ch.systemsx.cisd.hdf5

Class HDF5StringReader

java.lang.Object

ch.systemsx.cisd.hdf5.HDF5StringReader

All Implemented Interfaces:

IHDF5StringReader

Direct Known Subclasses:

HDF5StringWriter

public class HDF5StringReader
extends java.lang.Object
implements IHDF5StringReader

The implementation of IHDF5StringReader.

Method Summary

Modifier and Type	Method and Description
java.lang.String[]	getArrayAttr(java.lang.String objectPath, java.lang.String attributeName) Reads a string array attribute named attributeName from the object objectPath.
java.lang.String[]	getArrayAttrRaw(java.lang.String objectPath, java.lang.String attributeName) Reads a string 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 string data set to iterate over.
java.lang.Iterable<HDF5DataBlock<java.lang.String[]>>	getArrayNaturalBlocksRaw(java.lang.String dataSetPath) Provides all natural blocks of this one-dimensional string data set to iterate over.
java.lang.String	getAttr(java.lang.String objectPath, java.lang.String attributeName) Reads a string attribute named attributeName from the object objectPath.
java.lang.String	getAttrRaw(java.lang.String objectPath, java.lang.String attributeName) Reads a string 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 a multi-dimensional string array attribute named attributeName from the object objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	getMDArrayAttrRaw(java.lang.String objectPath, java.lang.String attributeName) Reads a multi-dimensional string 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 objectPath) Provides all natural blocks of this multi-dimensional string data set to iterate over.
java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>>	getMDArrayNaturalBlocksRaw(java.lang.String objectPath) Provides all natural blocks of this multi-dimensional string data set to iterate over.
java.lang.String	read(java.lang.String objectPath) Reads a string from the data set objectPath.
java.lang.String[]	readArray(java.lang.String objectPath) Reads a string array (of rank 1) from the data set objectPath.
java.lang.String[]	readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber) Reads a block of a string array (of rank 1) from the data set objectPath.
java.lang.String[]	readArrayBlockRaw(java.lang.String objectPath, int blockSize, long blockNumber) Reads a block of a string array (of rank 1) from the data set objectPath.
java.lang.String[]	readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset) Reads a block of a string array (of rank 1) from the data set objectPath.
java.lang.String[]	readArrayBlockWithOffsetRaw(java.lang.String objectPath, int blockSize, long offset) Reads a block of a string array (of rank 1) from the data set objectPath.
java.lang.String[]	readArrayRaw(java.lang.String objectPath) Reads a string array (of rank 1) from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArray(java.lang.String objectPath) Reads a string array (of rank N) from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber) Reads a block of a string array (of rank N) from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayBlockRaw(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber) Reads a block of a string array (of rank N) 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 block of a string array (of rank N) from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayBlockWithOffsetRaw(java.lang.String objectPath, int[] blockDimensions, long[] offset) Reads a block of a string array (of rank N) from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>	readMDArrayRaw(java.lang.String objectPath) Reads a string array (of rank N) from the data set objectPath.
java.lang.String	readRaw(java.lang.String objectPath) Reads a String from the data set objectPath.

Methods inherited from class java.lang.Object

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

Method Detail

getAttr

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

Description copied from interface: IHDF5StringReader

Reads a string attribute named attributeName from the object objectPath. Considers '\0' as end of string.

Specified by:

getAttr in interface IHDF5StringReader

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 attribute value read from the data set.

getAttrRaw

public java.lang.String getAttrRaw(java.lang.String objectPath,
                                   java.lang.String attributeName)

Description copied from interface: IHDF5StringReader

Reads a string attribute named attributeName from the object objectPath. Does not consider '\0' as end of string but reads the full length of the attribute.

Specified by:

getAttrRaw in interface IHDF5StringReader

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 attribute value read from the data set.

getArrayAttr

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

Description copied from interface: IHDF5StringReader

Reads a string array attribute named attributeName from the object objectPath. Considers '\0' as end of string.

