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MOAB: Mesh Oriented datABase
(version 5.4.1)
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MOAB: Mesh Oriented datABase
(version 5.4.1)
|
#include <stdlib.h>#include <string.h>#include <H5Tpublic.h>#include <H5Gpublic.h>#include <H5Dpublic.h>#include <H5Spublic.h>#include <H5Apublic.h>#include <H5Ppublic.h>#include "status.h"#include "file-handle.h"#include "mhdf.h"#include "util.h"#include "names-and-paths.h"
Include dependency graph for tags.c:Go to the source code of this file.
Functions | |
| hid_t | mhdf_getNativeType (hid_t input_type, int size, mhdf_Status *status) |
| Make type native-endian. | |
| static hid_t | get_tag (mhdf_FileHandle file_handle, const char *tag_name, hid_t *id_type, mhdf_Status *status) |
| static hid_t | get_tag_type (FileHandle *file_ptr, const char *tag_path, mhdf_Status *status) |
| static int | store_tag_val_in_attrib (hid_t tag_id, const char *attrib_name, hid_t type_id, const void *value, hsize_t value_size, mhdf_Status *status) |
| static hid_t | create_tag_common (mhdf_FileHandle file_handle, const char *tag_name, enum mhdf_TagDataType tag_type, int size, int storage, const void *default_value, int default_value_size_in, const void *global_value, int global_value_size_in, hid_t hdf_type, hid_t hdf_base_type, mhdf_Status *status) |
| hid_t | mhdf_getTagDataType (mhdf_FileHandle file_handle, const char *tag_name, mhdf_Status *status) |
| Get handle to HDF5 type object for tag data. | |
| void | mhdf_createTag (mhdf_FileHandle file_handle, const char *tag_name, enum mhdf_TagDataType tag_type, int size, int storage, const void *default_value, const void *global_value, hid_t hdf_type, hid_t hdf_base_type, mhdf_Status *status) |
| Add a tag to the file. | |
| void | mhdf_createVarLenTag (mhdf_FileHandle file_handle, const char *tag_name, enum mhdf_TagDataType tag_type, int storage, const void *default_value, int default_value_length, const void *global_value, int global_value_length, hid_t hdf_type, hid_t hdf_base_type, mhdf_Status *status) |
| Add variable-length tag to file. | |
| int | mhdf_getNumberTags (mhdf_FileHandle file_handle, mhdf_Status *status) |
| Get the number of tags in the file. | |
| char ** | mhdf_getTagNames (mhdf_FileHandle file_handle, int *num_names_out, mhdf_Status *status) |
| Get the name for each tag defined in the file. | |
| static int | get_attrib_array_length_handle (hid_t attrib_id) |
| static int | get_attrib_array_length_name (hid_t file, const char *path) |
| void | mhdf_getTagInfo (mhdf_FileHandle file_handle, const char *tag_name, enum mhdf_TagDataType *class_out, int *size_out, int *tstt_storage_out, int *have_default_out, int *have_global_out, int *have_sparse_out, mhdf_Status *status) |
| Get the description of a specified tag. | |
| static int | read_tag_attrib_data (hid_t tag_id, const char *attrib_name, hid_t type_id, void *data, int is_var_len, mhdf_Status *status) |
| void | mhdf_getTagValues (mhdf_FileHandle file_handle, const char *tag_name, hid_t output_data_type, void *default_value, void *global_value, mhdf_Status *status) |
| Get the default and global values of the tag. | |
| int | mhdf_haveDenseTag (mhdf_FileHandle file_handle, const char *tag_name, const char *type_handle, mhdf_Status *status) |
| Check if the file contains dense tag data for the specified tag and element group. | |
| hid_t | mhdf_createDenseTagData (mhdf_FileHandle file_handle, const char *tag_name, const char *type_handle, long num_values, mhdf_Status *status) |
| Create an object to hold dense tag values for a given element group. | |
| hid_t | mhdf_openDenseTagData (mhdf_FileHandle file_handle, const char *tag_name, const char *type_handle, long *num_values_out, mhdf_Status *status) |
