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

Class CMPH5FileData

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

Direct Known Subclasses:

CMPH5File

public class CMPH5FileData
extends CMPH5FileBase

This class wraps high level access to lazy data storage

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
CMPH5FileData(java.io.File file, int access, int num_cached_objects)

Method Summary

Methods

Modifier and Type	Method and Description
byte[]	getConsensusSequence(java.lang.String contig_id, long start, long stop)
int[]	getIPDSequence(java.lang.String contig_id, long start, long stop)
protected RawRead	getSingleRawRead(AlignmentIndexTable table, int row_idx) Deprecated.
RawRead	getSingleRawReadUsingCache(H5ScalarDS read_align_dataset, H5ScalarDS read_metrics_dataset, AlignmentIndexTable table, int row_idx)
RawRead	updateSingleRawReadUsingCache(RawRead read, H5ScalarDS read_metrics_dataset, AlignmentIndexTable table, int row_idx)

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, dispose, 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

CMPH5FileData

public CMPH5FileData(java.io.File file,
             int access,
             int num_cached_objects)
              throws HDF5ExceptionEx

Parameters:

file -

access -

Throws:

HDF5ExceptionEx

Method Detail

getConsensusSequence

public byte[] getConsensusSequence(java.lang.String contig_id,
                          long start,
                          long stop)

Parameters:

contig_index -

start -

stop -

Returns:

getIPDSequence

public int[] getIPDSequence(java.lang.String contig_id,
                   long start,
                   long stop)

Parameters:

contig_index -

start -

stop -

Returns:

getSingleRawRead

@Deprecated
protected RawRead getSingleRawRead(AlignmentIndexTable table,
                                  int row_idx)

Deprecated.

Parameters:

table -

row_idx -

Returns:

getSingleRawReadUsingCache

public RawRead getSingleRawReadUsingCache(H5ScalarDS read_align_dataset,
                                 H5ScalarDS read_metrics_dataset,
                                 AlignmentIndexTable table,
                                 int row_idx)

Parameters:

table -

row_idx -

Returns:

updateSingleRawReadUsingCache

public RawRead updateSingleRawReadUsingCache(RawRead read,
                                    H5ScalarDS read_metrics_dataset,
                                    AlignmentIndexTable table,
                                    int row_idx)

Parameters:

table -

row_idx -

Returns: