fr.profi.mzdb.io.reader.bb

Class SQLiteBlobReader

java.lang.Object

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

fr.profi.mzdb.io.reader.bb.SQLiteBlobReader

All Implemented Interfaces:

IBlobReader

public class SQLiteBlobReader
extends AbstractBlobReader

Class for manipulating Blob in SQLite datafile using sqlite4java.SQLiteBlob

Author:

Marc Dubois

See Also:

AbstractBlobReader

Field Summary

Fields

Modifier and Type	Field and Description
protected com.almworks.sqlite4java.SQLiteBlob	_blob SQLiteBlob Object

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

_dataEncodingBySpectrumId, _peaksCounts, _spectraCount, _spectrumHeaderById, _spectrumSliceStartPositions, logger

Constructor Summary

Constructors

Constructor and Description
SQLiteBlobReader(com.almworks.sqlite4java.SQLiteBlob blob, 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)
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

_blob

protected com.almworks.sqlite4java.SQLiteBlob _blob

SQLiteBlob Object

Constructor Detail

SQLiteBlobReader

public SQLiteBlobReader(com.almworks.sqlite4java.SQLiteBlob blob,
                        long firstSpectrumId,
                        long lastSpectrumId,
                        Map<Long,SpectrumHeader> spectrumHeaderById,
                        Map<Long,DataEncoding> dataEncodingBySpectrumId)
                 throws StreamCorruptedException

Constructor

Throws:

StreamCorruptedException

See Also:

SQLiteBlob, DataEncoding

Method Detail

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()

_indexSpectrumSlices

protected void _indexSpectrumSlices(int estimatedSpectraCount)
                             throws StreamCorruptedException

Throws:

StreamCorruptedException

See Also:

AbstractBlobReader, AbstractBlobReader#_buildMapPositions()

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