| Open the object containing dense tag values for a given element group. | |
| void | mhdf_createSparseTagData (mhdf_FileHandle file_handle, const char *tag_name, long num_values, hid_t handles_out[2], mhdf_Status *status) |
| Create file objects to store sparse tag data. | |
| void | mhdf_createVarLenTagData (mhdf_FileHandle file_handle, const char *tag_name, long num_entities, long num_values, hid_t handles_out[3], mhdf_Status *status) |
| Create file objects to store (sparse) variable-length tag data. | |
| void | mhdf_openSparseTagData (mhdf_FileHandle file_handle, const char *tag_name, long *num_entity_out, long *num_values_out, hid_t handles_out[3], mhdf_Status *status) |
| Create file objects to read sparse tag data. | |
| void | mhdf_writeSparseTagEntities (hid_t table_id, long offset, long count, hid_t int_type, const void *id_list, mhdf_Status *status) |
| Write Global ID list for sparse tag data. | |
| void | mhdf_writeSparseTagEntitiesWithOpt (hid_t table_id, long offset, long count, hid_t int_type, const void *id_list, hid_t io_prop, mhdf_Status *status) |
| void | mhdf_writeTagValues (hid_t table_id, long offset, long count, hid_t tag_type, const void *tag_data, mhdf_Status *status) |
| Write tag values. | |
| void | mhdf_writeTagValuesWithOpt (hid_t table_id, long offset, long count, hid_t tag_type, const void *tag_data, hid_t io_prop, mhdf_Status *status) |
| void | mhdf_writeSparseTagIndices (hid_t table_id, long offset, long count, hid_t int_type, const void *indices, mhdf_Status *status) |
| Write sparse tag end indices for variable-length tag data. | |
| void | mhdf_writeSparseTagIndicesWithOpt (hid_t table_id, long offset, long count, hid_t int_type, const void *indices, hid_t io_prop, mhdf_Status *status) |
| void | mhdf_readSparseTagEntities (hid_t table_id, long offset, long count, hid_t int_type, void *id_list, mhdf_Status *status) |
| Read Global ID list for sparse tag data. | |
| void | mhdf_readSparseTagEntitiesWithOpt (hid_t table_id, long offset, long count, hid_t int_type, void *id_list, hid_t io_prop, mhdf_Status *status) |
| void | mhdf_readTagValues (hid_t table_id, long offset, long count, hid_t tag_type, void *tag_data, mhdf_Status *status) |
| Read tag values. | |
| void | mhdf_readTagValuesWithOpt (hid_t table_id, long offset, long count, hid_t tag_type, void *tag_data, hid_t io_prop, mhdf_Status *status) |
| void | mhdf_readSparseTagIndices (hid_t table_id, long offset, long count, hid_t int_type, void *indices, mhdf_Status *status) |
| Read sparse tag end indices for variable-length tag data. | |
| void | mhdf_readSparseTagIndicesWithOpt (hid_t table_id, long offset, long count, hid_t int_type, void *indices, hid_t io_prop, mhdf_Status *status) |
| static hid_t create_tag_common | ( | mhdf_FileHandle | file_handle, |
| const char * | tag_name, | ||
| enum mhdf_TagDataType | tag_type, | ||
| int | size, | ||
| int | storage, | ||
| const void * | default_value, | ||
| int | default_value_size_in, | ||
| const void * | global_value, | ||
| int | global_value_size_in, | ||
| hid_t | hdf_type, | ||
| hid_t | hdf_base_type, | ||
| mhdf_Status * | status | ||
| ) | [static] |
Definition at line 235 of file tags.c.
References struct_FileHandle::hdf_handle, mhdf_BITFIELD, mhdf_BOOLEAN, mhdf_check_valid_file(), mhdf_create_scalar_attrib(), mhdf_ENTITY_ID, mhdf_FLOAT, mhdf_INTEGER, mhdf_name_to_path_copy(), mhdf_OPAQUE, mhdf_setFail(), mhdf_setOkay(), store_tag_val_in_attrib(), TAG_DEFAULT_ATTRIB, TAG_GLOBAL_ATTRIB, TAG_GROUP, TAG_HANDLE_TYPE_ATTRIB, TAG_TYPE_ATTRIB, and TAG_TYPE_NAME.
Referenced by mhdf_createTag(), and mhdf_createVarLenTag().
