ch.systemsx.cisd.hdf5

Class HDF5ReferenceWriter

java.lang.Object

ch.systemsx.cisd.hdf5.HDF5ReferenceReader

ch.systemsx.cisd.hdf5.HDF5ReferenceWriter

All Implemented Interfaces:

IHDF5ReferenceReader, IHDF5ReferenceWriter

public class HDF5ReferenceWriter
extends HDF5ReferenceReader
implements IHDF5ReferenceWriter

The implementation of IHDF5ReferenceWriter.

Method Summary

Modifier and Type	Method and Description
void	createArray(java.lang.String objectPath, int size) Creates an array (of rank 1) of object references.
void	createArray(java.lang.String objectPath, int size, HDF5IntStorageFeatures features) Creates an array (of rank 1) of object references.
void	createArray(java.lang.String objectPath, long size, int blockSize) Creates an array (of rank 1) of object references.
void	createArray(java.lang.String objectPath, long size, int blockSize, HDF5IntStorageFeatures features) Creates an array (of rank 1) of object references.
void	createMDArray(java.lang.String objectPath, int[] dimensions) Creates a multi-dimensional array of object references.
void	createMDArray(java.lang.String objectPath, int[] dimensions, HDF5IntStorageFeatures features) Creates a multi-dimensional array of object references.
void	createMDArray(java.lang.String objectPath, long[] dimensions, int[] blockDimensions) Creates a multi-dimensional array of object references.
void	createMDArray(java.lang.String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features) Creates a multi-dimensional array of object references.
void	setArrayAttr(java.lang.String objectPath, java.lang.String name, java.lang.String[] referencedObjectPaths) Sets a 1D object reference array attribute to referenced objects.
void	setAttr(java.lang.String objectPath, java.lang.String name, java.lang.String referencedObjectPath) Sets an object reference attribute to the referenced object.
void	setMDArrayAttr(java.lang.String objectPath, java.lang.String name, ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths) Sets an object reference array attribute to referenced objects.
void	write(java.lang.String objectPath, java.lang.String referencedObjectPath) Writes an object reference to the referenced object.
void	writeArray(java.lang.String objectPath, java.lang.String[] referencedObjectPath) Writes an array (of rank 1) of object references.
void	writeArray(java.lang.String objectPath, java.lang.String[] referencedObjectPaths, HDF5IntStorageFeatures features) Writes an array (of rank 1) of object references.
void	writeArrayBlock(java.lang.String objectPath, java.lang.String[] referencedObjectPaths, long blockNumber) Writes out a block of an array (of rank 1) of object references.
void	writeArrayBlockWithOffset(java.lang.String objectPath, java.lang.String[] referencedObjectPaths, int dataSize, long offset) Writes out a block of an array (of rank 1) of object references.
void	writeMDArray(java.lang.String objectPath, ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths) Writes an array (of rank N) of object references.
void	writeMDArray(java.lang.String objectPath, ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths, HDF5IntStorageFeatures features) Writes an array (of rank N) of object references.
void	writeMDArrayBlock(java.lang.String objectPath, ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths, long[] blockNumber) Writes out a block of a multi-dimensional array of object references.
void	writeMDArrayBlockWithOffset(java.lang.String objectPath, ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths, long[] offset) Writes out a block of a multi-dimensional array of object references.
void	writeMDArrayBlockWithOffset(java.lang.String objectPath, ch.systemsx.cisd.base.mdarray.MDLongArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) Writes out a block of a multi-dimensional array of object references.

Methods inherited from class ch.systemsx.cisd.hdf5.HDF5ReferenceReader

getArrayAttr, getArrayAttr, getArrayNaturalBlocks, getArrayNaturalBlocks, getAttr, getAttr, getMDArrayAttr, getMDArrayAttr, getMDArrayNaturalBlocks, getMDArrayNaturalBlocks, read, read, readArray, readArray, readArrayBlock, readArrayBlock, readArrayBlockWithOffset, readArrayBlockWithOffset, readMDArray, readMDArray, readMDArrayBlock, readMDArrayBlock, readMDArrayBlockWithOffset, readMDArrayBlockWithOffset, resolvePath

Methods inherited from class java.lang.Object

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

Methods inherited from interface ch.systemsx.cisd.hdf5.IHDF5ReferenceReader

getArrayAttr, getArrayAttr, getArrayNaturalBlocks, getArrayNaturalBlocks, getAttr, getAttr, getMDArrayAttr, getMDArrayAttr, getMDArrayNaturalBlocks, getMDArrayNaturalBlocks, read, read, readArray, readArray, readArrayBlock, readArrayBlock, readArrayBlockWithOffset, readArrayBlockWithOffset, readMDArray, readMDArray, readMDArrayBlock, readMDArrayBlock, readMDArrayBlockWithOffset, readMDArrayBlockWithOffset, resolvePath

Method Detail

setAttr

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

Description copied from interface: IHDF5ReferenceWriter

Sets an object reference attribute to the referenced object.

