ch.systemsx.cisd.hdf5

Class HDF5BooleanWriter

java.lang.Object

ch.systemsx.cisd.hdf5.HDF5BooleanReader

ch.systemsx.cisd.hdf5.HDF5BooleanWriter

All Implemented Interfaces:

IHDF5BooleanReader, IHDF5BooleanWriter

public class HDF5BooleanWriter
extends HDF5BooleanReader
implements IHDF5BooleanWriter

Implementation of IHDF5BooleanWriter.

Method Summary

Modifier and Type	Method and Description
void	createBitField(java.lang.String objectPath, int size) Creates a bit field (of rank 1).
void	createBitField(java.lang.String objectPath, int size, HDF5GenericStorageFeatures features) Creates a bit field array (of rank 1).
void	createBitField(java.lang.String objectPath, long size, int blockSize) Creates a bit field (of rank 1).
void	createBitField(java.lang.String objectPath, long size, int blockSize, HDF5GenericStorageFeatures features) Creates a bit field (of rank 1).
void	createBitFieldArray(java.lang.String objectPath, int bitFieldSize, long arrayBlockSize) Creates an empty array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2).
void	createBitFieldArray(java.lang.String objectPath, int bitFieldSize, long arrayBlockSize, HDF5IntStorageFeatures features) Creates an empty array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2).
void	createBitFieldArray(java.lang.String objectPath, int bitFieldSize, long arraySize, long arrayBlockSize) Creates an array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2).
void	createBitFieldArray(java.lang.String objectPath, int bitFieldSize, long arraySize, long arrayBlockSize, HDF5IntStorageFeatures features) Creates an array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2).
void	setAttr(java.lang.String objectPath, java.lang.String name, boolean value) Sets a boolean attribute to the referenced object.
void	write(java.lang.String objectPath, boolean value) Writes out a boolean value.
void	writeBitField(java.lang.String objectPath, java.util.BitSet data) Writes out a bit field ((which can be considered the equivalent to a boolean array of rank 1), provided as a Java BitSet.
void	writeBitField(java.lang.String objectPath, java.util.BitSet data, HDF5GenericStorageFeatures features) Writes out a bit field ((which can be considered the equivalent to a boolean array of rank 1), provided as a Java BitSet.
void	writeBitFieldArray(java.lang.String objectPath, java.util.BitSet[] data) Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.
void	writeBitFieldArray(java.lang.String objectPath, java.util.BitSet[] data, HDF5IntStorageFeatures features) Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.
void	writeBitFieldArrayBlock(java.lang.String objectPath, java.util.BitSet[] data, int dataSize, long blockNumber) Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.
void	writeBitFieldArrayBlock(java.lang.String objectPath, java.util.BitSet[] data, long blockNumber) Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.
void	writeBitFieldArrayBlockWithOffset(java.lang.String objectPath, java.util.BitSet[] data, int dataSize, long offset) Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.
void	writeBitFieldArrayBlockWithOffset(java.lang.String objectPath, java.util.BitSet[] data, long offset) Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.
void	writeBitFieldBlock(java.lang.String objectPath, java.util.BitSet data, int dataSize, long blockNumber) Writes out a block of a bit field (of rank 1).
void	writeBitFieldBlockWithOffset(java.lang.String objectPath, java.util.BitSet data, int dataSize, long offset) Writes out a block of a long array (of rank 1).

Methods inherited from class ch.systemsx.cisd.hdf5.HDF5BooleanReader

getAttr, isBitSet, read, readBitField, readBitFieldArray, readBitFieldArrayBlock, readBitFieldArrayBlockWithOffset, readBitFieldBlock, readBitFieldBlockWithOffset

Methods inherited from class java.lang.Object

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

Methods inherited from interface ch.systemsx.cisd.hdf5.IHDF5BooleanReader

getAttr, isBitSet, read, readBitField, readBitFieldArray, readBitFieldArrayBlock, readBitFieldArrayBlockWithOffset, readBitFieldBlock, readBitFieldBlockWithOffset

Method Detail

setAttr

public void setAttr(java.lang.String objectPath,
                    java.lang.String name,
                    boolean value)

Description copied from interface: IHDF5BooleanWriter

Sets a boolean attribute to the referenced object.

