ch.systemsx.cisd.hdf5

Interface IHDF5ReferenceReader

All Known Subinterfaces:

IHDF5ReferenceWriter

All Known Implementing Classes:

HDF5ReferenceReader, HDF5ReferenceWriter

public interface IHDF5ReferenceReader

An interface for reading references in HDF5 files.

Obtain an object implementing this interface by calling IHDF5Reader.reference().

For an explanation about references, see IHDF5ReferenceWriter.

Method Summary

Modifier and Type	Method and Description
java.lang.String[]	getArrayAttr(java.lang.String objectPath, java.lang.String attributeName) Reads a 1D object reference array attribute named attributeName from the object objectPath, resolving the names of the objects.
java.lang.String[]	getArrayAttr(java.lang.String objectPath, java.lang.String attributeName, boolean resolveName) Reads a 1D object reference array attribute named attributeName from the object objectPath.
java.lang.Iterable<HDF5DataBlock<java.lang.String[]>>	getArrayNaturalBlocks(java.lang.String dataSetPath) Provides all natural blocks of this one-dimensional data set to iterate over.
java.lang.Iterable<HDF5DataBlock<java.lang.String[]>>	getArrayNaturalBlocks(java.lang.String dataSetPath, boolean resolveName) Provides all natural blocks of this one-dimensional data set to iterate over.
java.lang.String	getAttr(java.lang.String objectPath, java.lang.String attributeName) Reads an object reference attribute named attributeName from the object objectPath, resolving the name of the object.
java.lang.String	getAttr(java.lang.String objectPath, java.lang.String attributeName, boolean resolveName) Reads an object reference attribute named attributeName from the object objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	getMDArrayAttr(java.lang.String objectPath, java.lang.String attributeName) Reads an object reference array attribute named attributeName from the object objectPath, resolving the names of the objects.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	getMDArrayAttr(java.lang.String objectPath, java.lang.String attributeName, boolean resolveName) Reads an object reference array attribute named attributeName from the object objectPath.
java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>>	getMDArrayNaturalBlocks(java.lang.String dataSetPath) Provides all natural blocks of this multi-dimensional data set to iterate over.
java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>>	getMDArrayNaturalBlocks(java.lang.String dataSetPath, boolean resolveName) Provides all natural blocks of this multi-dimensional data set to iterate over.
java.lang.String	read(java.lang.String objectPath) Reads an object reference from the object objectPath, resolving the name of the object.
java.lang.String	read(java.lang.String objectPath, boolean resolveName) Reads an object reference from the object objectPath.
java.lang.String[]	readArray(java.lang.String objectPath) Reads an array of object references from the object objectPath, resolving the names of the objects.
java.lang.String[]	readArray(java.lang.String objectPath, boolean resolveName) Reads an array of object references from the object objectPath.
java.lang.String[]	readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber) Reads a block from an array (of rank 1) of object references from the data set objectPath, resolving the names of the objects.
java.lang.String[]	readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber, boolean resolveName) Reads a block from an array (of rank 1) of object references from the data set objectPath.
java.lang.String[]	readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset) Reads a block from an array (of rank 1) of object references from the data set objectPath, resolving the names of the objects.
java.lang.String[]	readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset, boolean resolveName) Reads a block from an array (of rank 1) of object references from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArray(java.lang.String objectPath) Reads an array (or rank N) of object references from the object objectPath, resolving the names of the objects.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArray(java.lang.String objectPath, boolean resolveName) Reads an array (or rank N) of object references from the object objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber) Reads a multi-dimensional array of object references from the data set objectPath, resolving the names of the objects.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber, boolean resolveName) Reads a multi-dimensional array of object references from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayBlockWithOffset(java.lang.String objectPath, int[] blockDimensions, long[] offset) Reads a multi-dimensional array of object references from the data set objectPath, resolving the names of the objects.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayBlockWithOffset(java.lang.String objectPath, int[] blockDimensions, long[] offset, boolean resolveName) Reads a multi-dimensional array of object references from the data set objectPath.
java.lang.String	resolvePath(java.lang.String reference) Resolves the path of a reference which has been read without name resolution.

Method Detail

resolvePath

java.lang.String resolvePath(java.lang.String reference)
                      throws HDF5JavaException

Resolves the path of a reference which has been read without name resolution.

Parameters:

reference - Reference encoded as string.

Returns:

The path in the HDF5 file.

Throws:

HDF5JavaException - if reference is not a string-encoded reference.

See Also:

readArray(String, boolean)

getAttr

java.lang.String getAttr(java.lang.String objectPath,
                         java.lang.String attributeName)

Reads an object reference attribute named attributeName from the object objectPath, resolving the name of the object.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

attributeName - The name of the attribute to read.

Returns:

The path of the object that the reference refers to, or an empty string, if the object reference refers to an unnamed object.

getAttr

java.lang.String getAttr(java.lang.String objectPath,
                         java.lang.String attributeName,
                         boolean resolveName)

Reads an object reference attribute named attributeName from the object objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

attributeName - The name of the attribute to read.

resolveName - If true, resolves the name of the object referenced, otherwise returns the references itself.

Returns:

The path of the object that the reference refers to, or an empty string, if the object reference refers to an unnamed object.

getArrayAttr

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

Reads a 1D object reference array attribute named attributeName from the object objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

attributeName - The name of the attribute to read.

Returns:

The paths of the objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

getArrayAttr

java.lang.String[] getArrayAttr(java.lang.String objectPath,
                                java.lang.String attributeName,
                                boolean resolveName)

Reads a 1D object reference array attribute named attributeName from the object objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

attributeName - The name of the attribute to read.

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The paths of the objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

getMDArrayAttr

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> getMDArrayAttr(java.lang.String objectPath,
                                                                       java.lang.String attributeName)

Reads an object reference array attribute named attributeName from the object objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

attributeName - The name of the attribute to read.

Returns:

The paths of the objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

getMDArrayAttr

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> getMDArrayAttr(java.lang.String objectPath,
                                                                       java.lang.String attributeName,
                                                                       boolean resolveName)

Reads an object reference array attribute named attributeName from the object objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

attributeName - The name of the attribute to read.

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The paths of the objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

read

java.lang.String read(java.lang.String objectPath)

Reads an object reference from the object objectPath, resolving the name of the object.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

Returns:

The path of the object that the reference refers to, or an empty string, if the object reference refers to an unnamed object.

read

java.lang.String read(java.lang.String objectPath,
                      boolean resolveName)

Reads an object reference from the object objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

resolveName - If true, resolves the name of the object referenced, otherwise returns the references itself.

Returns:

The path of the object that the reference refers to, or an empty string, if the object reference refers to an unnamed object.

readArray

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

Reads an array of object references from the object objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

Returns:

The array of the paths of objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

readArray

java.lang.String[] readArray(java.lang.String objectPath,
                             boolean resolveName)

Reads an array of object references from the object objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The array of the paths of objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

readArrayBlock

java.lang.String[] readArrayBlock(java.lang.String objectPath,
                                  int blockSize,
                                  long blockNumber)

Reads a block from an array (of rank 1) of object references from the data set objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

blockSize - The block size (this will be the length of the long[] returned if the data set is long enough).

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

Returns:

The referenced data set paths read from the data set. The length will be min(size - blockSize*blockNumber, blockSize).

readArrayBlock

java.lang.String[] readArrayBlock(java.lang.String objectPath,
                                  int blockSize,
                                  long blockNumber,
                                  boolean resolveName)

Reads a block from an array (of rank 1) of object references from the data set objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

blockSize - The block size (this will be the length of the long[] returned if the data set is long enough).

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

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The referenced data set paths read from the data set. The length will be min(size - blockSize*blockNumber, blockSize).

readArrayBlockWithOffset

java.lang.String[] readArrayBlockWithOffset(java.lang.String objectPath,
                                            int blockSize,
                                            long offset)

Reads a block from an array (of rank 1) of object references from the data set objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

blockSize - The block size (this will be the length of the long[] returned).

offset - The offset of the block in the data set to start reading from (starting with 0).