{
hid_t temp_id, group_id, tag_id;
char* path;
FileHandle* file_ptr;
herr_t rval;
hsize_t arr_len;
int one = 1, var_len = 0;
hsize_t default_value_size = default_value_size_in;
hsize_t global_value_size = global_value_size_in;
int close_base_type = 0;
/* Force standard data types over user-specified types */
if( tag_type != mhdf_OPAQUE ) hdf_type = 0;
if( tag_type != mhdf_ENTITY_ID ) hdf_base_type = 0;
/* Validate input */
file_ptr = (FileHandle*)file_handle;
if( !mhdf_check_valid_file( file_ptr, status ) ) return -1;
if( !tag_name || !*tag_name )
{
mhdf_setFail( status, "Invalid tag name" );
return -1;
}
/* Open the tag group */
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
group_id = H5Gopen2( file_ptr->hdf_handle, TAG_GROUP, H5P_DEFAULT );
#else
group_id = H5Gopen( file_ptr->hdf_handle, TAG_GROUP );
#endif
if( group_id < 0 )
{
mhdf_setFail( status, "H5Gopen(\"%s\") failed.", TAG_GROUP );
return -1;
}
/* Create path string for tag object */
path = mhdf_name_to_path_copy( tag_name, status );
if( !path )
{
H5Gclose( group_id );
return -1;
}
/* Create group for this tag */
#if defined( H5Gcreate_vers ) && H5Gcreate_vers > 1
tag_id = H5Gcreate2( group_id, path, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
#else
tag_id = H5Gcreate( group_id, path, 3 );
#endif
if( tag_id < 0 )
{
mhdf_setFail( status, "H5Gcreate( \"%s\" ) failed.", path );
free( path );
H5Gclose( group_id );
return -1;
}
/* Store the tag name as the comment on the group entry */
rval = H5Gset_comment( group_id, path, tag_name );
H5Gclose( group_id );
free( path );
if( rval < 0 )
{
mhdf_setFail( status, "H5Gset_comment failed for tag \"%s\"", tag_name );
H5Gclose( tag_id );
return -1;
}
/* Store TSTT tag type as attribute */
rval = mhdf_create_scalar_attrib( tag_id, TAG_TYPE_ATTRIB, H5T_NATIVE_INT, &storage, status );
if( !rval )
{
H5Gclose( tag_id );
return -1;
}
if( hdf_type )
{
hdf_type = H5Tcopy( hdf_type );
arr_len = 1;
}
else
{
switch( tag_type )
{
default:
case mhdf_OPAQUE:
arr_len = 1;
hdf_type = H5Tcreate( H5T_OPAQUE, abs( size ) );
H5Tset_tag( hdf_type, "tag_data" );
break;
case mhdf_BITFIELD:
arr_len = 1;
if( size <= 0 )
{
mhdf_setFail( status, "Invalid size (%d) for bit tag.", (int)size );
return -1;
}
else if( size <= 8 )
hdf_type = H5Tcopy( H5T_NATIVE_B8 );
else if( size <= 16 )
hdf_type = H5Tcopy( H5T_NATIVE_B16 );
else if( size <= 32 )
hdf_type = H5Tcopy( H5T_NATIVE_B32 );
else if( size <= 64 )
hdf_type = H5Tcopy( H5T_NATIVE_B64 );
else
{
mhdf_setFail( status, "Cannot create a bit tag larger than 64-bits. %d bits requested.\n",
(int)size );
return -1;
}
if( 0 > H5Tset_precision( hdf_type, size ) )
{
mhdf_setFail( status, "H5Tset_precision failed." );
return -1;
}
break;
case mhdf_ENTITY_ID:
arr_len = abs( size );
hdf_type = H5Tcopy( H5T_NATIVE_ULONG );
break;
case mhdf_BOOLEAN:
arr_len = abs( size );
hdf_type = H5Tcopy( H5T_NATIVE_UCHAR );
break;
case mhdf_INTEGER:
arr_len = abs( size );
hdf_type = H5Tcopy( H5T_NATIVE_INT );
break;
case mhdf_FLOAT:
arr_len = abs( size );
hdf_type = H5Tcopy( H5T_NATIVE_DOUBLE );
break;
}
}
if( hdf_type <= 0 )
{
mhdf_setFail( status, "Failed to create tag type object." );
H5Gclose( tag_id );
return -1;
}
if( hdf_base_type && H5Tget_class( hdf_type ) != H5Tget_class( hdf_base_type ) )
{
mhdf_setFail( status, "Invalid base type for tag default/global data" );
H5Gclose( tag_id );
return -1;
}
if( size < -1 || !arr_len )
{
mhdf_setFail( status, "Invalid 'size' parameter passed to mhdf_createTag (%d)", (int)size );
H5Gclose( tag_id );
return -1;
}
else if( size == -1 )
{
/* Note: we don't do anything with this here. We rely on
* the app to ask us to create the index table later.
*/
arr_len = 1;
/* need to know this later, when storing default/global values */
var_len = 1;
}
else if( arr_len > 1 )
{
#if defined( H5Tarray_create_vers ) && H5Tarray_create_vers > 1
temp_id = H5Tarray_create2( hdf_type, 1, &arr_len );
#else
temp_id = H5Tarray_create( hdf_type, 1, &arr_len, NULL );
#endif
H5Tclose( hdf_type );
if( temp_id < 0 )
{
mhdf_setFail( status, "Failed to create tag type object." );
H5Gclose( tag_id );
return -1;
}
hdf_type = temp_id;
if( hdf_base_type )
{
if( H5Tequal( hdf_base_type, hdf_type ) > 0 )
{
hdf_base_type = hdf_type;
}
else
{
#if defined( H5Tarray_create_vers ) && H5Tarray_create_vers > 1
temp_id = H5Tarray_create2( hdf_base_type, 1, &arr_len );
#else
temp_id = H5Tarray_create( hdf_base_type, 1, &arr_len, NULL );
#endif
if( temp_id < 0 )
{
mhdf_setFail( status, "Failed to create tag type object." );
H5Gclose( tag_id );
H5Tclose( hdf_type );
return -1;
}
hdf_base_type = temp_id;
close_base_type = 1;
}
}
}
if( !hdf_base_type ) hdf_base_type = hdf_type;
/* Create tag type object, or write attribute if opaque */
#if defined( H5Tcommit_vers ) && H5Tcommit_vers > 1
rval = H5Tcommit2( tag_id, TAG_TYPE_NAME, hdf_type, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
#else
rval = H5Tcommit( tag_id, TAG_TYPE_NAME, hdf_type );
#endif
if( rval < 0 )
{
mhdf_setFail( status, "H5Tcommit failed for tag \"%s\"", tag_name );
if( close_base_type ) H5Tclose( hdf_base_type );
H5Tclose( hdf_type );
H5Gclose( tag_id );
return -1;
}
/* If tag is entity handle, make note of it */
if( tag_type == mhdf_ENTITY_ID )
{
rval = mhdf_create_scalar_attrib( tag_id, TAG_HANDLE_TYPE_ATTRIB, H5T_NATIVE_INT, &one, status );
if( !rval )
{
if( close_base_type ) H5Tclose( hdf_base_type );
H5Gclose( tag_id );
H5Tclose( hdf_type );
return -1;
}
}
/* Store the default value as a attribute of the tag group */
if( default_value )
{
rval = store_tag_val_in_attrib( tag_id, TAG_DEFAULT_ATTRIB, hdf_base_type, default_value,
var_len ? default_value_size : 1, status );
if( !rval )
{
if( close_base_type ) H5Tclose( hdf_base_type );
H5Gclose( tag_id );
H5Tclose( hdf_type );
return -1;
}
}
/* Store global tag value as attribute */
if( global_value )
{
rval = store_tag_val_in_attrib( tag_id, TAG_GLOBAL_ATTRIB, hdf_base_type, global_value,
var_len ? global_value_size : 1, status );
if( !rval )
{
if( close_base_type ) H5Tclose( hdf_base_type );
H5Gclose( tag_id );
H5Tclose( hdf_type );
return -1;
}
}
if( close_base_type ) H5Tclose( hdf_base_type );
H5Tclose( hdf_type );
mhdf_setOkay( status );
return tag_id;
}
| static int get_attrib_array_length_handle | ( | hid_t | attrib_id | ) | [static] |
Definition at line 741 of file tags.c.
