ch.systemsx.cisd.hdf5

Class HDF5OpaqueReader

java.lang.Object

ch.systemsx.cisd.hdf5.HDF5OpaqueReader

All Implemented Interfaces:

IHDF5OpaqueReader

Direct Known Subclasses:

HDF5OpaqueWriter

public class HDF5OpaqueReader
extends java.lang.Object
implements IHDF5OpaqueReader

Implementation of IHDF5OpaqueReader

Method Summary

Modifier and Type	Method and Description
byte[]	getArrayAttr(java.lang.String objectPath, java.lang.String attributeName) Gets the byte array values of an attribute attributeName of object objectPath.
java.lang.Iterable<HDF5DataBlock<byte[]>>	getArrayNaturalBlocks(java.lang.String dataSetPath) Provides all natural blocks of this one-dimensional data set to iterate over.
byte[]	readArray(java.lang.String objectPath) Reads the data set objectPath as byte array.
byte[]	readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber) Reads a block from data set objectPath as byte array.
byte[]	readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset) Reads a block from data set objectPath as byte array.
int	readArrayToBlockWithOffset(java.lang.String objectPath, byte[] buffer, int blockSize, long offset, int memoryOffset) Reads a block from data set objectPath as byte array into buffer.
java.lang.String	tryGetOpaqueTag(java.lang.String objectPath) Returns the tag of the opaque data type associated with objectPath, or null, if objectPath is not of an opaque data type (i.e.
HDF5OpaqueType	tryGetOpaqueType(java.lang.String objectPath) Returns the opaque data type or null, if objectPath is not of such a data type.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

tryGetOpaqueTag

public java.lang.String tryGetOpaqueTag(java.lang.String objectPath)

Description copied from interface: IHDF5OpaqueReader

Returns the tag of the opaque data type associated with objectPath, or null, if objectPath is not of an opaque data type (i.e. if reader.getDataSetInformation(objectPath).getTypeInformation().getDataClass() != HDF5DataClass.OPAQUE ).

Specified by:

tryGetOpaqueTag in interface IHDF5OpaqueReader

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The tag of the opaque data type, or null.

tryGetOpaqueType

public HDF5OpaqueType tryGetOpaqueType(java.lang.String objectPath)

Description copied from interface: IHDF5OpaqueReader

Returns the opaque data type or null, if objectPath is not of such a data type.

Specified by:

tryGetOpaqueType in interface IHDF5OpaqueReader

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The opaque data type, or null.

readArray

public byte[] readArray(java.lang.String objectPath)

Description copied from interface: IHDF5OpaqueReader

Reads the data set objectPath as byte array. The bytes read will be in the native byte-order of the machine and will be ordered 'row-first' in the case of multi-dimensional data sets, but will otherwise be unchanged.

Specified by:

readArray in interface IHDF5OpaqueReader

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

getArrayAttr

public byte[] getArrayAttr(java.lang.String objectPath,
                           java.lang.String attributeName)

Description copied from interface: IHDF5OpaqueReader

Gets the byte array values of an attribute attributeName of object objectPath. The bytes read will be in the native byte-order of the machine but will otherwise be unchanged.

Specified by:

getArrayAttr in interface IHDF5OpaqueReader

readArrayBlock

public byte[] readArrayBlock(java.lang.String objectPath,
                             int blockSize,
                             long blockNumber)
                      throws HDF5JavaException

Description copied from interface: IHDF5OpaqueReader

Reads a block from data set objectPath as byte array. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Specified by:

readArrayBlock in interface IHDF5OpaqueReader

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSize - The block size in numbers of elements (this will be the length of the byte[] returned, divided by the size of one element).

blockNumber - The number of the block to read (starting with 0, offset: multiply with blockSize).

Returns:

The data block read from the data set.

Throws:

HDF5JavaException - If the data set is not of rank 1 or is a String.

readArrayBlockWithOffset

public byte[] readArrayBlockWithOffset(java.lang.String objectPath,
                                       int blockSize,
                                       long offset)
                                throws HDF5JavaException

Description copied from interface: IHDF5OpaqueReader

Reads a block from data set objectPath as byte array. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Specified by:

readArrayBlockWithOffset in interface IHDF5OpaqueReader

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSize - The block size in numbers of elements (this will be the length of the byte[] returned, divided by the size of one element).

offset - The offset of the block to read as number of elements (starting with 0).

Returns:

The data block read from the data set.

Throws:

HDF5JavaException - If the data set is not of rank 1.

readArrayToBlockWithOffset

public int readArrayToBlockWithOffset(java.lang.String objectPath,
                                      byte[] buffer,
                                      int blockSize,
                                      long offset,
                                      int memoryOffset)
                               throws HDF5JavaException

Description copied from interface: IHDF5OpaqueReader

Reads a block from data set objectPath as byte array into buffer. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Specified by:

readArrayToBlockWithOffset in interface IHDF5OpaqueReader

Parameters:

objectPath - The name (including path information) of the data set object in the file.

buffer - The buffer to read the values in.

blockSize - The block size in numbers of elements (this will be the length of the byte[] returned, divided by the size of one element).

offset - The offset of the block in the data set as number of elements (zero-based).

memoryOffset - The offset of the block in buffer as number of elements (zero-based).

Returns:

The effective block size.

Throws:

HDF5JavaException - If the data set is not of rank 1.

getArrayNaturalBlocks

public java.lang.Iterable<HDF5DataBlock<byte[]>> getArrayNaturalBlocks(java.lang.String dataSetPath)
                                                                throws HDF5JavaException

Description copied from interface: IHDF5OpaqueReader

Provides all natural blocks of this one-dimensional data set to iterate over. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Specified by:

getArrayNaturalBlocks in interface IHDF5OpaqueReader

Throws:

HDF5JavaException - If the data set is not of rank 1.

See Also:

HDF5DataBlock