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authorAllen Byrne <byrn@hdfgroup.org>2018-06-26 14:35:07 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2018-06-26 14:35:07 (GMT)
commit7636342d959bfd3d023345bac76650932961d843 (patch)
treeaca513b9b30c2551e5f2d946bc180097ed4733bf /java/src
parentf89bdb7753786994887fb882c459a898b1bade63 (diff)
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Push updates from develop
Diffstat (limited to 'java/src')
-rw-r--r--java/src/hdf/hdf5lib/HDF5Constants.java3
-rw-r--r--java/src/hdf/hdf5lib/HDFArray.java5
-rw-r--r--java/src/jni/h5Constants.c2
-rw-r--r--java/src/jni/h5aImp.c322
-rw-r--r--java/src/jni/h5aImp.h18
-rw-r--r--java/src/jni/h5dImp.c206
-rw-r--r--java/src/jni/h5util.c297
-rw-r--r--java/src/jni/h5util.h21
8 files changed, 605 insertions, 269 deletions
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 43109f2..7eddac0 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -623,6 +623,7 @@ public class HDF5Constants {
public static final long H5T_UNIX_D64LE = H5T_UNIX_D64LE();
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 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();
@@ -1825,6 +1826,8 @@ public class HDF5Constants {
private static native final int H5T_VLEN();
+ private static native final int H5T_VL_T();
+
private static native final int H5Z_CB_CONT();
private static native final int H5Z_CB_ERROR();
diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java
index 529aecb..30f0fc8 100644
--- a/java/src/hdf/hdf5lib/HDFArray.java
+++ b/java/src/hdf/hdf5lib/HDFArray.java
@@ -1025,8 +1025,11 @@ class ArrayDescriptor {
NTsize = 8;
}
else if (css.startsWith("Ljava.lang.String")) {
+ NT = 'L';
+ className = "java.lang.String";
+ NTsize = 1;
throw new HDF5JavaException(new String(
- "ArrayDesciptor: Error: String array not supported yet"));
+ "ArrayDesciptor: Warning: String array not fully supported yet"));
}
else {
/*
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 0f4361f..c99745d 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -1231,6 +1231,8 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5T_1VARIABLE(JNIEnv *env, jclass cls) { return (int)H5T_VARIABLE; }
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5T_1VLEN(JNIEnv *env, jclass cls) { return H5T_VLEN; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5T_1VL_1T(JNIEnv *env, jclass cls) { return sizeof(hvl_t); }
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1CONT(JNIEnv *env, jclass cls) { return H5Z_CB_CONT; }
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index 26ec4fc..13f5207 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -49,6 +49,10 @@ extern jobject visit_callback;
/* Local Prototypes */
/********************/
+static herr_t H5AwriteVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
+static herr_t H5AwriteVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
+static herr_t H5AreadVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
+static herr_t H5AreadVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *op_data);
@@ -178,7 +182,6 @@ Java_hdf_hdf5lib_H5_H5Aread
} /* end if */
else {
status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP);
-
if (status < 0) {
ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
h5libraryError(env);
@@ -194,6 +197,323 @@ Java_hdf_hdf5lib_H5_H5Aread
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5AwriteVL
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5AwriteVL
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
+{
+ herr_t status = -1;
+ htri_t isStr = 0;
+ htri_t isVlenStr = 0;
+ htri_t isComplex = 0;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5AwriteVL: buf is NULL");
+ } /* end if */
+ else {
+ isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
+ if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) {
+ unsigned i;
+ int nm = H5Tget_nmembers(mem_type_id);
+ for(i = 0; i <nm; i++) {
+ hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i);
+ isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) ||
+ H5Tdetect_class((hid_t)nested_tid, H5T_VLEN);
+ H5Tclose(nested_tid);
+ }
+ }
+ else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) {
+ isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
+ }
+ if (isStr == 0 || isComplex>0 || isVlenStr) {
+ status = H5AwriteVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
+ }
+ else if (isStr > 0) {
+ status = H5AwriteVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
+ }
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */
+
+herr_t
+H5AwriteVL_str
+ (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+{
+ herr_t status = -1;
+ char **wdata;
+ jsize size;
+ jint i;
+
+ size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
+
+ wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
+ if (!wdata) {
+ h5JNIFatalError(env, "H5AwriteVL_str: 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);
+ } /* end if */
+ } /* end if */
+
+ ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
+ ENVPTR->DeleteLocalRef(ENVPAR obj);
+ } /* end if */
+ } /* end for (i = 0; i < size; ++i) */
+
+ status = H5Awrite((hid_t)aid, (hid_t)tid, wdata);
+
+ 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 (jint)status;
+}
+
+herr_t
+H5AwriteVL_asstr
+ (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+{
+ char **strs;
+ jstring jstr;
+ jint i;
+ jint n;
+ hid_t sid;
+ hsize_t dims[H5S_MAX_RANK];
+ herr_t status = -1;
+
+ n = ENVPTR->GetArrayLength(ENVPAR buf);
+ strs =(hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+
+ if (strs == NULL) {
+ h5JNIFatalError(env, "H5AwriteVL_asstr: failed to allocate buff for read variable length strings");
+ } /* end if */
+ else {
+ status = H5Awrite(aid, tid, strs);
+
+ if (status < 0) {
+ dims[0] = (hsize_t)n;
+ sid = H5Screate_simple(1, dims, NULL);
+ H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
+ H5Sclose(sid);
+ HDfree(strs);
+ h5JNIFatalError(env, "H5AwriteVL_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 H5AwriteVL_str */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5AreadVL
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5AreadVL
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
+{
+ herr_t status = -1;
+ htri_t isStr = 0;
+ htri_t isVlenStr = 0;
+ htri_t isComplex = 0;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5AreadVL: buf is NULL");
+ } /* end if */
+ else {
+ isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
+ if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) {
+ unsigned i;
+ int nm = H5Tget_nmembers(mem_type_id);
+ for(i = 0; i <nm; i++) {
+ hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i);
+ isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) ||
+ H5Tdetect_class((hid_t)nested_tid, H5T_VLEN);
+ H5Tclose(nested_tid);
+ }
+ }
+ else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) {
+ isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
+ }
+ if (isStr == 0 || isComplex>0 || isVlenStr) {
+ status = H5AreadVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
+ }
+ else if (isStr > 0) {
+ status = H5AreadVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
+ }
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1VL */
+
+herr_t
+H5AreadVL_asstr
+ (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+{
+ jint i;
+ jint n;
+ hid_t sid;
+ jstring jstr;
+ h5str_t h5str;
+ hvl_t *rdata;
+ hsize_t dims[H5S_MAX_RANK];
+ size_t size;
+ size_t max_len = 0;
+ herr_t status = -1;
+
+ /* Get size of string array */
+ n = ENVPTR->GetArrayLength(ENVPAR buf);
+ /* we will need to read n number of hvl_t structures */
+ rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+ if (rdata == NULL) {
+ h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buff for read");
+ } /* end if */
+ else {
+ status = H5Aread(aid, tid, rdata);
+
+ if (status < 0) {
+ dims[0] = (hsize_t)n;
+ sid = H5Screate_simple(1, dims, NULL);
+ H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
+ H5Sclose(sid);
+ HDfree(rdata);
+ h5JNIFatalError(env, "H5AreadVL_asstr: failed to read data");
+ } /* end if */
+ else {
+ /* calculate the largest size of all the hvl_t structures read */
+ max_len = 1;
+ for (i=0; i < n; i++) {
+ if ((rdata + i)->len > max_len)
+ max_len = (rdata + i)->len;
+ }
+
+ /* create one malloc to hold largest element */
+ size = H5Tget_size(tid) * max_len;
+ HDmemset(&h5str, 0, sizeof(h5str_t));
+ h5str_new(&h5str, 4 * size);
+
+ if (h5str.s == NULL) {
+ dims[0] = (hsize_t)n;
+ sid = H5Screate_simple(1, dims, NULL);
+ H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
+ H5Sclose(sid);
+ HDfree(rdata);
+ h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buf");
+ } /* end if */
+ else {
+ H5T_class_t tclass = H5Tget_class(tid);
+ /* convert each element to char string */
+ for (i=0; i < n; i++) {
+ h5str.s[0] = '\0';
+ h5str_vlsprintf(&h5str, aid, tid, rdata+i, 0);
+ jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
+ ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+ } /* end for */
+ h5str_free(&h5str);
+
+ dims[0] = (hsize_t)n;
+ sid = H5Screate_simple(1, dims, NULL);
+ H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
+ H5Sclose(sid);
+ HDfree(rdata);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return status;
+}
+
+herr_t
+H5AreadVL_str
+ (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+{
+ char **strs;
+ jstring jstr;
+ jint i;
+ jint n;
+ hid_t sid;
+ hsize_t dims[H5S_MAX_RANK];
+ herr_t status = -1;
+
+ n = ENVPTR->GetArrayLength(ENVPAR buf);
+ strs =(char**)HDcalloc((size_t)n, sizeof(char*));
+
+ if (strs == NULL) {
+ h5JNIFatalError(env, "H5AreadVL_str: failed to allocate buff for read variable length strings");
+ } /* end if */
+ else {
+ status = H5Aread(aid, tid, strs);
+
+ if (status < 0) {
+ dims[0] = (hsize_t)n;
+ sid = H5Screate_simple(1, dims, NULL);
+ H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
+ H5Sclose(sid);
+ HDfree(strs);
+ h5JNIFatalError(env, "H5AreadVL_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 H5AreadVL_str */
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Aget_space
* Signature: (J)J
*/
diff --git a/java/src/jni/h5aImp.h b/java/src/jni/h5aImp.h
index 62769fd..f3758eb 100644
--- a/java/src/jni/h5aImp.h
+++ b/java/src/jni/h5aImp.h
@@ -69,6 +69,24 @@ Java_hdf_hdf5lib_H5_H5Aread
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5AwriteVL
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5AwriteVL
+ (JNIEnv *, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5AreadVL
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5AreadVL
+ (JNIEnv *, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Aget_space
* Signature: (J)J
*/
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 9784055..1d7b823 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -993,96 +993,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double
/*
* Class: hdf_hdf5lib_H5
- * Method: H5DreadVL
- * Signature: (JJJJJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5DreadVL
- (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, "H5DreadVL: buf is NULL");
- } /* end if */
- else {
- isVlenStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
-
- if (isVlenStr)
- h5badArgument(env, "H5DreadVL: type is not variable length non-string");
- else
- status = H5DreadVL_asstr(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 else */
-
- return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Dread_1VL */
-
-herr_t
-H5DreadVL_asstr
- (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf)
-{
- jint i;
- jint n;
- jstring jstr;
- h5str_t h5str;
- hvl_t *rdata;
- size_t size;
- size_t max_len = 0;
- herr_t status = -1;
-
- n = ENVPTR->GetArrayLength(ENVPAR buf);
- rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
- if (rdata == NULL) {
- h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read");
- } /* end if */
- else {
- status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata);
-
- if (status < 0) {
- H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
- HDfree(rdata);
- h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data");
- } /* end if */
- else {
- max_len = 1;
- for (i=0; i < n; i++) {
- if ((rdata + i)->len > max_len)
- max_len = (rdata + i)->len;
- }
-
- size = H5Tget_size(tid) * max_len;
- HDmemset(&h5str, 0, sizeof(h5str_t));
- h5str_new(&h5str, 4 * size);
-
- if (h5str.s == NULL) {
- H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
- HDfree(rdata);
- h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buf");
- } /* end if */
- else {
- for (i=0; i < n; i++) {
- h5str.s[0] = '\0';
- h5str_sprintf(&h5str, did, tid, rdata+i, 0);
- jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
- ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