Specified by:

getArrayAttr in interface IHDF5StringReader

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 attribute value read from the data set.

getArrayAttrRaw

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

Description copied from interface: IHDF5StringReader

Reads a string array attribute named attributeName from the object objectPath. Does not consider '\0' as end of string but reads the full length.

Specified by:

getArrayAttrRaw in interface IHDF5StringReader

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 attribute value read from the data set.

getMDArrayAttr

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

Description copied from interface: IHDF5StringReader

Reads a multi-dimensional string array attribute named attributeName from the object objectPath. Considers '\0' as end of string.

Specified by:

getMDArrayAttr in interface IHDF5StringReader

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 attribute value read from the data set.

getMDArrayAttrRaw

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

Description copied from interface: IHDF5StringReader

Reads a multi-dimensional string array attribute named attributeName from the object objectPath. Does not consider '\0' as end of string but reads the full length.

Specified by:

getMDArrayAttrRaw in interface IHDF5StringReader

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 attribute value read from the data set.

read

public java.lang.String read(java.lang.String objectPath)
                      throws HDF5JavaException

Description copied from interface: IHDF5StringReader

Reads a string from the data set objectPath. Considers '\0' as end of string. This needs to be a string type.

Specified by:

read in interface IHDF5StringReader

Parameters:

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

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a string type.

readRaw

public java.lang.String readRaw(java.lang.String objectPath)
                         throws HDF5JavaException

Description copied from interface: IHDF5StringReader

Reads a String from the data set objectPath. Does not consider '\0' as end of string but reads the full length of the string. This needs to be a string type.

Specified by:

readRaw in interface IHDF5StringReader

Parameters:

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

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a string type.

readArrayRaw

public java.lang.String[] readArrayRaw(java.lang.String objectPath)
                                throws HDF5JavaException

Description copied from interface: IHDF5StringReader

Reads a string array (of rank 1) from the data set objectPath. The elements of this data set need to be a string type. Does not consider '\0' as end of string but reads the full length.

Specified by:

readArrayRaw in interface IHDF5StringReader

Parameters:

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

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a string type.

readArray

public java.lang.String[] readArray(java.lang.String objectPath)
                             throws HDF5JavaException

Description copied from interface: IHDF5StringReader

Reads a string array (of rank 1) from the data set objectPath. The elements of this data set need to be a string type. Considers '\0' as end of string.

Specified by:

readArray in interface IHDF5StringReader

Parameters:

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

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a string type.

readArrayBlock

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank 1) from the data set objectPath. The elements of this data set need to be a string type. Considers '\0' as end of string.

Specified by:

readArrayBlock in interface IHDF5StringReader

Parameters:

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

blockSize - The size of the block to read from the data set.

blockNumber - The number of the block to read from the data set (the offset is blockSize * blockNumber).

Returns:

The data read from the data set.

readArrayBlockRaw

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank 1) from the data set objectPath. The elements of this data set need to be a string type. Does not consider '\0' as end of string but reads the full length.

Specified by:

readArrayBlockRaw in interface IHDF5StringReader

Parameters:

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

blockSize - The size of the block to read from the data set.

blockNumber - The number of the block to read from the data set (the offset is blockSize * blockNumber).

Returns:

The data read from the data set.

readArrayBlockWithOffset

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank 1) from the data set objectPath. The elements of this data set need to be a string type. Considers '\0' as end of string.

Specified by:

readArrayBlockWithOffset in interface IHDF5StringReader

Parameters:

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

blockSize - The size of the block to read from the data set.

offset - The offset of the block in the data set.

Returns:

The data read from the data set.

readArrayBlockWithOffsetRaw

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank 1) from the data set objectPath. The elements of this data set need to be a string type. Does not consider '\0' as end of string but reads the full length.

Specified by:

readArrayBlockWithOffsetRaw in interface IHDF5StringReader

Parameters:

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

blockSize - The size of the block to read from the data set.

offset - The offset of the block in the data set.

