)this.version;
+ k += this.namenode_name.length();
+ k += this.user_name.length();
+ k += this.kerberos_ticket_cache.length();
+ k += namenode_port;
+ k += stream_buffer_size;
+ return k;
+ }
+
+ @Override
+ public String toString() {
+ return "H5FD_hdfs_fapl_t (Version: " + this.version + ") {" +
+ "\n namenode_name: '" + this.namenode_name +
+ "'\n namenode_port: " + this.namenode_port +
+ "\n user_name: '" + this.user_name +
+ "'\n kerberos_ticket_cache: '" + this.kerberos_ticket_cache +
+ "'\n stream_buffer_size: " + this.stream_buffer_size +
+ "\n}\n";
+ }
+}
+
+
diff --git a/source/java/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/source/java/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
new file mode 100644
index 0000000000000000000000000000000000000000..a899e10704a4519c949cf37b4e90adb68c701266
--- /dev/null
+++ b/source/java/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
@@ -0,0 +1,123 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Read-Only S3 Virtual File Driver (VFD) *
+ * Copyright (c) 2017-2018, 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package hdf.hdf5lib.structs;
+
+import java.io.Serializable;
+
+/*
+ * Java representation of the ROS3 VFD file access property list (fapl)
+ * structure.
+ *
+ * Used for the access of files hosted remotely on S3 by Amazon.
+ *
+ * For simplicity, implemented assuming that all ROS3 fapls have components:
+ * - version
+ * - authenticate
+ * - aws_region
+ * - secret_id
+ * - secret_key
+ *
+ * Future implementations may be created to enable different fapl "shapes"
+ * depending on provided version.
+ *
+ * proposed:
+ *
+ * H5FD_ros3_fapl_t (super class, has only version field)
+ * H5FD_ros3_fapl_v1_t (extends super with Version 1 components)
+ * H5FD_ros3_fapl_v2_t (extends super with Version 2 components)
+ * and so on, for each version
+ *
+ * "super" is passed around, and is version-checked and re-cast as
+ * appropriate
+ */
+
+public class H5FD_ros3_fapl_t implements Serializable {
+ private static final long serialVersionUID = 8985533001471224030L;
+
+ private int version;
+ private boolean authenticate;
+ private String aws_region;
+ private String secret_id;
+ private String secret_key;
+
+ /**
+ * Create a "default" fapl_t structure, for anonymous access.
+ */
+ public H5FD_ros3_fapl_t () {
+ /* H5FD_ros3_fapl_t("", "", ""); */ /* defer */
+ this.version = 1;
+ this.aws_region = "";
+ this.secret_id = "";
+ this.secret_key = "";
+ }
+
+ /**
+ * Create a fapl_t structure with the specified components.
+ * If all are the empty string, is anonymous (non-authenticating).
+ * Region and ID must both be supplied for authentication.