The referenced object must exist, that is it need to have been written before by one of the write() methods.

Specified by:

setAttr in interface IHDF5BooleanWriter

Parameters:

objectPath - The name of the object to add the attribute to.

name - The name of the attribute.

value - The value of the attribute.

write

public void write(java.lang.String objectPath,
                  boolean value)

Description copied from interface: IHDF5BooleanWriter

Writes out a boolean value.

Specified by:

write in interface IHDF5BooleanWriter

Parameters:

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

value - The value of the data set.

writeBitField

public void writeBitField(java.lang.String objectPath,
                          java.util.BitSet data)

Description copied from interface: IHDF5BooleanWriter

Writes out a bit field ((which can be considered the equivalent to a boolean array of rank 1), provided as a Java BitSet.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitField in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

writeBitField

public void writeBitField(java.lang.String objectPath,
                          java.util.BitSet data,
                          HDF5GenericStorageFeatures features)

Description copied from interface: IHDF5BooleanWriter

Writes out a bit field ((which can be considered the equivalent to a boolean array of rank 1), provided as a Java BitSet.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitField in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

features - The storage features of the data set.

createBitField

public void createBitField(java.lang.String objectPath,
                           int size)

Description copied from interface: IHDF5BooleanWriter

Creates a bit field (of rank 1).

Specified by:

createBitField in interface IHDF5BooleanWriter

Parameters:

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

size - The size (in 64 bit words) of the bit field to create. This will be the total size for non-extendable data sets and the size of one chunk for extendable (chunked) data sets. For extendable data sets the initial size of the array will be 0, see IHDF5WriterConfigurator.dontUseExtendableDataTypes().

createBitField

public void createBitField(java.lang.String objectPath,
                           long size,
                           int blockSize)

Description copied from interface: IHDF5BooleanWriter

Creates a bit field (of rank 1).

Specified by:

createBitField in interface IHDF5BooleanWriter

Parameters:

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

size - The size (in 64 bit words) of the bit field to create. When using extendable data sets ((see IHDF5WriterConfigurator.dontUseExtendableDataTypes())), then no data set smaller than this size can be created, however data sets may be larger.

blockSize - The size of one block (for block-wise IO). Ignored if no extendable data sets are used (see IHDF5WriterConfigurator.dontUseExtendableDataTypes()).

createBitField

public void createBitField(java.lang.String objectPath,
                           int size,
                           HDF5GenericStorageFeatures features)

Description copied from interface: IHDF5BooleanWriter

Creates a bit field array (of rank 1).

Specified by:

createBitField in interface IHDF5BooleanWriter

Parameters:

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

size - The size (in 64 bit words) of the bit field to create. This will be the total size for non-extendable data sets and the size of one chunk for extendable (chunked) data sets. For extendable data sets the initial size of the array will be 0, see HDF5IntStorageFeatures.

features - The storage features of the data set.

createBitField

public void createBitField(java.lang.String objectPath,
                           long size,
                           int blockSize,
                           HDF5GenericStorageFeatures features)

Description copied from interface: IHDF5BooleanWriter

Creates a bit field (of rank 1).

Specified by:

createBitField in interface IHDF5BooleanWriter

Parameters:

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

size - The size (in 64 bit words) of the bit field to create. When using extendable data sets ((see IHDF5WriterConfigurator.dontUseExtendableDataTypes())), then no data set smaller than this size can be created, however data sets may be larger.

blockSize - The size of one block (for block-wise IO). Ignored if no extendable data sets are used (see IHDF5WriterConfigurator.dontUseExtendableDataTypes()) and features is HDF5IntStorageFeature.INT_NO_COMPRESSION .

features - The storage features of the data set.

writeBitFieldBlock

public void writeBitFieldBlock(java.lang.String objectPath,
                               java.util.BitSet data,
                               int dataSize,
                               long blockNumber)

Description copied from interface: IHDF5BooleanWriter

Writes out a block of a bit field (of rank 1). The data set needs to have been created by IHDF5BooleanWriter.createBitField(String, long, int, HDF5GenericStorageFeatures) beforehand.

Note: For best performance, the block size in this method should be chosen to be equal to the blockSize argument of the IHDF5BooleanWriter.createBitField(String, long, int, HDF5GenericStorageFeatures) call that was used to create the data set.

Specified by:

writeBitFieldBlock in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. The length defines the block size. Must not be null or of length 0.

dataSize - The (real) size of data

blockNumber - The number of the block to write.

writeBitFieldBlockWithOffset

public void writeBitFieldBlockWithOffset(java.lang.String objectPath,
                                         java.util.BitSet data,
                                         int dataSize,
                                         long offset)

Description copied from interface: IHDF5BooleanWriter

Writes out a block of a long array (of rank 1). The data set needs to have been created by IHDF5BooleanWriter.createBitFieldArray(String, int, long, long, HDF5IntStorageFeatures) beforehand.

Use this method instead of IHDF5BooleanWriter.writeBitFieldBlock(String, BitSet, int, long) if the total size of the data set is not a multiple of the block size.

Note: For best performance, the typical dataSize in this method should be chosen to be equal to the blockSize argument of the IHDF5BooleanWriter.createBitField(String, long, int, HDF5GenericStorageFeatures) call that was used to create the data set.

Specified by:

writeBitFieldBlockWithOffset in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. The length defines the block size. Must not be null or of length 0.

dataSize - The (real) size of data

offset - The offset in the data set to start writing to.

writeBitFieldArray

public void writeBitFieldArray(java.lang.String objectPath,
                               java.util.BitSet[] data)

Description copied from interface: IHDF5BooleanWriter

Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitFieldArray in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

writeBitFieldArray

public void writeBitFieldArray(java.lang.String objectPath,
                               java.util.BitSet[] data,
                               HDF5IntStorageFeatures features)

Description copied from interface: IHDF5BooleanWriter

Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitFieldArray in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

features - The storage features of the data set.

createBitFieldArray

public void createBitFieldArray(java.lang.String objectPath,
                                int bitFieldSize,
                                long arraySize,
                                long arrayBlockSize,
                                HDF5IntStorageFeatures features)

Description copied from interface: IHDF5BooleanWriter

Creates an array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2).

Specified by:

createBitFieldArray in interface IHDF5BooleanWriter

Parameters:

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

bitFieldSize - The size of the bit fields in the array (in 64 bit words).

arraySize - The size of the array of bit fields to create. When using extendable data sets ((see IHDF5WriterConfigurator.dontUseExtendableDataTypes())), then no data set smaller than this size can be created, however data sets may be larger.

arrayBlockSize - The size of one block (for block-wise IO). Ignored if no extendable data sets are used (see IHDF5WriterConfigurator.dontUseExtendableDataTypes()) and features is HDF5IntStorageFeature.INT_NO_COMPRESSION.

features - The storage features of the data set.

createBitFieldArray

public void createBitFieldArray(java.lang.String objectPath,
                                int bitFieldSize,
                                long arrayBlockSize,
                                HDF5IntStorageFeatures features)

Description copied from interface: IHDF5BooleanWriter

Creates an empty array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2).