Returns:

The referenced data set paths block read from the data set.

readArrayBlockWithOffset

java.lang.String[] readArrayBlockWithOffset(java.lang.String objectPath,
                                            int blockSize,
                                            long offset,
                                            boolean resolveName)

Reads a block from an array (of rank 1) of object references from the data set objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

blockSize - The block size (this will be the length of the long[] returned).

offset - The offset of the block in the data set to start reading from (starting with 0).

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The referenced data set paths block read from the data set.

readMDArray

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArray(java.lang.String objectPath)

Reads an array (or rank N) of object references from the object objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

Returns:

The multi-dimensional array of the paths of objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

readMDArray

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArray(java.lang.String objectPath,
                                                                    boolean resolveName)

Reads an array (or rank N) of object references from the object objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The multi-dimensional array of the paths of objects that the references refers to. Each string may be empty, if the corresponding object reference refers to an unnamed object.

readMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlock(java.lang.String objectPath,
                                                                         int[] blockDimensions,
                                                                         long[] blockNumber)

Reads a multi-dimensional array of object references from the data set objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

blockDimensions - The extent of the block in each dimension.

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

Returns:

The referenced data set paths block read from the data set.

readMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlock(java.lang.String objectPath,
                                                                         int[] blockDimensions,
                                                                         long[] blockNumber,
                                                                         boolean resolveName)

Reads a multi-dimensional array of object references from the data set objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

blockDimensions - The extent of the block in each dimension.

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

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The referenced data set paths block read from the data set.

readMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlockWithOffset(java.lang.String objectPath,
                                                                                   int[] blockDimensions,
                                                                                   long[] offset)

Reads a multi-dimensional array of object references from the data set objectPath, resolving the names of the objects.
Note that resolving the name of the object is a time consuming operation. If you don't need the name, but want to dereference the dataset, you don't need to resolve the name if the reader / writer is configured for auto-dereferencing (see IHDF5ReaderConfigurator.noAutoDereference()).

Parameters:

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

blockDimensions - The extent of the block in each dimension.

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

Returns:

The referenced data set paths block read from the data set.

readMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlockWithOffset(java.lang.String objectPath,
                                                                                   int[] blockDimensions,
                                                                                   long[] offset,
                                                                                   boolean resolveName)

Reads a multi-dimensional array of object references from the data set objectPath.
Note: if the reader has been configured to automatically resolve references (see IHDF5ReaderConfigurator.noAutoDereference()), a reference can be provided in all places where an object path is expected. This is considerably faster than resolving the name/path of the reference if the name/path by itself is not needed.

Parameters:

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

blockDimensions - The extent of the block in each dimension.

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

resolveName - If true, resolves the names of the objects referenced, otherwise returns the references itself.

Returns:

The referenced data set paths block read from the data set.

getArrayNaturalBlocks

java.lang.Iterable<HDF5DataBlock<java.lang.String[]>> getArrayNaturalBlocks(java.lang.String dataSetPath)

Provides all natural blocks of this one-dimensional data set to iterate over.

Throws:

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

See Also:

HDF5DataBlock

getArrayNaturalBlocks

java.lang.Iterable<HDF5DataBlock<java.lang.String[]>> getArrayNaturalBlocks(java.lang.String dataSetPath,
                                                                            boolean resolveName)

Provides all natural blocks of this one-dimensional data set to iterate over.

Throws:

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

See Also:

HDF5DataBlock

getMDArrayNaturalBlocks

java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>> getMDArrayNaturalBlocks(java.lang.String dataSetPath)

Provides all natural blocks of this multi-dimensional data set to iterate over.

See Also:

HDF5MDDataBlock

getMDArrayNaturalBlocks

java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>> getMDArrayNaturalBlocks(java.lang.String dataSetPath,
                                                                                                                     boolean resolveName)

Provides all natural blocks of this multi-dimensional data set to iterate over.

See Also:

HDF5MDDataBlock