com.pacbio.secondary.vis.io.hdf.file.cmph5

Class CMPH5File

java.lang.Object

com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData

com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5File

public class CMPH5File
extends CMPH5FileData

Base class for accessing cmp.h5 files

Author:

mmilletti

Field Summary

Fields inherited from class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

file_version, movie_frame_rates, movie_names_info, read_group_info, read_type, reference_info

Fields inherited from class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

hdf_file_format, hdf_file_root_group, hdf_file_root_node, MAX_NUM_CACHED_OBJECTS, MAX_NUM_CACHED_OBJECTS_KINETOGRAM

Constructor Summary

Constructors

Constructor and Description
CMPH5File(java.io.File file, int access, int num_cached_objects)

Method Summary

Methods

Modifier and Type	Method and Description
void	dispose() this method must be called after using the file

Methods inherited from class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData

getConsensusSequence, getIPDSequence, getSingleRawRead, getSingleRawReadUsingCache, updateSingleRawReadUsingCache

Methods inherited from class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

clearDataSet, getAlignmentIndexDataChunk, getAlignmentIndexDataset, getAlignmentIndexTableForContig, getAlnGroupPathDataset, getContigIndexFromID, getContigNames, getFullSequenceName, getMovieFrameRateDataset, getMovieFrameRateFromMovieID, getMovieNameFromMovieID, getMovieNameIDsDataset, getMovieNamesDataset, getNumRows, getReadGroupAlignmentIndexPath, getReadGroupDataChunk, getReadGroupIDDataset, getReadGroupIndexFromReadGroupValue, getReadGroupMetricsPath, getReadGroupNormalizedIPDPath, getReadGroupPulseWidthPath, getReadGroupQualityValuePath, getReadGroupRawIPDPath, getRefGroupIDDataset, getRefGroupPathDataset, getRefGroupRefInfoIDDataset, getRefInfoFullNamesDataset, getSortedRefIndexDataset, isStrobeReadType, isVersion1_3, isVersion2_0, isVersionAtLeast1_2, readCmpH5ReferenceInfo, toString, updateMovieInfoFromMovieIDs

Methods inherited from class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

createEmptyDataset, createFilledDataset, createGroup, getAllAttributes, getAllChildDatasets, getAllChildGroups, getAttributeFloatValues, getAttributeLongValues, getAttributeStringValues, getChildDataset, getChildGroup, getDataset, getDatasetChunkInfo, getDatasetHyperslabInfo, getDataStreamFromDataset, getFileHandle, getFilePath, getGroup, getNamedRootObject, getUCharDataChunk, getUIntDataChunk, readDatasetHyperslab, readUnsignedDatasetHyperslab, testPrintDatasetInfo, writeChunkToDataset, writeStringAttribute, writeUIntAttribute

Methods inherited from class java.lang.Object

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

Constructor Detail

CMPH5File

public CMPH5File(java.io.File file,
         int access,
         int num_cached_objects)
          throws HDF5ExceptionEx

Throws:

HDF5ExceptionEx

Method Detail

dispose

public void dispose()

this method must be called after using the file

Overrides:

dispose in class HDF5File