References rank.
Referenced by get_attrib_array_length_name().
{
hid_t type_id;
int rank;
hsize_t dims[H5S_MAX_RANK];
int perm[H5S_MAX_RANK];
type_id = H5Aget_type( attrib_id );
switch( H5Tget_class( type_id ) )
{
case H5T_NO_CLASS:
dims[0] = -1;
break;
case H5T_OPAQUE:
dims[0] = H5Tget_size( type_id );
break;
case H5T_ARRAY:
#if defined( H5Tget_array_dims_vers ) && H5Tget_array_dims_vers > 1
(void)perm; /* suppress warning */
rank = H5Tget_array_dims2( type_id, dims );
#else
rank = H5Tget_array_dims( type_id, dims, perm );
#endif
if( rank == 1 )
break;
else
return -1;
default:
dims[0] = 1;
break;
}
H5Tclose( type_id );
return dims[0];
}
| static int get_attrib_array_length_name | ( | hid_t | file, |
| const char * | path | ||
| ) | [static] |
Definition at line 793 of file tags.c.
References get_attrib_array_length_handle().
Referenced by mhdf_getTagInfo(), and read_tag_attrib_data().
{
hid_t attrib_id;
int result;
attrib_id = H5Aopen_name( file, path );
if( attrib_id < 0 ) return -1;
result = get_attrib_array_length_handle( attrib_id );
H5Aclose( attrib_id );
return result;
}
| static hid_t get_tag | ( | mhdf_FileHandle | file_handle, |
| const char * | tag_name, | ||
| hid_t * | id_type, | ||
| mhdf_Status * | status | ||
| ) | [static] |
Definition at line 106 of file tags.c.
References struct_FileHandle::hdf_handle, struct_FileHandle::id_type, mhdf_check_valid_file(), mhdf_name_to_path_copy(), mhdf_setFail(), mhdf_setOkay(), and TAG_GROUP.
Referenced by mhdf_createSparseTagData(), mhdf_createVarLenTagData(), mhdf_getTagInfo(), mhdf_getTagValues(), and mhdf_openSparseTagData().
{
hid_t group_id, tag_id;
char* path;
FileHandle* file_ptr;
file_ptr = (FileHandle*)file_handle;
if( !mhdf_check_valid_file( file_ptr, status ) ) return -1;
if( NULL != id_type ) *id_type = file_ptr->id_type;
path = mhdf_name_to_path_copy( tag_name, status );
if( NULL == path ) return -1;
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
group_id = H5Gopen2( file_ptr->hdf_handle, TAG_GROUP, H5P_DEFAULT );
#else
group_id = H5Gopen( file_ptr->hdf_handle, TAG_GROUP );
#endif
if( group_id < 0 )
{
mhdf_setFail( status, "Failed to open tag group." );
free( path );
return -1;
}
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
tag_id = H5Gopen2( group_id, path, H5P_DEFAULT );
#else
tag_id = H5Gopen( group_id, path );
#endif
H5Gclose( group_id );
free( path );
if( tag_id < 0 )
{
mhdf_setFail( status, "Failed to open tag data for tag \"%s\".", tag_name );
return -1;
}
mhdf_setOkay( status );
return tag_id;
}
| static hid_t get_tag_type | ( | FileHandle * | file_ptr, |
| const char * | tag_path, | ||
| mhdf_Status * | status | ||
| ) | [static] |
Definition at line 149 of file tags.c.
References struct_FileHandle::hdf_handle, mhdf_setFail(), TAG_GROUP, and TAG_TYPE_NAME.
Referenced by mhdf_createDenseTagData(), and mhdf_getTagDataType().
{
hid_t group_id, tag_id, type_id;
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
group_id = H5Gopen2( file_ptr->hdf_handle, TAG_GROUP, H5P_DEFAULT );
#else
group_id = H5Gopen( file_ptr->hdf_handle, TAG_GROUP );
#endif
if( group_id < 0 )
{
mhdf_setFail( status, "Failed to open tag group." );
return -1;
}
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
tag_id = H5Gopen2( group_id, tag_path, H5P_DEFAULT );
#else
tag_id = H5Gopen( group_id, tag_path );
#endif
H5Gclose( group_id );
if( tag_id < 0 )
{
mhdf_setFail( status, "Failed to open group for tag \"%s\".", tag_path );
return -1;
}
#if defined( H5Topen_vers ) && H5Topen_vers > 1
type_id = H5Topen2( tag_id, TAG_TYPE_NAME, H5P_DEFAULT );
#else
type_id = H5Topen( tag_id, TAG_TYPE_NAME );
#endif
H5Gclose( tag_id );
if( type_id < 0 )
{
mhdf_setFail( status, "Failed to open type data for tag \"%s\".", tag_path );
return -1;
}
return type_id;
}
| static int read_tag_attrib_data | ( | hid_t | tag_id, |
| const char * | attrib_name, | ||
| hid_t | type_id, | ||
| void * | data, | ||
| int | is_var_len, | ||
| mhdf_Status * | status | ||
| ) | [static] |
Definition at line 1075 of file tags.c.
References get_attrib_array_length_name(), mhdf_find_attribute(), mhdf_read_scalar_attrib(), and mhdf_setFail().
Referenced by mhdf_getTagValues().
{
int rval, ilen;
unsigned idx;
hid_t read_type = type_id;
hsize_t len;
/* Check if tag has attribute */
rval = mhdf_find_attribute( tag_id, attrib_name, &idx, status );
if( rval < 0 )
return 0;
else if( 0 == rval )
return 1;
if( NULL == data )
{
mhdf_setFail( status, "Invalid input." );
return 0;
}
if( is_var_len )
{
/* len = get_attrib_array_length_index(tag_id, index); */
ilen = get_attrib_array_length_name( tag_id, attrib_name );
if( ilen < 0 )
{
mhdf_setFail( status, "Failed to read length of default/mesh value for tag" );
return 0;
}
len = ilen;
/* caller passes type_id == 0 for OPAQUE */
if( 0 == type_id )
read_type = H5Tcreate( H5T_OPAQUE, len );
else
{
#if defined( H5Tarray_create_vers ) && H5Tarray_create_vers > 1
read_type = H5Tarray_create2( type_id, 1, &len );
#else
read_type = H5Tarray_create( type_id, 1, &len, 0 );
#endif
}
if( read_type < 0 )
{
mhdf_setFail( status, "Failed to read mesh/default value for tag" );
return 0;
}
}
rval = mhdf_read_scalar_attrib( tag_id, attrib_name, read_type, data, status );
if( is_var_len ) H5Tclose( read_type );
return rval;
}
| static int store_tag_val_in_attrib | ( | hid_t | tag_id, |
| const char * | attrib_name, | ||
| hid_t | type_id, | ||
| const void * | value, | ||
| hsize_t | value_size, | ||
| mhdf_Status * | status | ||
| ) | [static] |
Helper function to write default and mesh values for tag
| tag_id | The file object upon which to attach the attribute |
| attrib_name | The name of the attribute object |
| type_id | The data type of the attribute data |
| value | Pointer to attribute data |
| value_size | Size of attribute data, as multiple of type indicated by type_id. Should be 1 except for variable-length tag data. |
Definition at line 199 of file tags.c.
References mhdf_create_scalar_attrib(), and mhdf_setFail().
Referenced by create_tag_common().
{
hid_t write_type;
int rval;
if( value_size == 1 )
write_type = type_id;
else if( H5Tget_class( type_id ) == H5T_OPAQUE )
{
write_type = H5Tcreate( H5T_OPAQUE, value_size );
}
else
{
#if defined( H5Tarray_create_vers ) && H5Tarray_create_vers > 1
write_type = H5Tarray_create2( type_id, 1, &value_size );
#else
write_type = H5Tarray_create( type_id, 1, &value_size, 0 );
#endif
}
if( write_type < 0 )
{
mhdf_setFail( status, "Error constructing type object for tag mesh/default value" );
return -1;
}
rval = mhdf_create_scalar_attrib( tag_id, attrib_name, write_type, value, status );
if( write_type != type_id ) H5Tclose( write_type );
return rval;
}
1.7.6.1