- } /* end for */
- h5str_free(&h5str);
-
- H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
- HDfree(rdata);
- } /* end else */
- } /* end else */
- } /* end else */
-
- return status;
-}
-
-/*
- * Class: hdf_hdf5lib_H5
* Method: H5Dread_string
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
@@ -1218,6 +1128,120 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1string
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1string */
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5DreadVL
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5DreadVL
+ (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 isStr = 0;
+ htri_t isVlenStr = 0;
+ htri_t isComplex = 0;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5DreadVL: buf is NULL");
+ } /* end if */
+ else {
+ isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
+ if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) {
+ unsigned i;
+ int nm = H5Tget_nmembers(mem_type_id);
+ for(i = 0; i <nm; i++) {
+ hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i);
+ isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) ||
+ H5Tdetect_class((hid_t)nested_tid, H5T_VLEN);
+ H5Tclose(nested_tid);
+ }
+ }
+ else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) {
+ isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
+ }
+ if (isStr == 0 || isComplex>0 || isVlenStr) {
+ status = H5DreadVL_asstr(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);
+ }
+ else if (isStr > 0) {
+ 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 else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1VL */
+
+herr_t
+H5DreadVL_asstr
+ (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf)
+{
+ jint i;
+ jint n;
+ jstring jstr;
+ h5str_t h5str;
+ hvl_t *rdata;
+ size_t size;
+ size_t max_len = 0;
+ herr_t status = -1;
+
+ /* Get size of string array */
+ n = ENVPTR->GetArrayLength(ENVPAR buf);
+ /* we will need to read n number of hvl_t structures */
+ rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+ if (rdata == NULL) {
+ h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read");
+ } /* end if */
+ else {
+ status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata);
+
+ if (status < 0) {
+ H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+ HDfree(rdata);
+ h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data");
+ } /* end if */
+ else {
+ /* calculate the largest size of all the hvl_t structures read */
+ max_len = 1;
+ for (i=0; i < n; i++) {
+ if ((rdata + i)->len > max_len)
+ max_len = (rdata + i)->len;
+ }
+
+ /* create one malloc to hold largest element */
+ size = H5Tget_size(tid) * max_len;
+ HDmemset(&h5str, 0, sizeof(h5str_t));
+ h5str_new(&h5str, 4 * size);
+
+ if (h5str.s == NULL) {
+ H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+ HDfree(rdata);
+ h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buf");
+ } /* end if */
+ else {
+ H5T_class_t tclass = H5Tget_class(tid);
+ /* convert each element to char string */
+ for (i=0; i < n; i++) {
+ h5str.s[0] = '\0';
+ h5str_vlsprintf(&h5str, did, tid, rdata+i, 0);
+ jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
+ ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+ } /* end for */
+ h5str_free(&h5str);
+
+ H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+ HDfree(rdata);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return status;
+}
+
/**
* Read VLEN data into array of arrays.
* Object[] buf contains VL arrays of data points
@@ -1433,7 +1457,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref
h5str_new(&h5str, 1024);
for (i=0; i<n; i++) {
h5str.s[0] = '\0';
- h5str_sprintf(&h5str, did, tid, ref_data[i], 0);
+ h5str_sprintf(&h5str, did, tid, ref_data[i], 0, 0);
jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 9a98202..385bfc7 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -21,6 +21,7 @@
extern "C" {
#endif /* __cplusplus */
+#include <jni.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
@@ -152,6 +153,100 @@ h5str_append
return HDstrcat(str->s, cstr);
} /* end h5str_append */
+/** print value of a vlen data point into string.
+ Return Value:
+ On success, the total number of characters printed is returned.
+ On error, a negative number is returned.
+ */
+size_t
+h5str_vlsprintf
+ (h5str_t *str, hid_t container, hid_t tid, hvl_t *ptr, int expand_data)
+{
+ unsigned char tmp_uchar = 0;
+ char tmp_char = 0;
+ unsigned short tmp_ushort = 0;
+ short tmp_short = 0;
+ unsigned int tmp_uint = 0;
+ int tmp_int = 0;
+ unsigned long tmp_ulong = 0;
+ long tmp_long = 0;
+ unsigned long long tmp_ullong = 0;
+ long long tmp_llong = 0;
+ float tmp_float = 0.0;
+ double tmp_double = 0.0;
+ long double tmp_ldouble = 0.0;
+ static char fmt_llong[8], fmt_ullong[8];
+
+ hid_t mtid = -1;
+ size_t offset;
+ size_t nll;
+ char *this_str;
+ size_t this_strlen;
+ int n;
+ H5T_class_t tclass = H5Tget_class(tid);
+ size_t size = H5Tget_size(tid);
+ H5T_sign_t nsign = H5Tget_sign(tid);
+ int bdata_print = 0;
+
+ if (!str || !ptr)
+ return 0;
+
+ /* Build default formats for long long types */
+ if (!fmt_llong[0]) {
+ sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH);
+ sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH);
+ } /* end if */
+
+ this_str = NULL;
+ this_strlen = 0;
+
+ switch (tclass) {
+ case H5T_COMPOUND:
+ {
+ unsigned i;
+ n = H5Tget_nmembers(tid);
+ h5str_append(str, " {");
+
+ for (i = 0; i < n; i++) {
+ offset = H5Tget_member_offset(tid, i);
+ mtid = H5Tget_member_type(tid, i);
+ h5str_sprintf(str, container, mtid, ((char *) (ptr->p)) + offset, ptr->len, expand_data);
+ if ((i + 1) < n)
+ h5str_append(str, ", ");
+ H5Tclose(mtid);
+ }
+ h5str_append(str, "} ");
+ }
+ break;
+ case H5T_ARRAY:
+ {
+ int rank = 0;
+ hsize_t i, dims[H5S_MAX_RANK], total_elmts;
+ h5str_append(str, "[ ");
+
+ mtid = H5Tget_super(tid);
+ size = H5Tget_size(mtid);
+ rank = H5Tget_array_ndims(tid);
+
+ H5Tget_array_dims2(tid, dims);
+
+ total_elmts = 1;
+ for (i = 0; i < rank; i++)
+ total_elmts *= dims[i];
+
+ h5str_sprintf(str, container, mtid, ((char *) (ptr->p)), ptr->len, expand_data);
+ H5Tclose(mtid);
+ h5str_append(str, " ] ");
+ }
+ break;
+ default:
+ this_strlen = h5str_sprintf(str, container, tid, ((char *) (ptr->p)), ptr->len, expand_data);
+ break;
+ } /* end switch */
+
+ return this_strlen;
+} /* end h5str_vlsprintf */
+
/** print value of a data point into string.
Return Value:
On success, the total number of characters printed is returned.
@@ -159,7 +254,7 @@ h5str_append
*/
size_t
h5str_sprintf
- (h5str_t *str, hid_t container, hid_t tid, void *ptr, int expand_data)
+ (h5str_t *str, hid_t container, hid_t tid, void *ptr, int ptr_len, int expand_data)
{
unsigned char tmp_uchar = 0;
char tmp_char = 0;
@@ -182,9 +277,8 @@ h5str_sprintf
char *this_str;
size_t this_strlen;
int n;
- hvl_t *vlptr;
- char *cptr = (char*) ptr;
- unsigned char *ucptr = (unsigned char*) ptr;
+ char *cptr = (char*) (ptr);
+ unsigned char *ucptr = (unsigned char*) (ptr);
H5T_class_t tclass = H5Tget_class(tid);
size_t size = H5Tget_size(tid);
H5T_sign_t nsign = H5Tget_sign(tid);
@@ -206,20 +300,20 @@ h5str_sprintf
case H5T_FLOAT:
if (sizeof(float) == size) {
/* if (H5Tequal(tid, H5T_NATIVE_FLOAT)) */
- HDmemcpy(&tmp_float, ptr, sizeof(float));
+ HDmemcpy(&tmp_float, cptr, sizeof(float));
this_str = (char*)HDmalloc(25);
sprintf(this_str, "%g", tmp_float);
}
else if (sizeof(double) == size) {
/* if (H5Tequal(tid, H5T_NATIVE_DOUBLE)) */
- HDmemcpy(&tmp_double, ptr, sizeof(double));
+ HDmemcpy(&tmp_double, cptr, sizeof(double));
this_str = (char*)HDmalloc(25);
sprintf(this_str, "%g", tmp_double);
}
#if H5_SIZEOF_LONG_DOUBLE !=0
else if (sizeof(long double) == size) {
/* if (H5Tequal(tid, H5T_NATIVE_LDOUBLE)) */
- HDmemcpy(&tmp_ldouble, ptr, sizeof(long double));
+ HDmemcpy(&tmp_ldouble, cptr, sizeof(long double));
