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

Class CMPH5FileBase

java.lang.Object

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

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

Direct Known Subclasses:

CMPH5FileData

public class CMPH5FileBase
extends HDF5File

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	file_version
protected float[]	movie_frame_rates
protected java.lang.String[]	movie_names_info
protected CMPH5ReadGroupInfo	read_group_info
protected java.lang.String	read_type
protected java.util.ArrayList<CMPH5ReferenceInfo>	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
CMPH5FileBase(java.io.File file, int access, int num_cached_objects)

Method Summary

Methods

Modifier and Type	Method and Description
void	clearDataSet(H5ScalarDS dataset) Clears memory held by the dataset, such as data buffer
UIntMatrixArray	getAlignmentIndexDataChunk(H5ScalarDS dataset, HDF5HyperslabInfo info) Reads a chunk of data from alignment index dataset.
H5ScalarDS	getAlignmentIndexDataset() returns the alignment index dataset
AlignmentIndexTable	getAlignmentIndexTableForContig(java.lang.String contig_id) Simple method to get cmp.h5 alignment index data for a specific contig.
protected H5ScalarDS	getAlnGroupPathDataset() returns the aln group path dataset
protected int	getContigIndexFromID(java.lang.String contig_id) Returns index of contig in cmp.h5 from contig id (ref00001, ref00002...)
java.lang.String[]	getContigNames(boolean full) Returns list of references in this file.
protected java.lang.String	getFullSequenceName(java.lang.String[] read_group_names, java.lang.String[] ref_info_full_names, int[] read_group_ref_info_id, int read_group_index) Reads full sequence (contig) name from cmp.h5 metadata
protected H5ScalarDS	getMovieFrameRateDataset() returns the movie framerate
float	getMovieFrameRateFromMovieID(int index) public as it is used in cmp.h5 wrapper
java.lang.String	getMovieNameFromMovieID(int index) public as it is used in cmp.h5 wrapper
protected H5ScalarDS	getMovieNameIDsDataset() returns the movie name ids
protected H5ScalarDS	getMovieNamesDataset() returns the movie names
long	getNumRows(H5ScalarDS dataset) Returns total rows in dataset
java.lang.String	getReadGroupAlignmentIndexPath(int index) public as it is used in cmp.h5 wrapper
UCharMatrixArray	getReadGroupDataChunk(H5ScalarDS dataset, HDF5HyperslabInfo info) Reads a chunk of data from a readgroup dataset.
protected H5ScalarDS	getReadGroupIDDataset() returns the read group id
int	getReadGroupIndexFromReadGroupValue(int value) public as it is used in cmp.h5 wrapper
java.lang.String	getReadGroupMetricsPath(int index, int mode) Returns path to selected metrics array
protected java.lang.String	getReadGroupNormalizedIPDPath(int index) Returns path to normalized IPD metrics
protected java.lang.String	getReadGroupPulseWidthPath(int index) Returns path to Pulse Width metrics
protected java.lang.String	getReadGroupQualityValuePath(int index) Returns path to QV metrics
protected java.lang.String	getReadGroupRawIPDPath(int index) Returns path to raw IPD metrics
protected H5ScalarDS	getRefGroupIDDataset() returns the ref group id dataset
protected H5ScalarDS	getRefGroupPathDataset() returns the ref group path dataset
protected H5ScalarDS	getRefGroupRefInfoIDDataset() returns the ref group refinfo id dataset
protected H5ScalarDS	getRefInfoFullNamesDataset() returns the refinfo fullname
protected H5ScalarDS	getSortedRefIndexDataset() returns the sorted ref index dataset
boolean	isStrobeReadType() ReadType attribute
boolean	isVersion1_3() Version specific tags
boolean	isVersion2_0() Version specific tags
boolean	isVersionAtLeast1_2() Version specific tags
protected void	readCmpH5ReferenceInfo() reads reference info from file and stores in local arraylist
java.lang.String	toString()
protected void	updateMovieInfoFromMovieIDs() reads movie ids and eventually update table of movie names and frame rates

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

Field Detail

file_version

protected java.lang.String file_version

read_type

protected java.lang.String read_type

reference_info

protected java.util.ArrayList<CMPH5ReferenceInfo> reference_info

read_group_info

protected CMPH5ReadGroupInfo read_group_info

movie_names_info

protected java.lang.String[] movie_names_info

movie_frame_rates

protected float[] movie_frame_rates

Constructor Detail

CMPH5FileBase

public CMPH5FileBase(java.io.File file,
             int access,
             int num_cached_objects)
              throws HDF5ExceptionEx

Parameters:

file - the path to the file to open or create

access - mode: FileFormat.READ, FileFormat.WRITE, FileFormat.CREATE

Throws:

HDF5ExceptionEx

Method Detail

readCmpH5ReferenceInfo

protected void readCmpH5ReferenceInfo()

reads reference info from file and stores in local arraylist

updateMovieInfoFromMovieIDs

protected void updateMovieInfoFromMovieIDs()

reads movie ids and eventually update table of movie names and frame rates

clearDataSet

public void clearDataSet(H5ScalarDS dataset)

Clears memory held by the dataset, such as data buffer

Parameters:

dataset -

getFullSequenceName

protected java.lang.String getFullSequenceName(java.lang.String[] read_group_names,
                                   java.lang.String[] ref_info_full_names,
                                   int[] read_group_ref_info_id,
                                   int read_group_index)
                                        throws HDF5Exception

Reads full sequence (contig) name from cmp.h5 metadata

Parameters:

read_group_ref_info_id -

ref_info_full_names -

read_group -

Returns:

full sequence name for this read group

Throws:

HDF5Exception

getAlignmentIndexTableForContig

public AlignmentIndexTable getAlignmentIndexTableForContig(java.lang.String contig_id)

Simple method to get cmp.h5 alignment index data for a specific contig. Requires SortedRefindex info to locate contig data.