Specified by:

createBitFieldArray in interface IHDF5BooleanWriter

Parameters:

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

bitFieldSize - The size of the bit fields in the array (in 64 bit words).

arrayBlockSize - The size of the long array to create. When requesting a chunked data set (e.g. HDF5IntStorageFeatures.INT_CHUNKED), the initial size of the array will be 0 and the chunk size will be arraySize. When allowing a chunked data set (e.g. HDF5IntStorageFeatures.INT_NO_COMPRESSION when the writer is not configured to avoid extendable data types, see IHDF5WriterConfigurator.dontUseExtendableDataTypes()), the initial size and the chunk size of the array will be arraySize. When enforcing a on-extendable data set (e.g. HDF5IntStorageFeatures.INT_CONTIGUOUS), the initial size equals the total size and will be arraySize.

features - The storage features of the data set.

createBitFieldArray

public void createBitFieldArray(java.lang.String objectPath,
                                int bitFieldSize,
                                long arraySize,
                                long arrayBlockSize)

Description copied from interface: IHDF5BooleanWriter

Creates an array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2).

Specified by:

createBitFieldArray in interface IHDF5BooleanWriter

Parameters:

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

bitFieldSize - The size of the bit fields in the array (in 64 bit words).

arraySize - The size of the array of bit fields to create. When using extendable data sets ((see IHDF5WriterConfigurator.dontUseExtendableDataTypes())), then no data set smaller than this size can be created, however data sets may be larger.

arrayBlockSize - The size of one block (for block-wise IO). Ignored if no extendable data sets are used (see IHDF5WriterConfigurator.dontUseExtendableDataTypes()) and features is HDF5IntStorageFeature.INT_NO_COMPRESSION.

createBitFieldArray

public void createBitFieldArray(java.lang.String objectPath,
                                int bitFieldSize,
                                long arrayBlockSize)

Description copied from interface: IHDF5BooleanWriter

Creates an empty array of bit fields (of rank 1) (which can be considered the equivalent to a boolean array of rank 2). This method always creates an extendable data sets.

Specified by:

createBitFieldArray in interface IHDF5BooleanWriter

Parameters:

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

bitFieldSize - The size of the bit fields in the array (in 64 bit words).

arrayBlockSize - When the writer is configured to use extendable data types (see IHDF5WriterConfigurator.dontUseExtendableDataTypes()), the initial size and the chunk size of the array will be arraySize. When the writer is configured to enforce a on-extendable data set, the initial size equals the total size and will be arraySize.

writeBitFieldArrayBlockWithOffset

public void writeBitFieldArrayBlockWithOffset(java.lang.String objectPath,
                                              java.util.BitSet[] data,
                                              int dataSize,
                                              long offset)

Description copied from interface: IHDF5BooleanWriter

Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitFieldArrayBlockWithOffset in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

dataSize - The number of entries from data to write to the bitfield array (must be smaller or equals to data.length.

offset - The offset in the bitfield array where to start writing the data.

writeBitFieldArrayBlockWithOffset

public void writeBitFieldArrayBlockWithOffset(java.lang.String objectPath,
                                              java.util.BitSet[] data,
                                              long offset)

Description copied from interface: IHDF5BooleanWriter

Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitFieldArrayBlockWithOffset in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

offset - The offset in the bitfield array where to start writing the data.

writeBitFieldArrayBlock

public void writeBitFieldArrayBlock(java.lang.String objectPath,
                                    java.util.BitSet[] data,
                                    int dataSize,
                                    long blockNumber)

Description copied from interface: IHDF5BooleanWriter

Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitFieldArrayBlock in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

dataSize - The number of entries from data to write to the bitfield array (must be smaller or equals to data.length.

blockNumber - The block number in the array (offset: multiply with dataSize>).

writeBitFieldArrayBlock

public void writeBitFieldArrayBlock(java.lang.String objectPath,
                                    java.util.BitSet[] data,
                                    long blockNumber)

Description copied from interface: IHDF5BooleanWriter

Writes out an array of bit fields (which can be considered the equivalent to a boolean array of rank 2), provided as a Java array of BitSets.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read back by IHDF5LongReader.readArray(String) but will throw a HDF5DatatypeInterfaceException.

Specified by:

writeBitFieldArrayBlock in interface IHDF5BooleanWriter

Parameters:

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

data - The data to write. Must not be null.

blockNumber - The block number in the array (offset: multiply with data.length).