fr.profi.mzdb.io.reader.bb

Class AbstractBlobReader

java.lang.Object

fr.profi.mzdb.io.reader.bb.AbstractBlobReader

All Implemented Interfaces:

IBlobReader

Direct Known Subclasses:

BytesReader, SQLiteBlobReader, StreamReader

public abstract class AbstractBlobReader
extends Object
implements IBlobReader

Abstract Class containing commons objects and attributes through the implementations

Author:

marco, David Bouyssie

See Also:

IBlobReader

Field Summary

Fields

Modifier and Type	Field and Description
protected Map<Long,DataEncoding>	_dataEncodingBySpectrumId
protected int[]	_peaksCounts
protected int	_spectraCount
protected Map<Long,SpectrumHeader>	_spectrumHeaderById
protected int[]	_spectrumSliceStartPositions
protected org.slf4j.Logger	logger

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractBlobReader(long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId) Abstract constructor

Method Summary

Modifier and Type	Method and Description
protected void	checkDataEncodingIsNotNull(DataEncoding de, long spectrumId)
protected void	checkSpectrumIndexRange(int idx)
long[]	getAllSpectrumIds()
SpectrumSlice[]	readAllSpectrumSlices(int runSliceId)
protected SpectrumData	readSpectrumSliceData(ByteBuffer bbByteBuffer, int spectrumSliceStartPos, int peaksBytesLength, DataEncoding de, double minMz, double maxMz) Read spectrum slice data by using a ByteBuffer as input

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.profi.mzdb.io.reader.bb.IBlobReader

disposeBlob, getSpectraCount, getSpectrumIdAt, readFilteredSpectrumSliceDataAt, readSpectrumSliceAt, readSpectrumSliceDataAt

Field Detail

logger

protected final org.slf4j.Logger logger

_spectraCount

protected int _spectraCount

_spectrumSliceStartPositions

protected int[] _spectrumSliceStartPositions

_peaksCounts

protected int[] _peaksCounts

_spectrumHeaderById

protected Map<Long,SpectrumHeader> _spectrumHeaderById

_dataEncodingBySpectrumId

protected Map<Long,DataEncoding> _dataEncodingBySpectrumId

Constructor Detail

AbstractBlobReader

protected AbstractBlobReader(long firstSpectrumId,
                             long lastSpectrumId,
                             Map<Long,SpectrumHeader> spectrumHeaderById,
                             Map<Long,DataEncoding> dataEncodingBySpectrumId)

Abstract constructor

Parameters:

spectrumHeaderById - SpectrumHeader by spectrum id

dataEncById - DataEncoding by spectrum id

See Also:

DataEncoding

Method Detail

getAllSpectrumIds

public long[] getAllSpectrumIds()

Specified by:

getAllSpectrumIds in interface IBlobReader

readSpectrumSliceData

protected SpectrumData readSpectrumSliceData(ByteBuffer bbByteBuffer,
                                             int spectrumSliceStartPos,
                                             int peaksBytesLength,
                                             DataEncoding de,
                                             double minMz,
                                             double maxMz)

Read spectrum slice data by using a ByteBuffer as input

Parameters:

bbByteBuffer - array of bytes containing the SpectrumSlices of interest

spectrumSliceStartPos, - the starting position

peaksBytesLength, - length of bytes used by peaks

structSize, - size of the struct for a given peak

de, - the corresponding DataEncoding

minMz, - the minimum m/z value

maxMz, - the maximum m/z value

Returns:

checkSpectrumIndexRange

protected void checkSpectrumIndexRange(int idx)

checkDataEncodingIsNotNull

protected void checkDataEncodingIsNotNull(DataEncoding de,
                                          long spectrumId)
                                   throws StreamCorruptedException

Throws:

StreamCorruptedException

readAllSpectrumSlices

public SpectrumSlice[] readAllSpectrumSlices(int runSliceId)

Specified by:

readAllSpectrumSlices in interface IBlobReader

Parameters:

runSliceId - needed to correctly annotate the SpectrumSlice

Returns:

array of spectrumSlice representing the bounding box

See Also:

IBlobReader.readAllSpectrumSlices(int)