this_str = (char*)HDmalloc(27);
sprintf(this_str, "%Lf", tmp_ldouble);
}
@@ -256,13 +350,13 @@ h5str_sprintf
if (sizeof(char) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_UCHAR)) */
- HDmemcpy(&tmp_uchar, ptr, sizeof(unsigned char));
+ HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char));
this_str = (char*)HDmalloc(7);
sprintf(this_str, "%u", tmp_uchar);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_SCHAR)) */
- HDmemcpy(&tmp_char, ptr, sizeof(char));
+ HDmemcpy(&tmp_char, cptr, sizeof(char));
this_str = (char*)HDmalloc(7);
sprintf(this_str, "%hhd", tmp_char);
}
@@ -270,13 +364,13 @@ h5str_sprintf
else if (sizeof(int) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_UINT)) */
- HDmemcpy(&tmp_uint, ptr, sizeof(unsigned int));
+ HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int));
this_str = (char*)HDmalloc(14);
sprintf(this_str, "%u", tmp_uint);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_INT)) */
- HDmemcpy(&tmp_int, ptr, sizeof(int));
+ HDmemcpy(&tmp_int, cptr, sizeof(int));
this_str = (char*)HDmalloc(14);
sprintf(this_str, "%d", tmp_int);
}
@@ -284,13 +378,13 @@ h5str_sprintf
else if (sizeof(short) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_USHORT)) */
- HDmemcpy(&tmp_ushort, ptr, sizeof(unsigned short));
+ HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short));
this_str = (char*)HDmalloc(9);
sprintf(this_str, "%u", tmp_ushort);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_SHORT)) */
- HDmemcpy(&tmp_short, ptr, sizeof(short));
+ HDmemcpy(&tmp_short, cptr, sizeof(short));
this_str = (char*)HDmalloc(9);
sprintf(this_str, "%d", tmp_short);
}
@@ -298,13 +392,13 @@ h5str_sprintf
else if (sizeof(long) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_ULONG)) */
- HDmemcpy(&tmp_ulong, ptr, sizeof(unsigned long));
+ HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long));
this_str = (char*)HDmalloc(23);
sprintf(this_str, "%lu", tmp_ulong);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_LONG)) */
- HDmemcpy(&tmp_long, ptr, sizeof(long));
+ HDmemcpy(&tmp_long, cptr, sizeof(long));
this_str = (char*)HDmalloc(23);
sprintf(this_str, "%ld", tmp_long);
}
@@ -312,13 +406,13 @@ h5str_sprintf
else if (sizeof(long long) == size) {
if(H5T_SGN_NONE == nsign) {
/* if (H5Tequal(tid, H5T_NATIVE_ULLONG)) */
- HDmemcpy(&tmp_ullong, ptr, sizeof(unsigned long long));
+ HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long));
this_str = (char*)HDmalloc(25);
sprintf(this_str, fmt_ullong, tmp_ullong);
}
else {
/* if (H5Tequal(tid, H5T_NATIVE_LLONG)) */
- HDmemcpy(&tmp_llong, ptr, sizeof(long long));
+ HDmemcpy(&tmp_llong, cptr, sizeof(long long));
this_str = (char*)HDmalloc(25);
sprintf(this_str, fmt_llong, tmp_llong);
}
@@ -333,8 +427,8 @@ h5str_sprintf
for (i = 0; i < n; i++) {
offset = H5Tget_member_offset(tid, i);
mtid = H5Tget_member_type(tid, i);
- h5str_sprintf(str, container, mtid, cptr + offset, expand_data);
- if (i < n - 1)
+ h5str_sprintf(str, container, mtid, cptr + offset, ptr_len, expand_data);
+ if ((i + 1) < n)
h5str_append(str, ", ");
H5Tclose(mtid);
}
@@ -344,7 +438,7 @@ h5str_sprintf
case H5T_ENUM:
{
char enum_name[1024];
- if (H5Tenum_nameof(tid, ptr, enum_name, sizeof enum_name) >= 0) {
+ if (H5Tenum_nameof(tid, cptr, enum_name, sizeof enum_name) >= 0) {
h5str_append(str, enum_name);
}
else {
@@ -363,7 +457,7 @@ h5str_sprintf
}
break;
case H5T_REFERENCE:
- if (h5str_is_zero(ptr, size)) {
+ if (h5str_is_zero(cptr, size)) {
h5str_append(str, "NULL");
}
else {
@@ -379,9 +473,9 @@ h5str_sprintf
H5S_sel_type region_type;
/* get name of the dataset the region reference points to using H5Rget_name */
