com.pacbio.secondary.vis.io.hdf.test

Class HDFTest

java.lang.Object

com.pacbio.secondary.vis.io.hdf.test.HDFTest

public class HDFTest
extends java.lang.Object

Test class for hdf library, exercises methods for accessing file data and metadata

Author:

mmilletti

Constructor Summary

Constructors

Constructor and Description
HDFTest()

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(java.lang.String[] args) runs all tests
protected static void	testDataStreaming(CMPH5File cmp_file, H5ScalarDS dataset, StreamingDataConsumer consumer) Demo/Test method only.
protected static void	testGetAlignmentIndexTableForInterval(CMPH5File cmp_file, java.lang.String contig_id, long start, long end) Demo/Test method.
static boolean	testReadCMPH5File(java.io.File file, int access) simple cmp.h5 file read access test
protected static void	testStreamAlignmentIndexData(CMPH5File cmp_file) Demo/Test method only.
protected static void	testStreamFirstReadGroupData(CMPH5File cmp_file) Demo/Test method only.
static boolean	testWriteCMPH5File(java.io.File file, int access) simple cmp.h5 file write access test
protected static boolean	testWriteDataSet(CMPH5File cmp_file) Demo/Test method only.

Methods inherited from class java.lang.Object

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

Constructor Detail

HDFTest

public HDFTest()

Method Detail

main

public static void main(java.lang.String[] args)

runs all tests

Parameters:

args -

testReadCMPH5File

public static boolean testReadCMPH5File(java.io.File file,
                        int access)

simple cmp.h5 file read access test

Parameters:

file - file to open

access - access mode

Returns:

true if successful, false otherwise

testWriteCMPH5File

public static boolean testWriteCMPH5File(java.io.File file,
                         int access)

simple cmp.h5 file write access test

Parameters:

file - file to open

access - access mode

Returns:

true if successful, false otherwise

testGetAlignmentIndexTableForInterval

protected static void testGetAlignmentIndexTableForInterval(CMPH5File cmp_file,
                                         java.lang.String contig_id,
                                         long start,
                                         long end)

Demo/Test method. Gets reads info from the alignmentindex table for specific contig and interval.

Parameters:

contig_id - id of contig

start - inclusive start of interval

end - inclusive end of interval

testStreamAlignmentIndexData

protected static void testStreamAlignmentIndexData(CMPH5File cmp_file)

Demo/Test method only. Shows how to read a 2D dataset of unsigned ints (alignment index) in chunks

Parameters:

dump -

testStreamFirstReadGroupData

protected static void testStreamFirstReadGroupData(CMPH5File cmp_file)

Demo/Test method only. Shows how to read a 1D dataset of unsigned chars (first read group) in chunks

Parameters:

dump -

testDataStreaming

protected static void testDataStreaming(CMPH5File cmp_file,
                     H5ScalarDS dataset,
                     StreamingDataConsumer consumer)

Demo/Test method only. Performs multiple tests of streaming data transfer: all data, random access, first row, last row

Parameters:

dataset - scalar dataset

consumer - streamingdataconsumer instance to receive callbacks with data chunks

testWriteDataSet

protected static boolean testWriteDataSet(CMPH5File cmp_file)

Demo/Test method only. Performs multiple tests of writing data: bytes, chars, etc.

Returns: