fr.profi.mzdb.io.reader.bb

Class StreamReader

java.lang.Object

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

fr.profi.mzdb.io.reader.bb.StreamReader

All Implemented Interfaces:

IBlobReader

public class StreamReader
extends AbstractBlobReader

This class aloow to read a SQLite blob using a stream reader. We process data only in one direction in a sequential way The goal is to request only one time the blob

Author:

marco

Field Summary

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

_dataEncodingBySpectrumId, _peaksCounts, _spectraCount, _spectrumHeaderById, _spectrumSliceStartPositions, logger

Constructor Summary

Constructors

Constructor and Description
StreamReader(InputStream inputStream, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId)

Method Summary

Modifier and Type	Method and Description
void	disposeBlob() Cleanup the blob if necessary
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

Constructor Detail

StreamReader

public StreamReader(InputStream inputStream,
                    long firstSpectrumId,
                    long lastSpectrumId,
                    Map<Long,SpectrumHeader> spectrumHeaderById,
                    Map<Long,DataEncoding> dataEncodingBySpectrumId)

Parameters:

dataEnc - SpectrumID the key, dataEncoding the value

s - inputStream

See Also:

AbstractBlobReader, AbstractBlobReader._dataEncodingBySpectrumId

Method Detail

disposeBlob

public void disposeBlob()

Description copied from interface: IBlobReader

Cleanup the blob if necessary

See Also:

IBlobReader.disposeBlob()

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

readFilteredSpectrumSliceDataAt

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

Parameters:

idx - index of specified spectrum

Returns:

SpectrumData of the specified spectrum