[svn-r29226] HDFFV-9552: merge in java code.

1 files changed, 1758 insertions, 0 deletions

diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
new file mode 100644
index 0000000..f70cb5e
--- /dev/null
+++ b/java/src/jni/h5dImp.c
@@ -0,0 +1,1758 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ *  For details of the HDF libraries, see the HDF Documentation at:
+ *    http://hdfdfgroup.org/HDF5/doc/
+ *
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#include <jni.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "hdf5.h"
+#include "h5util.h"
+#include "h5dImp.h"
+
+extern JavaVM *jvm;
+extern jobject visit_callback;
+
+#ifdef __cplusplus
+  #ifdef _WINDOWS
+    #include <direct.h>
+  #endif
+  #define CBENVPTR (cbenv)
+  #define CBENVPAR
+  #define JVMPTR (jvm)
+  #define JVMPAR
+  #define JVMPAR2
+#else
+  #define CBENVPTR (*cbenv)
+  #define CBENVPAR cbenv,
+  #define JVMPTR (*jvm)
+  #define JVMPAR jvm
+  #define JVMPAR2 jvm,
+#endif
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+static herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
+static herr_t H5DreadVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
+static herr_t H5DwriteVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
+static herr_t H5DwriteVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
+
+/********************/
+/* Local Macros     */
+/********************/
+
+#define PIN_BYTE_ARRAY() { \
+    if (isCriticalPinning) \
+        buffP = (jbyte*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+    else \
+        buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_BYTE_ARRAY(mode) { \
+    if (isCriticalPinning) \
+        ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+    else \
+        ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_SHORT_ARRAY() { \
+    if (isCriticalPinning) \
+        buffP = (jshort*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+    else \
+        buffP = ENVPTR->GetShortArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_SHORT_ARRAY(mode) { \
+    if (isCriticalPinning) \
+        ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+    else \
+        ENVPTR->ReleaseShortArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_INT_ARRAY() { \
+    if (isCriticalPinning) \
+        buffP = (jint*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+    else \
+        buffP = ENVPTR->GetIntArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_INT_ARRAY(mode) { \
+    if (isCriticalPinning) \
+        ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+    else \
+        ENVPTR->ReleaseIntArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_LONG_ARRAY() { \
+    if (isCriticalPinning) \
+        buffP = (jlong*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+    else \
+        buffP = ENVPTR->GetLongArrayElements(ENVPAR buf,&isCopy); \
+}
+
+#define UNPIN_LONG_ARRAY(mode) { \
+    if (isCriticalPinning) \
+        ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+    else \
+        ENVPTR->ReleaseLongArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_FLOAT_ARRAY() { \
+    if (isCriticalPinning) \
+        buffP = (jfloat*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+    else \
+        buffP = ENVPTR->GetFloatArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_FLOAT_ARRAY(mode) { \
+    if (isCriticalPinning) \
+        ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+    else \
+        ENVPTR->ReleaseFloatArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_DOUBLE_ARRAY() { \
+    if (isCriticalPinning) \
+        buffP = (jdouble*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+    else \
+        buffP = ENVPTR->GetDoubleArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_DOUBLE_ARRAY(mode) { \
+    if (isCriticalPinning) \
+        ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+    else \
+        ENVPTR->ReleaseDoubleArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dcreate
+ * Signature: (JLjava/lang/String;JJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dcreate(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong type_id,
+          jlong space_id, jlong create_plist_id)
+{
+    hid_t       dset_id = -1;
+    const char *fileName;
+
+    PIN_JAVA_STRING(name, fileName, -1);
+
+    dset_id = H5Dcreate2((hid_t)loc_id, fileName, (hid_t)type_id, (hid_t)space_id, H5P_DEFAULT, (hid_t)create_plist_id, H5P_DEFAULT);
+
+    UNPIN_JAVA_STRING(name, fileName);
+
+    if (dset_id < 0)
+        h5libraryError(env);
+
+    return (jlong)dset_id;
+} /* end Java_hdf_hdf5lib_H5__1H5Dcreate */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dopen
+ * Signature: (JLjava/lang/String;)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dopen(JNIEnv *env, jclass clss, jlong loc_id, jstring name)
+{
+    hid_t       dset_id = -1;
+    const char *fileName;
+
+    PIN_JAVA_STRING(name, fileName, -1);
+
+    dset_id = H5Dopen2((hid_t)loc_id, fileName, H5P_DEFAULT);
+
+    UNPIN_JAVA_STRING(name, fileName);
+    if (dset_id < 0)
+        h5libraryError(env);
+
+    return (jlong)dset_id;
+} /* end Java_hdf_hdf5lib_H5__1H5Dopen */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dget_space
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dget_1space(JNIEnv *env, jclass clss, jlong dataset_id)
+{
+    hid_t retVal = -1;
+
+    retVal = H5Dget_space((hid_t)dataset_id);
+    if (retVal < 0)
+        h5libraryError(env);
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5__1H5Dget_1space */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dget_type
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dget_1type(JNIEnv *env, jclass clss, jlong dataset_id)
+{
+    hid_t retVal = -1;
+
+    retVal = H5Dget_type((hid_t)dataset_id);
+    if (retVal < 0)
+        h5libraryError(env);
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5__1H5Dget_1type */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dget_create_plist
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dget_1create_1plist(JNIEnv *env, jclass clss, jlong dataset_id)
+{
+    hid_t retVal = -1;
+
+    retVal = H5Dget_create_plist((hid_t)dataset_id);
+    if (retVal < 0)
+        h5libraryError(env);
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5__1H5Dget_1create_1plist */
+
+static htri_t
+H5Tdetect_variable_str(hid_t tid) {
+    htri_t ret_val = 0;
+
+    if (H5Tget_class(tid) == H5T_COMPOUND) {
+        unsigned i;
+        unsigned nm = (unsigned)H5Tget_nmembers(tid);
+        for(i = 0; i < nm; i++) {
+            htri_t status = 0;
+            hid_t mtid = 0;
+            if((mtid = H5Tget_member_type(tid, i)) < 0)
+                return -1; /* exit immediately on error */
+            if((status = H5Tdetect_variable_str(mtid)) < 0)
+                return status; /* exit immediately on error */
+            ret_val |= status;
+            H5Tclose (mtid);
+        } /* end for */
+    } /* end if */
+    else
+        ret_val = H5Tis_variable_str(tid);
+
+    return ret_val;
+} /* end H5Tdetect_variable_str */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread
+ * Signature: (JJJJJ[BZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status;
+    jbyte   *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dread:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dread: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dread:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dread: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dread:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_BYTE_ARRAY();
+
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dread:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                if (status < 0) {
+                    UNPIN_BYTE_ARRAY(JNI_ABORT);
+                    h5libraryError(env);
+                } /* end if */
+                else {
+                    UNPIN_BYTE_ARRAY(0); /* update java buffer for return */
+                } /* end else */
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite
+ * Signature: (JJJJJ[BZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status;
+    jbyte   *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dwrite:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dwrite: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dwrite:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dwrite: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dwrite:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_BYTE_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dwrite:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                UNPIN_BYTE_ARRAY(JNI_ABORT); /* no need to update buffer */
+
+                if (status < 0)
+                    h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dclose
+ * Signature: (J)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5__1H5Dclose(JNIEnv *env, jclass clss, jlong dataset_id)
+{
+    herr_t retVal = -1;
+
+    retVal = H5Dclose((hid_t)dataset_id);
+
+    if (retVal < 0)
+        h5libraryError(env);
+
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5__1H5Dclose */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dget_storage_size
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Dget_1storage_1size(JNIEnv *env, jclass clss, jlong dataset_id)
+{
+    hsize_t retVal = (hsize_t)-1;
+
+    if (dataset_id < 0) {
+        h5badArgument(env, "H5Dget_storage_size: not a dataset");
+    } /* end if */
+    else {
+        retVal = H5Dget_storage_size((hid_t)dataset_id);
+    } /* end else */
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Dget_1storage_1size */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dvlen_reclaim
+ * Signature: (JJJ[B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim(JNIEnv *env, jclass clss, jlong type_id, jlong space_id,
+          jlong xfer_plist_id, jbyteArray buf)
+{
+    herr_t   status = -1;
+    jbyte   *byteP;
+    jboolean isCopy;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dvlen_reclaim:  buf is NULL");
+    } /* end if */
+    else {
+        byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
+        if (byteP == NULL) {
+            h5JNIFatalError(env, "H5Dvlen_reclaim:  buf not pinned");
+        } /* end if */
+        else {
+            status = H5Dvlen_reclaim((hid_t)type_id, (hid_t)space_id, (hid_t)xfer_plist_id, byteP);
+
+            ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
+
+            if (status < 0)
+                h5libraryError(env);
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim */
+
+/*
+    ////////////////////////////////////////////////////////////////////
+    //                                                                //
+    //         New APIs for read data from library                    //
+    //  Using H5Dread(..., Object buf) requires function calls        //
+    //  theArray.emptyBytes() and theArray.arrayify(buf), which       //
+    //  triples the actual memory needed by the data set.             //
+    //  Using the following APIs solves the problem.                  //
+    //                                                                //
+    ////////////////////////////////////////////////////////////////////
+*/
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_short
+ * Signature: (JJJJJ[SZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jshortArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jshort  *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dread_short:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dread: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dread_short:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dread_short: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dread_short:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_SHORT_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dread_short:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                if (status < 0) {
+                    UNPIN_SHORT_ARRAY(JNI_ABORT);
+                    h5libraryError(env);
+                } /* end if */
+                else {
+                    UNPIN_SHORT_ARRAY(0);
+                } /* end else */
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1short */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite_short
+ * Signature: (JJJJJ[SZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jshortArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jshort  *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL ) {
+        h5nullArgument(env, "H5Dwrite_short:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dwrite_short: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dwrite_short:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dwrite_short: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dwrite_short:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_SHORT_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dwrite_short:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                UNPIN_SHORT_ARRAY(JNI_ABORT);
+
+                if (status < 0)