+ *
+ * @param region "aws region" for authenticating request
+ * @param id "secret id" or "access id" for authenticating request
+ * @param key "secret key" or "access key" for authenticating request
+ */
+ public H5FD_ros3_fapl_t (String region, String id, String key) {
+ this.version = 1; /* must equal H5FD_CURR_ROS3_FAPL_T_VERSION */
+ /* as found in H5FDros3.h */
+ this.aws_region = region;
+ this.secret_id = id;
+ this.secret_key = key;
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (o == null)
+ return false;
+ if (!(o instanceof H5FD_ros3_fapl_t))
+ return false;
+
+ H5FD_ros3_fapl_t other = (H5FD_ros3_fapl_t)o;
+ if (this.version != other.version)
+ return false;
+ if (!this.aws_region.equals(other.aws_region))
+ return false;
+ if (!this.secret_key.equals(other.secret_key))
+ return false;
+ if (!this.secret_id.equals(other.secret_id))
+ return false;
+ return true;
+ }
+
+ @Override
+ public int hashCode() {
+ /* this is a _very bad_ hash algorithm for purposes of hashing! */
+ /* implemented to satisfy the "contract" regarding equality */
+ int k = (int)this.version;
+ k += this.aws_region.length();
+ k += this.secret_id.length();
+ k += this.secret_key.length();
+ return k;
+ }
+
+ @Override
+ public String toString() {
+ return "H5FD_ros3_fapl_t (Version:" + this.version + ") {" +
+ "\n aws_region : " + this.aws_region +
+ "\n secret_id : " + this.secret_id +
+ "\n secret_key : " + this.secret_key +
+ "\n}\n";
+ }
+}
+
+
diff --git a/source/java/hdf/hdf5lib/structs/H5L_info_t.java b/source/java/hdf/hdf5lib/structs/H5L_info_t.java
index 3bbb189b6b407234df7a4acf959490769d3b9bf0..377e6175c0b1054cb793942134a128d8c386b867 100644
--- a/source/java/hdf/hdf5lib/structs/H5L_info_t.java
+++ b/source/java/hdf/hdf5lib/structs/H5L_info_t.java
@@ -15,22 +15,39 @@ package hdf.hdf5lib.structs;
import java.io.Serializable;
-//Information struct for link (for H5Lget_info/H5Lget_info_by_idx)
-public class H5L_info_t implements Serializable{
+import hdf.hdf5lib.HDF5Constants;
+
+// Information struct for link (for H5Lget_info/H5Lget_info_by_idx)
+public class H5L_info_t implements Serializable {
private static final long serialVersionUID = -4754320605310155033L;
- public int type;
- public boolean corder_valid;
- public long corder;
- public int cset;
- public long address_val_size;
+ public int type;
+ public boolean corder_valid;
+ public long corder;
+ public int cset;
+ public H5O_token_t token;
+ public long val_size;
+
+ // 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)
+ {
+ this.type = type;
+ this.corder_valid = corder_valid;
+ this.corder = corder;
+ this.cset = cset;
+ this.token = token;
+ this.val_size = -1;
+ }
+ // Constructor for using val_size portion of C union
H5L_info_t (int type, boolean corder_valid, long corder,
- int cset, long address_val_size)
+ int cset, long val_size)
{
this.type = type;
this.corder_valid = corder_valid;
this.corder = corder;
this.cset = cset;
- this.address_val_size = address_val_size;
+ this.token = HDF5Constants.H5O_TOKEN_UNDEF;
+ this.val_size = val_size;
}
}
diff --git a/source/java/hdf/hdf5lib/structs/H5O_hdr_info_t.java b/source/java/hdf/hdf5lib/structs/H5O_hdr_info_t.java
index a39c1edbb497cac9ae6c6d8b8abfde336f071dda..8d0cc2472e668bc8f15824e9e340b764d7052853 100644
--- a/source/java/hdf/hdf5lib/structs/H5O_hdr_info_t.java
+++ b/source/java/hdf/hdf5lib/structs/H5O_hdr_info_t.java
@@ -16,7 +16,7 @@ package hdf.hdf5lib.structs;
import java.io.Serializable;
// Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
-public class H5O_hdr_info_t implements 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 */
@@ -44,4 +44,38 @@ public class H5O_hdr_info_t implements Serializable{
this.mesg_present = mesg_present;
this.mesg_shared = mesg_shared;
}
+
+ @Override
+ public boolean equals(Object o) {
+ if (this == o)
+ return true;
+
+ if (!(o instanceof H5O_hdr_info_t))
+ return false;
+
+ H5O_hdr_info_t info = (H5O_hdr_info_t) o;
+
+ if (this.version != info.version)
+ return false;
+ if (this.nmesgs != info.nmesgs)
+ return false;
+ if (this.nchunks != info.nchunks)
+ return false;
+ if (this.flags != info.flags)
+ return false;
+ if (this.space_total != info.space_total)
+ return false;