Parameters:

contig_index - index of selected contig

start -

end -

Returns:

getNumRows

public long getNumRows(H5ScalarDS dataset)

Returns total rows in dataset

Parameters:

dataset - the dataset to search for lastRow

Returns:

number of rows in this dataset

getContigNames

public java.lang.String[] getContigNames(boolean full)

Returns list of references in this file. Either ref id or ref full name.

Parameters:

full - if false returns sequence id (ref00001..) if true returns full sequence name (chr1..)

Returns:

getContigIndexFromID

protected int getContigIndexFromID(java.lang.String contig_id)

Returns index of contig in cmp.h5 from contig id (ref00001, ref00002...)

Parameters:

contig_id - contig we want to retrieve index

Returns:

index of contig in cmp.h5 or 1 (default for single contig) if not found

toString

public java.lang.String toString()

Overrides:

toString in class HDF5File

getAlignmentIndexDataChunk

public UIntMatrixArray getAlignmentIndexDataChunk(H5ScalarDS dataset,
                                         HDF5HyperslabInfo info)

Reads a chunk of data from alignment index dataset. Returns a memory-space-saving unsigned integer array wrapper. Consider using the more generic getDataStreamFromDataset(). This method should be used when explicit control over data transfer is desired.

See Also:

ncsa.hdf.object.ScalarDS.convertFromUnsignedC()

getReadGroupDataChunk

public UCharMatrixArray getReadGroupDataChunk(H5ScalarDS dataset,
                                     HDF5HyperslabInfo info)

Reads a chunk of data from a readgroup dataset. Returns a memory-space-saving unsigned char array wrapper. Consider using the more generic getDataStreamFromDataset(). This method should be used when explicit control over data transfer is desired.

See Also:

ncsa.hdf.object.ScalarDS.convertFromUnsignedC()

getReadGroupMetricsPath

public java.lang.String getReadGroupMetricsPath(int index,
                                       int mode)

Returns path to selected metrics array

Parameters:

index -

mode -

Returns:

getReadGroupQualityValuePath

protected java.lang.String getReadGroupQualityValuePath(int index)

Returns path to QV metrics

Parameters:

index -

Returns:

getReadGroupRawIPDPath

protected java.lang.String getReadGroupRawIPDPath(int index)

Returns path to raw IPD metrics

Parameters:

index -

Returns:

getReadGroupNormalizedIPDPath

protected java.lang.String getReadGroupNormalizedIPDPath(int index)

Returns path to normalized IPD metrics

Parameters:

index -

Returns:

getReadGroupPulseWidthPath

protected java.lang.String getReadGroupPulseWidthPath(int index)

Returns path to Pulse Width metrics

Parameters:

index -

Returns:

getReadGroupAlignmentIndexPath

public java.lang.String getReadGroupAlignmentIndexPath(int index)

public as it is used in cmp.h5 wrapper

getReadGroupIndexFromReadGroupValue

public int getReadGroupIndexFromReadGroupValue(int value)

public as it is used in cmp.h5 wrapper

getMovieNameFromMovieID

public java.lang.String getMovieNameFromMovieID(int index)

public as it is used in cmp.h5 wrapper

getMovieFrameRateFromMovieID

public float getMovieFrameRateFromMovieID(int index)

public as it is used in cmp.h5 wrapper

isVersionAtLeast1_2

public boolean isVersionAtLeast1_2()

Version specific tags

Returns:

isVersion1_3

public boolean isVersion1_3()

Version specific tags

Returns:

isVersion2_0

public boolean isVersion2_0()

Version specific tags

Returns:

isStrobeReadType

public boolean isStrobeReadType()

ReadType attribute

Returns:

true if cmp.h5 contains strobe reads

getSortedRefIndexDataset

protected H5ScalarDS getSortedRefIndexDataset()

returns the sorted ref index dataset

getRefGroupIDDataset

protected H5ScalarDS getRefGroupIDDataset()

returns the ref group id dataset

getRefGroupPathDataset

protected H5ScalarDS getRefGroupPathDataset()

returns the ref group path dataset

getRefGroupRefInfoIDDataset

protected H5ScalarDS getRefGroupRefInfoIDDataset()

returns the ref group refinfo id dataset

getAlnGroupPathDataset

protected H5ScalarDS getAlnGroupPathDataset()

returns the aln group path dataset

getReadGroupIDDataset

protected H5ScalarDS getReadGroupIDDataset()

returns the read group id

getAlignmentIndexDataset

public H5ScalarDS getAlignmentIndexDataset()

returns the alignment index dataset

getMovieNamesDataset

protected H5ScalarDS getMovieNamesDataset()

returns the movie names

getMovieNameIDsDataset

protected H5ScalarDS getMovieNameIDsDataset()

returns the movie name ids

getMovieFrameRateDataset

protected H5ScalarDS getMovieFrameRateDataset()

returns the movie framerate

getRefInfoFullNamesDataset

protected H5ScalarDS getRefInfoFullNamesDataset()

returns the refinfo fullname