Both the object referenced with objectPath and referencedObjectPath must exist, that is it need to have been written before by one of the write() or create() methods.

Specified by:

setAttr in interface IHDF5ReferenceWriter

Parameters:

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

name - The name of the attribute.

referencedObjectPath - The path of the object to reference.

setArrayAttr

public void setArrayAttr(java.lang.String objectPath,
                         java.lang.String name,
                         java.lang.String[] referencedObjectPaths)

Description copied from interface: IHDF5ReferenceWriter

Sets a 1D object reference array attribute to referenced objects.

Both the object referenced with objectPath and all referencedObjectPaths must exist, that is it need to have been written before by one of the write() or create() methods.

Specified by:

setArrayAttr in interface IHDF5ReferenceWriter

Parameters:

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

name - The name of the attribute.

referencedObjectPaths - The paths of the objects to reference.

setMDArrayAttr

public void setMDArrayAttr(java.lang.String objectPath,
                           java.lang.String name,
                           ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths)

Description copied from interface: IHDF5ReferenceWriter

Sets an object reference array attribute to referenced objects.

Both the object referenced with objectPath and all referencedObjectPaths must exist, that is it need to have been written before by one of the write() or create() methods.

Specified by:

setMDArrayAttr in interface IHDF5ReferenceWriter

Parameters:

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

name - The name of the attribute.

referencedObjectPaths - The paths of the objects to reference.

write

public void write(java.lang.String objectPath,
                  java.lang.String referencedObjectPath)

Description copied from interface: IHDF5ReferenceWriter

Writes an object reference to the referenced object.

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

Specified by:

write in interface IHDF5ReferenceWriter

Parameters:

objectPath - The name of the object to write.

referencedObjectPath - The path of the object to reference.

writeArray

public void writeArray(java.lang.String objectPath,
                       java.lang.String[] referencedObjectPath)

Description copied from interface: IHDF5ReferenceWriter

Writes an array (of rank 1) of object references.

Specified by:

writeArray in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPath - The names of the object to write.

writeArray

public void writeArray(java.lang.String objectPath,
                       java.lang.String[] referencedObjectPaths,
                       HDF5IntStorageFeatures features)

Description copied from interface: IHDF5ReferenceWriter

Writes an array (of rank 1) of object references.

Specified by:

writeArray in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPaths - The names of the object to write.

features - The storage features of the data set.

createArray

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

Description copied from interface: IHDF5ReferenceWriter

Creates an array (of rank 1) of object references.

Specified by:

createArray in interface IHDF5ReferenceWriter

Parameters:

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

size - The size of the array 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().

createArray

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

Description copied from interface: IHDF5ReferenceWriter

Creates an array (of rank 1) of object references.

Specified by:

createArray in interface IHDF5ReferenceWriter

Parameters:

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

size - The size of the array 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()).

createArray

public void createArray(java.lang.String objectPath,
                        int size,
                        HDF5IntStorageFeatures features)

Description copied from interface: IHDF5ReferenceWriter

Creates an array (of rank 1) of object references.

Specified by:

createArray in interface IHDF5ReferenceWriter

Parameters:

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

size - The size of the array 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.

createArray

public void createArray(java.lang.String objectPath,
                        long size,
                        int blockSize,
                        HDF5IntStorageFeatures features)

Description copied from interface: IHDF5ReferenceWriter

Creates an array (of rank 1) of object references.

Specified by:

createArray in interface IHDF5ReferenceWriter

Parameters:

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

size - The size of the array 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.INTNO_COMPRESSION.

features - The storage features of the data set.

writeArrayBlock

public void writeArrayBlock(java.lang.String objectPath,
                            java.lang.String[] referencedObjectPaths,
                            long blockNumber)

Description copied from interface: IHDF5ReferenceWriter

Writes out a block of an array (of rank 1) of object references. The data set needs to have been created by IHDF5ReferenceWriter.createArray(String, long, int, HDF5IntStorageFeatures) beforehand.

Note: For best performance, the block size in this method should be chosen to be equal to the blockSize argument of the IHDF5ReferenceWriter.createArray(String, long, int, HDF5IntStorageFeatures) call that was used to create the data set.

Specified by:

writeArrayBlock in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPaths - The paths of the referenced objects to write. The length defines the block size. Must not be null or of length 0.

blockNumber - The number of the block to write.

writeArrayBlockWithOffset

public void writeArrayBlockWithOffset(java.lang.String objectPath,
                                      java.lang.String[] referencedObjectPaths,
                                      int dataSize,
                                      long offset)

Description copied from interface: IHDF5ReferenceWriter

Writes out a block of an array (of rank 1) of object references. The data set needs to have been created by IHDF5ReferenceWriter.createArray(String, long, int, HDF5IntStorageFeatures) beforehand.

