fr.profi.mzdb.io.reader.bb

Class BytesReader

java.lang.Object

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

fr.profi.mzdb.io.reader.bb.BytesReader

All Implemented Interfaces:

IBlobReader

public class BytesReader
extends AbstractBlobReader

Author:

marco This implementation is mainly used is mzDbReader

Use a ByteBuffer to store the blob's bytes This class extends AbstractBlobReader.

Field Summary

Fields

Modifier and Type	Field and Description
protected ByteBuffer	_bbByteBuffer the data
protected int	_blobSize size of the Blob
protected DataEncoding	_firstDataEncondig

Fields inherited from class fr.profi.mzdb.io.reader.bb.AbstractBlobReader

_dataEncodingBySpectrumId, _peaksCounts, _spectraCount, _spectrumHeaderById, _spectrumSliceStartPositions, logger

Constructor Summary

Constructors

Constructor and Description
BytesReader(byte[] bytes, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId) Constructor

Method Summary

Modifier and Type	Method and Description
protected void	_indexSpectrumSlices(int estimatedSpectraCount) Do a first parse of the blob to determine beginning index of each spectrum slice
void	disposeBlob() Cleanup the blob if necessary
int	getBlobSize()
int	getSpectraCount()
long	getSpectrumIdAt(int idx)
SpectrumData	readFilteredSpectrumSliceDataAt(int idx, double minMz, double maxMz)
SpectrumSlice	readSpectrumSliceAt(int idx)
SpectrumData	readSpectrumSliceDataAt(int idx)

Methods inherited from class fr.profi.mzdb.io.reader.bb.AbstractBlobReader

checkDataEncodingIsNotNull, checkSpectrumIndexRange, getAllSpectrumIds, readAllSpectrumSlices, readSpectrumSliceData

Methods inherited from class java.lang.Object

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

Field Detail

_bbByteBuffer

protected ByteBuffer _bbByteBuffer

the data

_blobSize

protected int _blobSize

size of the Blob

_firstDataEncondig

protected DataEncoding _firstDataEncondig

Constructor Detail

BytesReader

public BytesReader(byte[] bytes,
                   long firstSpectrumId,
                   long lastSpectrumId,
                   Map<Long,SpectrumHeader> spectrumHeaderById,
                   Map<Long,DataEncoding> dataEncodingBySpectrumId)
            throws StreamCorruptedException

Constructor

Parameters:

dataEncodings, - DataEncoding object for each spectrum, usually given by a mzDbReaderInstance

data, - array of byte of the blob

Throws:

StreamCorruptedException

See Also:

MzDbReader, DataEncoding

Method Detail

_indexSpectrumSlices

protected void _indexSpectrumSlices(int estimatedSpectraCount)
                             throws StreamCorruptedException

Do a first parse of the blob to determine beginning index of each spectrum slice

Throws:

StreamCorruptedException

See Also:

AbstractBlobReader, AbstractBlobReader._buildMpaPositions()

disposeBlob

public void disposeBlob()

Description copied from interface: IBlobReader

Cleanup the blob if necessary

See Also:

IBlobReader.disposeBlob()

getBlobSize

public int getBlobSize()

See Also:

IBlobReader#getBlobSize()

getSpectraCount

public int getSpectraCount()

Returns:

the spectra count in the blob.

See Also:

IBlobReader.getSpectraCount()

getSpectrumIdAt

public long getSpectrumIdAt(int idx)

Parameters:

idx - index of spectrum starting at 1

Returns:

long, the ID of the spectrum at the specified index in the blob

See Also:

IBlobReader#idOfSpectrumAt(int)

readSpectrumSliceAt

public SpectrumSlice readSpectrumSliceAt(int idx)

Parameters:

idx - index of specified spectrum

Returns:

SpectrumSlice of the specified spectrum

See Also:

IBlobReader.readSpectrumSliceAt(int)

readSpectrumSliceDataAt

public SpectrumData readSpectrumSliceDataAt(int idx)

Parameters:

idx - index of specified spectrum

Returns:

SpectrumData of the specified spectrum

See Also:

IBlobReader.readSpectrumSliceAt(int)

readFilteredSpectrumSliceDataAt

public SpectrumData readFilteredSpectrumSliceDataAt(int idx,
                                                    double minMz,
                                                    double maxMz)

Parameters:

idx - index of specified spectrum

Returns:

SpectrumData of the specified spectrum