- region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, ptr);
+ region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, cptr);
if (region_obj >= 0) {
- region = H5Rget_region(container, H5R_DATASET_REGION, ptr);
+ region = H5Rget_region(container, H5R_DATASET_REGION, cptr);
if (region >= 0) {
if(expand_data) {
region_type = H5Sget_select_type(region);
@@ -393,7 +487,7 @@ h5str_sprintf
}
}
else {
- if(H5Rget_name(region_obj, H5R_DATASET_REGION, ptr, (char*)ref_name, 1024) >= 0) {
+ if(H5Rget_name(region_obj, H5R_DATASET_REGION, cptr, (char*)ref_name, 1024) >= 0) {
h5str_append(str, ref_name);
}
@@ -424,7 +518,7 @@ h5str_sprintf
hid_t obj;
this_str = (char*)HDmalloc(64);
- obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, ptr);
+ obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, cptr);
H5Oget_info2(obj, &oi, H5O_INFO_ALL);
/* Print object data and close object */
@@ -450,31 +544,30 @@ h5str_sprintf
total_elmts *= dims[i];
for (i = 0; i < total_elmts; i++) {
- h5str_sprintf(str, container, mtid, cptr + i * size, expand_data);
- if (i < total_elmts - 1)
+ h5str_sprintf(str, container, mtid, cptr + i * size, ptr_len, expand_data);
+ if ((i + 1) < total_elmts)
h5str_append(str, ", ");
}
H5Tclose(mtid);
- h5str_append(str, "] ");
+ h5str_append(str, " ] ");
}
break;
case H5T_VLEN:
- {
- unsigned int i;
- mtid = H5Tget_super(tid);
- size = H5Tget_size(mtid);
-
- vlptr = (hvl_t *) cptr;
-
- nll = vlptr->len;
- for (i = 0; i < (int)nll; i++) {
- h5str_sprintf(str, container, mtid, ((char *) (vlptr->p)) + i * size, expand_data);
- if (i < (int)nll - 1)
- h5str_append(str, ", ");
+ {
+ unsigned int i;
+ mtid = H5Tget_super(tid);
+ size = H5Tget_size(mtid);
+
+ h5str_append(str, "{");
+ for (i = 0; i < (int)ptr_len; i++) {
+ h5str_sprintf(str, container, mtid, cptr + i * size, ptr_len, expand_data);
+ if ((i + 1) < (int)ptr_len)
+ h5str_append(str, ", ");
+ }
+ H5Tclose(mtid);
+ h5str_append(str, "}");
}
- H5Tclose(mtid);
- }
- break;
+ break;
default:
{
@@ -563,7 +656,7 @@ h5str_print_region_data_blocks
if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) {
if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) {
for (numindex = 0; numindex < numelem; numindex++) {
- h5str_sprintf(str, region_id, type_id, ((char*)region_buf + numindex * type_size), 1);
+ h5str_sprintf(str, region_id, type_id, ((char*)region_buf + numindex * type_size), 0, 1);
if (numindex + 1 < numelem)
h5str_append(str, ", ");
@@ -763,7 +856,7 @@ h5str_print_region_data_points
for (jndx = 0; jndx < npoints; jndx++) {
if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) {
- h5str_sprintf(str, region_id, type_id, ((char*)region_buf + jndx * type_size), 1);
+ h5str_sprintf(str, region_id, type_id, ((char*)region_buf + jndx * type_size), 0, 1);
if (jndx + 1 < npoints)
h5str_append(str, ", ");
@@ -1883,7 +1976,7 @@ h5tools_dump_simple_data
/* Render the data element*/
h5str_new(&buffer, 32 * size);
- bytes_in = h5str_sprintf(&buffer, container, type, memref, 1);
+ bytes_in = h5str_sprintf(&buffer, container, type, memref, 0, 1);
if(i > 0) {
HDfprintf(stream, ", ");
if (line_count >= H5TOOLS_TEXT_BLOCK) {
@@ -1909,116 +2002,6 @@ h5tools_dump_simple_data
/*
* Class: hdf_hdf5lib_H5
- * Method: H5AwriteVL
- * Signature: (JJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AwriteVL
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
-{
- herr_t status = -1;
- char **wdata;
- jsize size;
- jint i;
-
- size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
-
- wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
- if (!wdata) {
- h5JNIFatalError(env, "H5AwriteVL: 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);
- } /* end if */
- } /* end if */
-
- ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
- ENVPTR->DeleteLocalRef(ENVPAR obj);
- } /* end if */
- } /* end for (i = 0; i < size; ++i) */
-
- status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, wdata);
-
- 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 (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5AwriteVL */
-
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5AreadVL
- * Signature: (JJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AreadVL
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
-{
- herr_t status = -1;
- jstring jstr;
- char **strs;
- int i, n;
- hid_t sid;
- hsize_t dims[H5S_MAX_RANK];
-
- n = ENVPTR->GetArrayLength(ENVPAR buf);
-
- strs =(char **)HDmalloc((size_t)n * sizeof(char *));
- if (strs == NULL) {
- h5JNIFatalError( env, "H5AreadVL: failed to allocate buff for read variable length strings");
- } /* end if */
- else {
- status = H5Aread(attr_id, mem_type_id, strs);
- if (status < 0) {
- dims[0] = (hsize_t)n;
- sid = H5Screate_simple(1, dims, NULL);
- H5Dvlen_reclaim(mem_type_id, sid, H5P_DEFAULT, strs);
- H5Sclose(sid);
- HDfree(strs);
- h5JNIFatalError(env, "H5AreadVL: 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);
- HDfree (strs[i]);
- } /* end for */
-
- /*
- for repeatedly reading an attribute 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 "free(strs[i])" to free individual strings
- after it is done.
- H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
- */
-
- HDfree(strs);
- } /* end else */
- } /* end else */
- return status;
-} /* end Java_hdf_hdf5lib_H5_H5AreadVL */
-
-/*
- * Class: hdf_hdf5lib_H5
* Method: H5AreadComplex
* Signature: (JJ[Ljava/lang/String;)I
*/
@@ -2059,7 +2042,7 @@ Java_hdf_hdf5lib_H5_H5AreadComplex
else {
for (i = 0; i < n; i++) {
h5str.s[0] = '\0';
- h5str_sprintf(&h5str, attr_id, mem_type_id, rdata + ((size_t)i * size), 0);
+ h5str_sprintf(&h5str, attr_id, mem_type_id, rdata + ((size_t)i * size), 0, 0);
jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
} /* end for */
diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h
index 434a107..c6b41d2 100644
--- a/java/src/jni/h5util.h
+++ b/java/src/jni/h5util.h
@@ -39,7 +39,8 @@ extern void h5str_new (h5str_t *str, size_t len);
extern void h5str_free (h5str_t *str);
extern void h5str_resize (h5str_t *str, size_t new_len);
extern char* h5str_append (h5str_t *str, const char* cstr);
-extern size_t h5str_sprintf(h5str_t *str, hid_t container, hid_t tid, void *buf, int expand_data);
+extern size_t h5str_vlsprintf(h5str_t *str, hid_t container, hid_t tid, hvl_t *buf, int expand_data);
+extern size_t h5str_sprintf(h5str_t *str, hid_t container, hid_t tid, void *buf, int ptrlen, int expand_data);
extern void h5str_array_free(char **strs, size_t len);
extern int h5str_dump_simple_dset(FILE *stream, hid_t dset, int binary_order);
extern int h5str_dump_region_blocks_data(h5str_t *str, hid_t region, hid_t region_obj);
@@ -47,24 +48,6 @@ extern int h5str_dump_region_points_data(h5str_t *str, hid_t region, hid_t r
/*
* Class: hdf_hdf5lib_H5
- * Method: H5AwriteVL
- * Signature: (JJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AwriteVL
- (JNIEnv *, jclass, jlong, jlong, jobjectArray);
-
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5AreadVL
- * Signature: (JJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AreadVL
- (JNIEnv *, jclass, jlong, jlong, jobjectArray);
-
-/*
- * Class: hdf_hdf5lib_H5
* Method: H5AreadComplex
* Signature: (JJ[Ljava/lang/String;)I
*/