+                    h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1short */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_int
+ * Signature: (JJJJJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jintArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jint    *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dread_int:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dread_int: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dread_int:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dread_int: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dread_int:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_INT_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dread_int:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                if (status < 0) {
+                    UNPIN_INT_ARRAY(JNI_ABORT);
+                    h5libraryError(env);
+                } /* end if */
+                else {
+                    UNPIN_INT_ARRAY(0);
+                } /* end else */
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1int */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite_int
+ * Signature: (JJJJJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jintArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jint    *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dwrite_int:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dwrite_int: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dwrite_int:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dwrite_int: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dwrite_int:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_INT_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dwrite_int:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                UNPIN_INT_ARRAY(JNI_ABORT);
+
+                if (status < 0)
+                    h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1int */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_long
+ * Signature: (JJJJJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1long(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jlongArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jlong   *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dread_long:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dread_long: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dread_long:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dread_long: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dread_long:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_LONG_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dread_long:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                if (status < 0) {
+                    UNPIN_LONG_ARRAY(JNI_ABORT);
+                    h5libraryError(env);
+                } /* end if */
+                else {
+                    UNPIN_LONG_ARRAY(0);
+                } /* end else */
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1long */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite_long
+ * Signature: (JJJJJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite_1long(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jlongArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jlong   *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dwrite_long:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dwrite_long: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dwrite_long:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dwrite_long: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dwrite_long:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_LONG_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dwrite_long:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                UNPIN_LONG_ARRAY(JNI_ABORT);
+                if (status < 0)
+                    h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1long */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_float
+ * Signature: (JJJJJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1float(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jfloatArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jfloat  *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dread_float:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dread_float: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dread_float:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dread_float: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dread_float:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_FLOAT_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dread_float:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                if (status < 0) {
+                    UNPIN_FLOAT_ARRAY(JNI_ABORT);
+                    h5libraryError(env);
+                } /* end if */
+                else {
+                    UNPIN_FLOAT_ARRAY(0);
+                } /* end else */
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1float */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite_float
+ * Signature: (JJJJJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite_1float(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jfloatArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jfloat  *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dwrite_float:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dwrite_float: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dwrite_float:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dwrite_float: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dwrite_float:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_FLOAT_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dwrite_float:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                UNPIN_FLOAT_ARRAY(JNI_ABORT);
+                if (status < 0)
+                    h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1float */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_double
+ * Signature: (JJJJJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jdoubleArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jdouble *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dread_double:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dread_double: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dread_double:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dread_double: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dread_double:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_DOUBLE_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dread_double:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                if (status < 0) {
+                    UNPIN_DOUBLE_ARRAY(JNI_ABORT);
+                    h5libraryError(env);
+                } /* end if */
+                else {
+                    UNPIN_DOUBLE_ARRAY(0);
+                } /* end else */
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1double */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite_double
+ * Signature: (JJJJJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jdoubleArray buf, jboolean isCriticalPinning)
+{
+    herr_t   status = -1;
+    jdouble *buffP;
+    jboolean isCopy;
+    htri_t data_class;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dwrite_double:  buf is NULL");
+    } /* end if */
+    else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+        h5JNIFatalError(env, "H5Dwrite_double: H5Tdetect_class() failed");
+    } /* end else if */
+    else  if(data_class == 1) {
+        h5badArgument(env, "H5Dwrite_double:  buf does not support variable length type");
+    } /* end else if */
+    else {
+        /* recursive detect any vlen string in type (compound, array ...) */
+        if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+            h5JNIFatalError(env, "H5Dwrite_double: H5Tdetect_variable_str() failed");
+        } /* end if */
+        else  if(data_class == 1) {
+            h5badArgument(env, "H5Dwrite_double:  buf does not support variable length type");
+        } /* end else if */
+        else {
+            PIN_DOUBLE_ARRAY();
+            if (buffP == NULL) {
+                h5JNIFatalError(env, "H5Dwrite_double:  buf not pinned");
+            } /* end if */
+            else {
+                status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP);
+
+                UNPIN_DOUBLE_ARRAY(JNI_ABORT);
+                if (status < 0)
+                    h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1double */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_string
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1string(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jobjectArray j_buf)
+{
+    herr_t  status = -1;
+    char   *c_buf;
+    char   *cstr;
+    size_t  str_len;
+    jsize   i;
+    jsize   n;
+    size_t  pos;
+    jstring jstr;
+
+    c_buf = cstr = NULL;
+    if (j_buf == NULL) {
+        h5nullArgument(env, "H5Dread_string:  buf is NULL");
+    } /* end if */
+    else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) {
+        h5nullArgument(env, "H5Dread_string:  buf length <= 0");
+    } /* end else if */
+    else if ((str_len = H5Tget_size((hid_t)mem_type_id)) <=0) {
+        h5libraryError(env);
+    } /* end else if */
+    else {
+        if ((cstr = (char*)HDmalloc(str_len + 1)) == NULL) {
+            h5JNIFatalError(env, "H5Dread_string: memory allocation failed.");
+        } /* end if */
+        else {
+            if ((c_buf = (char*)HDmalloc((size_t)n * str_len)) == NULL) {
+                if (cstr)
+                    HDfree(cstr);
+                cstr = NULL;
+                h5JNIFatalError(env, "H5Dread_string: memory allocation failed.");
+            } /* end if */
+            else {
+                status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                                (hid_t)file_space_id, (hid_t)xfer_plist_id, c_buf);
+
+                if (status < 0) {
+                    if (cstr)
+                        HDfree(cstr);
+                    cstr = NULL;
+                    if (c_buf)
+                        HDfree(c_buf);
+                    c_buf = NULL;
+                    h5libraryError(env);
+                } /* end if */
+                else {
+                    pos = 0;
+                    for (i = 0; i < n; i++) {
+                        HDmemcpy(cstr, c_buf+pos, str_len);
+                        cstr[str_len] = '\0';
+                        jstr = ENVPTR->NewStringUTF(ENVPAR cstr);
+                        ENVPTR->SetObjectArrayElement(ENVPAR j_buf, i, jstr);
+                        pos += str_len;
+                    } /* end for */
+                } /* end else */
+
+                if (c_buf)
+                    HDfree(c_buf);
+            } /* end else cbuf allocation*/
+
+            if (cstr)
+                HDfree(cstr);
+        } /* end else cstr allocation*/
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1string */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite_string
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite_1string(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jobjectArray j_buf)
+{
+    herr_t  status = -1;
+    char   *c_buf;
+    jsize  str_len;
+    jsize   i;
+    jsize   n;
+
+    if (j_buf == NULL) {
+        h5nullArgument(env, "H5Dwrite_string:  buf is NULL");
+    } /* end if */
+    else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) {
+        h5nullArgument(env, "H5Dwrite_string:  buf length <= 0");
+    } /* end else if */
+    else if ((str_len = (jsize)H5Tget_size((hid_t)mem_type_id)) <=0) {
+        h5libraryError(env);
+    } /* end else if */
+    else {
+        if ((c_buf = (char*)HDmalloc((size_t)n * (size_t)str_len)) == NULL) {
+            h5JNIFatalError(env, "H5Dwrite_string: memory allocation failed.");
+        } /* end if */
+        else {
+            for (i = 0; i < n; i++) {
+                jstring obj = (jstring)ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray)j_buf, i);
+                if (obj != 0) {
+                    jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
+                    const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
+
+                    if (utf8) {
+                        strncpy(&c_buf[i * str_len], utf8, str_len);
+                    } /* end if */
+
+                    ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
+                    ENVPTR->DeleteLocalRef(ENVPAR obj);
+                } /* end if */
+            } /* end for */
+
+            status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+                            (hid_t)file_space_id, (hid_t)xfer_plist_id, c_buf);
+
+            if (c_buf)
+                HDfree(c_buf);
+            c_buf = NULL;
+
+            if (status < 0) {
+                h5libraryError(env);
+            } /* end if */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1string */
+
+/**
+ *  Read VLEN data into array of arrays.
+ *  Object[] buf contains VL arrays of data points
+ *  Currently only deal with variable length of atomic data types
+ */
+/* old version */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_VLStrings
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
+{
+    herr_t  status = -1;
+    htri_t  isVlenStr=0;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dread_VLStrings:  buf is NULL");
+    } /* end if */
+    else {
+        isVlenStr = H5Tis_variable_str((hid_t)mem_type_id);
+
+        if (isVlenStr) {
+            status = H5DreadVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id,
+                                        (hid_t)mem_space_id, (hid_t)file_space_id,
+                                        (hid_t)xfer_plist_id, buf);
+        } /* end if */
+        else
+            h5badArgument(env, "H5Dread_VLStrings: type is not variable length String");
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
+
+herr_t
+H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t
+        file_sid, hid_t xfer_plist_id, jobjectArray buf)
+{
+    char  **strs;
+    jstring jstr;
+    jint    i;
+    jint    n;
+    herr_t  status = -1;
+
+    n = ENVPTR->GetArrayLength(ENVPAR buf);
+    strs =(char**)HDcalloc((size_t)n, sizeof(char*));
+
+    if (strs == NULL) {
+        h5JNIFatalError(env, "H5DreadVL_str:  failed to allocate buff for read variable length strings");
+    } /* end if */
+    else {
+        status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, strs);
+
+        if (status < 0) {
+            H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs);
+            HDfree(strs);
+            h5JNIFatalError(env, "H5DreadVL_str: failed to read variable length strings");
+        } /* end if */
+        else {
+            for (i=0; i < n; i++) {
+                jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
+                ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+                H5free_memory (strs[i]);
+            } /* end for */
+
+            /*
+            for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings,
+            H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect
+            free space in time. Instead, use "H5free_memory(strs[i])" above to free individual strings
+            after it is done.
+            H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs);
+            */
+
+            HDfree(strs);
+        } /* end else */
+    } /* end else */
+
+    return status;
+} /* end H5DreadVL_str */
+
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dwrite_VLStrings
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
+{
+    herr_t  status = -1;
+    htri_t  isVlenStr=0;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dwrite_VLStrings:  buf is NULL");
+    } /* end if */
+    else {
+        isVlenStr = H5Tis_variable_str((hid_t)mem_type_id);
+
+        if (isVlenStr) {
+            status = H5DwriteVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id,
+                                        (hid_t)mem_space_id, (hid_t)file_space_id,
+                                        (hid_t)xfer_plist_id, buf);
+        } /* end if */
+        else
+            h5badArgument(env, "H5Dwrite_VLStrings: type is not variable length String");
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings */
+
+herr_t
+H5DwriteVL_str(JNIEnv *env, hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
+        hid_t file_space_id, hid_t xfer_plist_id, jobjectArray buf)
+{
+    herr_t  status = -1;
+    char  **wdata;
+    jsize   size;
+    jsize    i;
+
+    size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
+    wdata = (char**)HDmalloc((size_t)size * sizeof (char*));
+
+    if (!wdata) {
+        h5JNIFatalError(env, "H5DwriteVL_string:  cannot allocate buffer");
+    } /* end if */
+    else {
+        HDmemset(wdata, 0, (size_t)size * sizeof(char*));
+        for (i = 0; i < size; ++i) {
+            jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray)buf, i);
+            if (obj != 0) {
+                jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
+                const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
+
+                if (utf8) {
+                    wdata[i] = (char*)HDmalloc((size_t)length + 1);
+                    if (wdata[i]) {
+                        HDmemset(wdata[i], 0, (size_t)length + 1);
+                        HDstrncpy(wdata[i], utf8, (size_t)length + 1);
+                    } /* end if */
+                } /* end if */
+
+                ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
+                ENVPTR->DeleteLocalRef(ENVPAR obj);
+            } /* end if */
+        } /* end for (i = 0; i < size; ++i) */
+
+        status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, wdata);
+
+        /* now free memory*/
+        for (i = 0; i < size; i++) {
+            if(wdata[i]) {
+                HDfree(wdata[i]);
+            } /* end if */
+        } /* end for */
+        HDfree(wdata);
+
+        if (status < 0)
+            h5libraryError(env);
+    } /* end else */
+
+    return status;
+} /* end H5DwriteVL_str */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_reg_ref
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref (JNIEnv *env, jclass clss,
+        jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+        jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
+{
+    herr_t    status = -1;
+    h5str_t   h5str;
+    size_t    size;
+    hdset_reg_ref_t *ref_data;
+    jint      i;
+    jint      n;
+    jstring   jstr;
+
+    hid_t region = -1;
+    hid_t did = (hid_t) dataset_id;
+    hid_t tid = (hid_t) mem_type_id;
+    hid_t mem_sid = (hid_t) mem_space_id;
+    hid_t file_sid = (hid_t) file_space_id;
+
+    n = ENVPTR->GetArrayLength(ENVPAR buf);
+    size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/
+    ref_data = (hdset_reg_ref_t*)HDmalloc(size * (size_t)n);
+
+    if (ref_data == NULL) {
+        h5JNIFatalError(env, "H5Dread_reg_ref:  failed to allocate buff for read");
+        return -1;
+    } /* end if */
+
+    status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data);
+
+    if (status < 0) {
+        HDfree(ref_data);
+        h5JNIFatalError(env, "H5Dread_reg_ref: failed to read data");
+        return -1;
+    } /* end if */
+
+    HDmemset(&h5str, 0, sizeof(h5str_t));
+    h5str_new(&h5str, 1024);
+    for (i=0; i<n; i++) {
+        h5str.s[0] = '\0';
+        h5str_sprintf(&h5str, did, tid, ref_data[i], 0);
+        jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
+
+        ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+    } /* end for */
+
+    h5str_free(&h5str);
+    HDfree(ref_data);
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dread_reg_ref_data
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data (JNIEnv *env, jclass clss,
+        jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+        jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
+{
+    herr_t    status = -1;
+    h5str_t   h5str;
+    size_t    size;
+    hdset_reg_ref_t *ref_data;
+    jint      i;
+    jint      n;
+    jstring   jstr;
+
+    hid_t        region_obj;
+    H5S_sel_type region_type;
+
+    hid_t region = -1;
+    hid_t did = (hid_t) dataset_id;
+    hid_t tid = (hid_t) mem_type_id;
+    hid_t mem_sid = (hid_t) mem_space_id;
+    hid_t file_sid = (hid_t) file_space_id;
+
+    n = ENVPTR->GetArrayLength(ENVPAR buf);
+    size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/
+    ref_data = (hdset_reg_ref_t*)HDmalloc(size * (size_t)n);
+
+    if (ref_data == NULL) {
+        h5JNIFatalError(env, "H5Dread_reg_ref_data:  failed to allocate buff for read");
+        return -1;
+    } /* end if */
+
+    status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data);
+
+    if (status < 0) {
+        HDfree(ref_data);
+        h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to read data");
+        return -1;
+    } /* end if */
+
+    HDmemset(&h5str, 0, sizeof(h5str_t));
+    h5str_new(&h5str, 1024);
+    for (i=0; i<n; i++) {
+        h5str.s[0] = '\0';
+
+        /* get name of the dataset the region reference points to using H5Rget_name */
+        region_obj = H5Rdereference2(did, H5P_DEFAULT, H5R_DATASET_REGION, ref_data[i]);
+        if (region_obj >= 0) {
+            region = H5Rget_region(did, H5R_DATASET_REGION, ref_data[i]);
+            if (region >= 0) {
+                region_type = H5Sget_select_type(region);
+                if(region_type==H5S_SEL_POINTS) {
+                    h5str_dump_region_points_data(&h5str, region, region_obj);
+                } /* end if */
+                else {
+                    h5str_dump_region_blocks_data(&h5str, region, region_obj);
+                } /* end else */
+
+                H5Sclose(region);
+            } /* end if */
+            H5Dclose(region_obj);
+        } /* end if */
+        jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
+
+        ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+    } /* end for */
+
+    h5str_free(&h5str);
+    HDfree(ref_data);
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dcreate2
+ * Signature: (JLjava/lang/String;JJJJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dcreate2(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong type_id,
+          jlong space_id, jlong link_plist_id, jlong create_plist_id, jlong access_plist_id)
+{
+    hid_t       dset_id = -1;
+    const char *fileName;
+
+    PIN_JAVA_STRING(name, fileName, -1);
+
+    dset_id = H5Dcreate2((hid_t)loc_id, fileName, (hid_t)type_id, (hid_t)space_id, (hid_t)link_plist_id, (hid_t)create_plist_id, (hid_t)access_plist_id);
+
+    UNPIN_JAVA_STRING(name, fileName);
+    if (dset_id < 0)
+        h5libraryError(env);
+
+    return (jlong)dset_id;
+} /* end Java_hdf_hdf5lib_H5__1H5Dcreate2 */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dopen2
+ * Signature: (JLjava/lang/String;J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dopen2(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong access_plist)
+{
+    hid_t       dset_id;
+    const char *fileName;
+
+    PIN_JAVA_STRING(name, fileName, -1);
+
+    dset_id = H5Dopen2((hid_t)loc_id, fileName, (hid_t)access_plist);
+
+    UNPIN_JAVA_STRING(name, fileName);
+    if (dset_id < 0)
+        h5libraryError(env);
+
+    return (jlong)dset_id;
+} /* end Java_hdf_hdf5lib_H5__1H5Dopen2 */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    _H5Dcreate_anon
+ * Signature: (JJJJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5__1H5Dcreate_1anon(JNIEnv *env, jclass clss, jlong loc_id, jlong type_id, jlong space_id, jlong dcpl_id, jlong dapl_id)
+{
+    hid_t dset_id = -1;
+
+    dset_id = H5Dcreate_anon((hid_t)loc_id, (hid_t)type_id, (hid_t)space_id, (hid_t)dcpl_id, (hid_t)dapl_id);
+    if (dset_id < 0)
+        h5libraryError(env);
+
+    return (jlong)dset_id;
+} /* end Java_hdf_hdf5lib_H5__1H5Dcreate_1anon */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dget_space_status
+ * Signature: (J)I;
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Dget_1space_1status(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    H5D_space_status_t space_status = H5D_SPACE_STATUS_ERROR;
+
+    if (H5Dget_space_status((hid_t)loc_id, &space_status) < 0)
+        h5libraryError(env);
+
+    return (jint)space_status;
+} /* end Java_hdf_hdf5lib_H5_H5Dget_1space_1status */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dget_access_plist
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Dget_1access_1plist(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    hid_t retVal = -1;
+
+    retVal = H5Dget_access_plist((hid_t)loc_id);
+    if (retVal < 0)
+        h5libraryError(env);
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Dget_1access_1plist */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dget_offset
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Dget_1offset(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    haddr_t offset = HADDR_UNDEF;
+
+    offset = H5Dget_offset((hid_t)loc_id);
+    if (offset == HADDR_UNDEF)
+        h5libraryError(env);
+
+    return (jlong)offset;
+} /* end Java_hdf_hdf5lib_H5_H5Dget_1offset */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dvlen_get_buf_size
+ * Signature: (JJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size(JNIEnv *env, jclass clss, jlong dataset_id, jlong type_id, jlong space_id)
+{
+  hsize_t sz = 0;
+
+  if (H5Dvlen_get_buf_size((hid_t)dataset_id, (hid_t)type_id, (hid_t)space_id, &sz) < 0)
+      h5libraryError(env);
+
+  return (jlong)sz;
+} /* end Java_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size_1long */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dfill
+ * Signature: ([BJ[BJJ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Dfill(JNIEnv *env, jclass clss, jbyteArray fill, jlong fill_type_id, jbyteArray buf, jlong buf_type_id, jlong space_id)
+{
+    herr_t    status;
+    jbyte    *fillP;
+    jbyte    *buffP;
+    jboolean  isCopy1;
+    jboolean  isCopy2;
+
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dfill:  buf is NULL");
+        return;
+    } /* end if */
+    buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy2);
+    if (buffP == NULL) {
+        h5JNIFatalError(env, "H5Dfill:  buf not pinned");
+        return;
+    } /* end if */
+
+    if(fill) {
+        fillP = ENVPTR->GetByteArrayElements(ENVPAR fill, &isCopy1);
+        if (fillP == NULL) {
+            ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT);
+            h5JNIFatalError( env, "H5Dfill:  fill not pinned");
+            return;
+        } /* end if */
+    } /* end if */
+    else
+        fillP = NULL;
+
+    status = H5Dfill((const void*)fillP, (hid_t)fill_type_id, (void*)buffP, (hid_t)buf_type_id, (hid_t)space_id);
+    if(fillP) {
+        /* free the buffer without copying back */
+        /* end if */ ENVPTR->ReleaseByteArrayElements(ENVPAR fill, fillP, JNI_ABORT);
+    }
+    if (status < 0) {
+        ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT);
+        h5libraryError(env);
+    } /* end if */
+    else {
+        if (isCopy2 == JNI_TRUE) {
+            ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, 0);
+        } /* end if */
+    } /* end else */
+} /* end Java_hdf_hdf5lib_H5_H5Dfill */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dset_extent
+ * Signature: (J[J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Dset_1extent(JNIEnv *env, jclass clss, jlong loc_id, jlongArray buf)
+{
+    herr_t    status;
+    hsize_t  *dims;
+    jlong    *buffP;
+    jsize     rank;
+    jboolean  isCopy;
+    int       i = 0;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5Dset_extent:  buf is NULL");
+        return;
+    } /* end if */
+
+    rank = ENVPTR->GetArrayLength(ENVPAR buf);
+    if (rank <= 0) {
+        h5JNIFatalError(env, "H5Dset_extent:  rank <=0");
+    } /* end if */
+    else {
+        buffP = ENVPTR->GetLongArrayElements(ENVPAR buf, &isCopy);
+        if (buffP == NULL) {
+            h5JNIFatalError( env, "H5Dset_extent:  buf not pinned");
+        } /* end if */
+        else {
+            dims = (hsize_t*)HDmalloc((size_t)rank * sizeof(hsize_t));
+            for (i = 0; i< rank; i++)
+                dims[i] = (hsize_t)buffP[i];
+
+            status = H5Dset_extent((hid_t)loc_id, (hsize_t*)dims);
+
+            HDfree (dims);
+
+            /* free the buffer without copying back */
+            ENVPTR->ReleaseLongArrayElements(ENVPAR buf, buffP, JNI_ABORT);
+
+            if (status < 0) {
+                h5libraryError(env);
+            } /* end if */
+        } /* end else */
+    } /* end else */
+} /* end Java_hdf_hdf5lib_H5_H5Dset_1extent */
+
+static herr_t
+H5D_iterate_cb(void* elem, hid_t elem_id, unsigned ndim, const hsize_t *point, void *op_data) {
+    JNIEnv    *cbenv;
+    jint       status;
+    jclass     cls;
+    jmethodID  mid;
+    jbyteArray elemArray;
+    jlongArray pointArray;
+    jsize      size;
+
+    if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
+        JVMPTR->DetachCurrentThread(JVMPAR);
+        return -1;
+    } /* end if */
+    cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback);
+    if (cls == 0) {
+       JVMPTR->DetachCurrentThread(JVMPAR);
+       return -1;
+    } /* end if */
+    mid = CBENVPTR->GetMethodID(CBENVPAR cls, "callback", "([BJI[JLhdf/hdf5lib/callbacks/H5D_iterate_t;)I");
+    if (mid == 0) {
+        JVMPTR->DetachCurrentThread(JVMPAR);
+        return -1;
+    } /* end if */
+
+    if (elem == NULL) {
+        JVMPTR->DetachCurrentThread(JVMPAR);
+        return -1;
+    } /* end if */
+    if (point == NULL) {
+        JVMPTR->DetachCurrentThread(JVMPAR);
+        return -1;
+    } /* end if */
+
+    size = (jsize)H5Tget_size(elem_id);
+    elemArray = CBENVPTR->NewByteArray(CBENVPAR size);
+    if (elemArray == NULL) {
+        JVMPTR->DetachCurrentThread(JVMPAR);
+        return -1;
+    } /* end if */
+    CBENVPTR->SetByteArrayRegion(CBENVPAR elemArray, 0, size, (jbyte *)elem);
+
+    pointArray = CBENVPTR->NewLongArray(CBENVPAR 2);
+    if (pointArray == NULL) {
+        JVMPTR->DetachCurrentThread(JVMPAR);
+        return -1;
+    } /* end if */
+    CBENVPTR->SetLongArrayRegion(CBENVPAR pointArray, 0, 2, (const jlong *)point);
+
+    status = CBENVPTR->CallIntMethod(CBENVPAR visit_callback, mid, (void*)elemArray, elem_id, ndim, pointArray, op_data);
+
+    CBENVPTR->GetByteArrayRegion(CBENVPAR elemArray, 0, size, (jbyte *)elem);
+
+    JVMPTR->DetachCurrentThread(JVMPAR);
+
+    return status;
+} /* end H5D_iterate_cb */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Diterate
+ * Signature: ([BJJLjava/lang/Object;Ljava/lang/Object;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Diterate(JNIEnv *env, jclass clss, jbyteArray buf, jlong buf_type, jlong space,
+          jobject callback_op, jobject op_data)
+{
+    herr_t        status = -1;
+    jboolean      isCopy;
+    jbyte        *buffP;
+
+    ENVPTR->GetJavaVM(ENVPAR &jvm);
+    visit_callback = callback_op;
+
+    if (op_data == NULL) {
+        h5nullArgument(env,  "H5Diterate:  op_data is NULL");
+        return -1;
+    } /* end if */
+    if (callback_op == NULL) {
+        h5nullArgument(env,  "H5Diterate:  callback_op is NULL");
+        return -1;
+    } /* end if */
+
+    if (buf == NULL) {
+        h5nullArgument(env,  "H5Diterate:  buf is NULL");
+        return -1;
+    } /* end if */
+    buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
+    if (buffP == NULL) {
+        h5JNIFatalError(env, "H5Diterate:  buf not pinned");
+    } /* end if */
+    else {
+        status = H5Diterate((void*)buffP, (hid_t)buf_type, (hid_t)space, (H5D_operator_t)H5D_iterate_cb, (void*)op_data);
+
+        if (status < 0) {
+        ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT);
+        h5libraryError(env);
+        } /* end if */
+        else {
+            if (isCopy == JNI_TRUE) {
+                ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, 0);
+            } /* end if */
+        } /* end else */
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Diterate */
+
+
+#ifdef __cplusplus
+} /* end extern "C" */
+#endif /* __cplusplus */