Note: For best performance, the block size in this method should be chosen to be equal to the blockSize argument of the IHDF5ReferenceWriter.createArray(String, long, int, HDF5IntStorageFeatures) call that was used to create the data set.

Specified by:

writeArrayBlockWithOffset in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPaths - The paths of the referenced objects to write. The length defines the block size. Must not be null or of length 0.

dataSize - The (real) size of data (needs to be <= data.length )

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

writeMDArray

public void writeMDArray(java.lang.String objectPath,
                         ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths)

Description copied from interface: IHDF5ReferenceWriter

Writes an array (of rank N) of object references.

Specified by:

writeMDArray in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPaths - The names of the object to write.

writeMDArray

public void writeMDArray(java.lang.String objectPath,
                         ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths,
                         HDF5IntStorageFeatures features)

Description copied from interface: IHDF5ReferenceWriter

Writes an array (of rank N) of object references.

Specified by:

writeMDArray in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPaths - The names of the object to write.

features - The storage features of the data set.

createMDArray

public void createMDArray(java.lang.String objectPath,
                          int[] dimensions)

Description copied from interface: IHDF5ReferenceWriter

Creates a multi-dimensional array of object references.

Specified by:

createMDArray in interface IHDF5ReferenceWriter

Parameters:

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

dimensions - The dimensions of the array to create. This will be the total dimensions for non-extendable data sets and the dimensions of one chunk (extent along each axis) for extendable (chunked) data sets. For extendable data sets the initial size of the array along each axis will be 0, see IHDF5WriterConfigurator.dontUseExtendableDataTypes().

createMDArray

public void createMDArray(java.lang.String objectPath,
                          long[] dimensions,
                          int[] blockDimensions)

Description copied from interface: IHDF5ReferenceWriter

Creates a multi-dimensional array of object references.

Specified by:

createMDArray in interface IHDF5ReferenceWriter

Parameters:

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

dimensions - The dimensions of the array.

blockDimensions - The dimensions of one block (chunk) of the array.

createMDArray

public void createMDArray(java.lang.String objectPath,
                          int[] dimensions,
                          HDF5IntStorageFeatures features)

Description copied from interface: IHDF5ReferenceWriter

Creates a multi-dimensional array of object references.

Specified by:

createMDArray in interface IHDF5ReferenceWriter

Parameters:

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

dimensions - The dimensions of the array to create. This will be the total dimensions for non-extendable data sets and the dimensions of one chunk (extent along each axis) for extendable (chunked) data sets. For extendable data sets the initial size of the array along each axis will be 0, see IHDF5WriterConfigurator.dontUseExtendableDataTypes().

features - The storage features of the data set.

createMDArray

public void createMDArray(java.lang.String objectPath,
                          long[] dimensions,
                          int[] blockDimensions,
                          HDF5IntStorageFeatures features)

Description copied from interface: IHDF5ReferenceWriter

Creates a multi-dimensional array of object references.

Specified by:

createMDArray in interface IHDF5ReferenceWriter

Parameters:

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

dimensions - The dimensions of the array.

blockDimensions - The dimensions of one block (chunk) of the array.

features - The storage features of the data set.

writeMDArrayBlock

public void writeMDArrayBlock(java.lang.String objectPath,
                              ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths,
                              long[] blockNumber)

Description copied from interface: IHDF5ReferenceWriter

Writes out a block of a multi-dimensional array of object references.

Specified by:

writeMDArrayBlock in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPaths - The paths of the object references to write. Must not be null. All columns need to have the same length.

blockNumber - The block number in each dimension (offset: multiply with the extend in the according dimension).

writeMDArrayBlockWithOffset

public void writeMDArrayBlockWithOffset(java.lang.String objectPath,
                                        ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> referencedObjectPaths,
                                        long[] offset)

Description copied from interface: IHDF5ReferenceWriter

Writes out a block of a multi-dimensional array of object references.

Specified by:

writeMDArrayBlockWithOffset in interface IHDF5ReferenceWriter

Parameters:

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

referencedObjectPaths - The paths of the object references to write. Must not be null.

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

writeMDArrayBlockWithOffset

public void writeMDArrayBlockWithOffset(java.lang.String objectPath,
                                        ch.systemsx.cisd.base.mdarray.MDLongArray data,
                                        int[] blockDimensions,
                                        long[] offset,
                                        int[] memoryOffset)

Description copied from interface: IHDF5ReferenceWriter

Writes out a block of a multi-dimensional array of object references.

Specified by:

writeMDArrayBlockWithOffset in interface IHDF5ReferenceWriter

Parameters:

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

data - The paths of the object references to write. Must not be null.

blockDimensions - The dimensions of the block to write to the data set.

offset - The offset of the block in the data set to start writing to in each dimension.

memoryOffset - The offset of the block in the data array.