Returns:

The data read from the data set.

readMDArray

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

Description copied from interface: IHDF5StringReader

Reads a string array (of rank N) from the data set objectPath. The elements of this data set need to be a string type. Considers '\0' as end of string.

Specified by:

readMDArray in interface IHDF5StringReader

Parameters:

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

Returns:

The data read from the data set.

readMDArrayRaw

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

Description copied from interface: IHDF5StringReader

Reads a string array (of rank N) from the data set objectPath. The elements of this data set need to be a string type. Does not considers '\0' as end of string but reads the full length.

Specified by:

readMDArrayRaw in interface IHDF5StringReader

Parameters:

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

Returns:

The data read from the data set.

readMDArrayBlockWithOffset

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank N) from the data set objectPath. The elements of this data set need to be a string type. Considers '\0' as end of string.

Specified by:

readMDArrayBlockWithOffset in interface IHDF5StringReader

Parameters:

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

blockDimensions - The dimensions (along each axis) of the block to read from the data set.

offset - The offset of the block in the data set.

Returns:

The data read from the data set.

readMDArrayBlockWithOffsetRaw

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank N) from the data set objectPath. The elements of this data set need to be a string type. Does not consider '\0' as end of string but reads the full length.

Specified by:

readMDArrayBlockWithOffsetRaw in interface IHDF5StringReader

Parameters:

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

blockDimensions - The dimensions (along each axis) of the block to read from the data set.

offset - The offset of the block in the data set.

Returns:

The data read from the data set.

readMDArrayBlock

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank N) from the data set objectPath. The elements of this data set need to be a string type. Considers '\0' as end of string. Considers '\0' as end of string.

Specified by:

readMDArrayBlock in interface IHDF5StringReader

Parameters:

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

blockDimensions - The dimensions (along each axis) of the block to read from the data set.

blockNumber - The number of the block to read from the data set (the offset in each dimension i is blockSize[i] * blockNumber[i]).

Returns:

The data read from the data set.

readMDArrayBlockRaw

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

Description copied from interface: IHDF5StringReader

Reads a block of a string array (of rank N) from the data set objectPath. The elements of this data set need to be a string type. Does not consider '\0' as end of string but reads the full length.

Specified by:

readMDArrayBlockRaw in interface IHDF5StringReader

Parameters:

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

blockDimensions - The dimensions (along each axis) of the block to read from the data set.

blockNumber - The number of the block to read from the data set (the offset in each dimension i is blockSize[i] * blockNumber[i]).

Returns:

The data read from the data set.

getArrayNaturalBlocks

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

Description copied from interface: IHDF5StringReader

Provides all natural blocks of this one-dimensional string data set to iterate over. Considers '\0' as end of string.

Specified by:

getArrayNaturalBlocks in interface IHDF5StringReader

Parameters:

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

Throws:

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

See Also:

HDF5DataBlock

getArrayNaturalBlocksRaw

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

Description copied from interface: IHDF5StringReader

Provides all natural blocks of this one-dimensional string data set to iterate over. Does not consider '\0' as end of string but reads the full length.

Specified by:

getArrayNaturalBlocksRaw in interface IHDF5StringReader

Parameters:

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

Throws:

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

See Also:

HDF5DataBlock

getMDArrayNaturalBlocks

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

Description copied from interface: IHDF5StringReader

Provides all natural blocks of this multi-dimensional string data set to iterate over. Considers '\0' as end of string.

Specified by:

getMDArrayNaturalBlocks in interface IHDF5StringReader

See Also:

HDF5MDDataBlock

getMDArrayNaturalBlocksRaw

public java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>> getMDArrayNaturalBlocksRaw(java.lang.String objectPath)

Description copied from interface: IHDF5StringReader

Provides all natural blocks of this multi-dimensional string data set to iterate over. Does not consider '\0' as end of string but reads the full length.

Specified by:

getMDArrayNaturalBlocksRaw in interface IHDF5StringReader

See Also:

HDF5MDDataBlock