+ if (this.space_meta != info.space_meta)
+ return false;
+ if (this.space_mesg != info.space_mesg)
+ return false;
+ if (this.space_free != info.space_free)
+ return false;
+ if (this.mesg_present != info.mesg_present)
+ return false;
+ if (this.mesg_shared != info.mesg_shared)
+ return false;
+
+ return true;
+ }
}
diff --git a/source/java/hdf/hdf5lib/structs/H5O_info_t.java b/source/java/hdf/hdf5lib/structs/H5O_info_t.java
index ac32f6adfba4b0fd9f40bf4e23ca38659f80e393..6a26a102c8f0b79d28fe6071c1e8294f1e9aa26c 100644
--- a/source/java/hdf/hdf5lib/structs/H5O_info_t.java
+++ b/source/java/hdf/hdf5lib/structs/H5O_info_t.java
@@ -15,38 +15,30 @@ package hdf.hdf5lib.structs;
import java.io.Serializable;
-//Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
-public class H5O_info_t implements Serializable{
+// Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+public class H5O_info_t implements Serializable {
private static final long serialVersionUID = 4691681163544054518L;
- public long fileno; /* File number that object is located in */
- public long addr; /* Object address 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 */
- public H5O_hdr_info_t hdr; /* Object header information */
- /* Extra metadata storage for obj & attributes */
- public H5_ih_info_t meta_size_obj; /* v1/v2 B-tree & local/fractal heap for groups, B-tree for chunked datasets */
- public H5_ih_info_t meta_size_attr; /* v2 B-tree & heap for attributes */
+ 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 */
- public H5O_info_t (long fileno, long addr, int type,
- int rc, long num_attrs, long atime, long mtime, long ctime, long btime,
- H5O_hdr_info_t hdr, H5_ih_info_t meta_size_obj, H5_ih_info_t meta_size_attr)
+ 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)
{
this.fileno = fileno;
- this.addr = addr;
+ this.token = token;
this.type = type;
this.rc = rc;
- this.num_attrs = num_attrs;
this.atime = atime;
this.mtime = mtime;
this.ctime = ctime;
this.btime = btime;
- this.hdr = hdr;
- this.meta_size_obj = meta_size_obj;
- this.meta_size_attr = meta_size_attr;
+ this.num_attrs = num_attrs;
}
}
diff --git a/source/java/hdf/hdf5lib/structs/H5O_native_info_t.java b/source/java/hdf/hdf5lib/structs/H5O_native_info_t.java
new file mode 100644
index 0000000000000000000000000000000000000000..4e808494119e7237b0718b8c415f8f396f8fd0bf
--- /dev/null
+++ b/source/java/hdf/hdf5lib/structs/H5O_native_info_t.java
@@ -0,0 +1,52 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * 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://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package hdf.hdf5lib.structs;
+
+import java.io.Serializable;
+
+// Information struct for native HDF5 object info, such as object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx).
+public class H5O_native_info_t implements Serializable {
+ private static final long serialVersionUID = 7883826382952577189L;
+
+ public H5O_hdr_info_t hdr_info; /* Object header information */
+
+ /* 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 */
+
+ H5O_native_info_t (H5O_hdr_info_t oheader_info, H5_ih_info_t obj_info, H5_ih_info_t attr_info)
+ {
+ this.hdr_info = oheader_info;
+ this.obj_info = obj_info;
+ this.attr_info = attr_info;
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (this == o)
+ return true;
+
+ if (!(o instanceof H5O_native_info_t))
+ return false;
+
+ H5O_native_info_t info = (H5O_native_info_t) o;
+
+ if (!this.hdr_info.equals(info.hdr_info)
+ || !this.obj_info.equals(info.obj_info)
+ || !this.attr_info.equals(info.attr_info))
+ return false;
+
+ return true;
+ }
+}
\ No newline at end of file
diff --git a/source/java/hdf/hdf5lib/structs/H5O_token_t.java b/source/java/hdf/hdf5lib/structs/H5O_token_t.java
new file mode 100644
index 0000000000000000000000000000000000000000..8ec0b7f8d033b454f6d33bac1f7363715e514d00
--- /dev/null
+++ b/source/java/hdf/hdf5lib/structs/H5O_token_t.java
@@ -0,0 +1,45 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package hdf.hdf5lib.structs;
+
+import java.io.Serializable;
+import java.util.Arrays;
+
+import hdf.hdf5lib.HDF5Constants;
+
+// Object token, which is a unique and permanent identifier, for an HDF5 object within a container.
+public class H5O_token_t implements Serializable {
+ private static final long serialVersionUID = -4754320605310155032L;
+ public byte[] data;
+
+ H5O_token_t (byte[] data) {
+ this.data = data;
+ }
+
+ public boolean isUndefined() {
+ return this.equals(HDF5Constants.H5O_TOKEN_UNDEF);
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (this == o)
+ return true;
+
+ if (!(o instanceof H5O_token_t))
+ return false;
+
+ H5O_token_t token = (H5O_token_t) o;
+
+ return Arrays.equals(this.data, token.data);
+ }
+}
\ No newline at end of file
diff --git a/source/java/hdf/hdf5lib/structs/H5_ih_info_t.java b/source/java/hdf/hdf5lib/structs/H5_ih_info_t.java
index ea36d85e5479a17c7d54090a661e0109b89ce324..7159f0223e35d3aba44f26417c70058d60178a33 100644
--- a/source/java/hdf/hdf5lib/structs/H5_ih_info_t.java
+++ b/source/java/hdf/hdf5lib/structs/H5_ih_info_t.java
@@ -26,4 +26,22 @@ public class H5_ih_info_t implements Serializable {
this.index_size = index_size;
this.heap_size = heap_size;
}
+
+ @Override
+ public boolean equals(Object o) {
+ if (this == o)
+ return true;
+
+ if (!(o instanceof H5_ih_info_t))
+ return false;
+
+ H5_ih_info_t info = (H5_ih_info_t) o;
+
+ if (this.index_size != info.index_size)
+ return false;
+ if (this.heap_size != info.heap_size)
+ return false;
+
+ return true;
+ }
}
diff --git a/source/java/hdf/overview.html b/source/java/hdf/overview.html
index 9c19442a11d7b604452b3f7d7f45f0347b661756..f181510ff75d8b5609b0ab5fb5f4183eb87ba0c0 100644
--- a/source/java/hdf/overview.html
+++ b/source/java/hdf/overview.html
@@ -6,18 +6,19 @@
The <b>Java HD5 Interface (JHI5)</b> is a Java package
(<a href="../../hdf-java-html/javadocs/hdf/hdf5lib/package-summary.html">hdf.hdf5lib</a>)
that ``wraps around'' the HDF5 library.
-<p />There are a large number of functions in the HDF5
-library (version 1.10). Some of the functions are not supported in JHI5. Most
+<p>There are a large number of functions in the HDF5
+library (version 1.12). Some of the functions are not supported in JHI5. Most
of the unsupported functions have C function pointers, which is not currently
-implemented in JHI5.
+implemented in JHI5.</p>
-<center><table BORDER=1 COLS=1 WIDTH="71%" BGCOLOR="#dbeaf5" >
+<table style="width:71%;text-align:center;background-color:#dbeaf5" border="1">
+<caption>Java HDF5 Interface (JHI5)</caption>
<tr>
-<td>
-<center>Note: The JHI5 does not support HDF4 or earlier.</center>
+<td style="text-align:center;">
+Note: The JHI5 does not support HDF4 or earlier.
</td>
</tr>
-</table></center>
+</table>
<p>The JHI5 may be used by any Java application that needs to access HDF5
files. It is extremely important to emphasize that <i>this package is not
@@ -89,8 +90,7 @@ like this:
The <i><b>H5</b> </i>class automatically loads the native method implementations
and the HDF5 library.
-<h3>
-<a NAME="DOWNLOAD"></a>To Obtain</h3>
-The JHI5 is included with the <a href="http://www.hdfgroup.org/HDF5/index.html">HDF5</a> library.
+<h3>To Obtain</h3>
+The JHI5 is included with the <a href="https://portal.hdfgroup.org/display/support/Downloads">HDF5</a> library.
</body>