fr.profi.mzdb

Class AbstractMzDbReader

java.lang.Object

fr.profi.mzdb.AbstractMzDbReader

Direct Known Subclasses:

MzDbAsyncReader, MzDbReader

public abstract class AbstractMzDbReader
extends Object

Allows to manipulates data contained in the mzDB file.

Author:

David

Field Summary

Fields

Modifier and Type	Field and Description
protected IMzDBParamNameGetter	_paramNameGetter
protected AcquisitionMode	acquisitionMode Define some lazy fields
protected BBSizes	bbSizes
protected static ExecutorService	computationThreadPool
protected File	dbLocation Some fields initialized in the constructor
protected IsolationWindow[]	diaIsolationWindows
protected MzDbEntityCache	entityCache
protected List<InstrumentConfiguration>	instrumentConfigs
protected Boolean	isNoLossMode The is no loss mode.
protected org.slf4j.Logger	logger
protected MzDbHeader	mzDbHeader
protected List<Run>	runs
protected static rx.Scheduler	rxCompScheduler
protected List<Sample>	samples
protected List<Software>	softwareList
protected List<SourceFile>	sourceFiles

Constructor Summary

Constructors

Constructor and Description
AbstractMzDbReader()

Method Summary

Modifier and Type	Method and Description
protected void	_setBBSizes(IMzDBParamNameGetter paramNameGetter)
abstract void	close() Close the file to avoid memory leaks.
void	enableParamTreeLoading()
void	enablePrecursorListLoading()
void	enableScanListLoading()
protected AcquisitionMode	getAcquisitionMode(com.almworks.sqlite4java.SQLiteConnection connection) Lazy loading of the acquisition mode, parameter
BBSizes	getBBSizes()
abstract AbstractDataEncodingReader	getDataEncodingReader()
String	getDbLocation()
protected IsolationWindow[]	getDIAIsolationWindows(com.almworks.sqlite4java.SQLiteConnection connection) Get the DIA IsolationWindows
MzDbEntityCache	getEntityCache() Gets the entity cache.
String	getFirstSourceFileName()
abstract List<InstrumentConfiguration>	getInstrumentConfigurations()
protected Peak[]	getMsnPeaksInMzRtRanges(double parentMz, double minFragMz, double maxFragMz, float minRt, float maxRt, com.almworks.sqlite4java.SQLiteConnection connection)
protected SpectrumSlice[]	getMsnSpectrumSlices(double parentMz, double minFragMz, double maxFragMz, float minRt, float maxRt, com.almworks.sqlite4java.SQLiteConnection connection)
protected Peak[]	getMsnXic(double parentMz, double fragmentMz, double fragmentMzTolInDa, float minRt, float maxRt, XicMethod method, com.almworks.sqlite4java.SQLiteConnection connection)
protected Peak[]	getMsPeaksInMzRtRanges(double minMz, double maxMz, float minRt, float maxRt, com.almworks.sqlite4java.SQLiteConnection connection) Gets the peaks.
protected SpectrumSlice[]	getMsSpectrumSlices(double minMz, double maxMz, float minRt, float maxRt, com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum slices.
protected Peak[]	getMsXic(double mz, double mzTolInDa, float minRt, float maxRt, XicMethod method, com.almworks.sqlite4java.SQLiteConnection connection)
protected Peak[]	getMsXicInMzRange(double minMz, double maxMz, XicMethod method, com.almworks.sqlite4java.SQLiteConnection connection) Gets the xic.
protected Peak[]	getMsXicInMzRtRanges(double minMz, double maxMz, float minRt, float maxRt, XicMethod method, com.almworks.sqlite4java.SQLiteConnection connection)
MzDbHeader	getMzDbHeader()
abstract List<Run>	getRuns()
protected RunSliceData	getRunSliceData(int runSliceId, com.almworks.sqlite4java.SQLiteConnection connection) Gets the run slice data.
abstract AbstractRunSliceHeaderReader	getRunSliceHeaderReader()
abstract List<Sample>	getSamples()
abstract List<Software>	getSoftwareList()
abstract List<SourceFile>	getSourceFiles()
protected Spectrum	getSpectrum(long spectrumId, com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum.
protected SpectrumData	getSpectrumData(long spectrumId, com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum data.
abstract AbstractSpectrumHeaderReader	getSpectrumHeaderReader()
protected Peak[]	getSpectrumPeaks(int spectrumId, com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum peaks.
boolean	isNoLossMode()
boolean	isParamTreeLoadingEnabled()
boolean	isPrecursorListLoadingEnabled()
boolean	isScanListLoadingEnabled()

Methods inherited from class java.lang.Object

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

Field Detail

computationThreadPool

protected static final ExecutorService computationThreadPool

rxCompScheduler

protected static final rx.Scheduler rxCompScheduler

logger

protected final org.slf4j.Logger logger

bbSizes

protected final BBSizes bbSizes

dbLocation

protected File dbLocation

Some fields initialized in the constructor

entityCache

protected MzDbEntityCache entityCache

mzDbHeader

protected MzDbHeader mzDbHeader

_paramNameGetter

protected IMzDBParamNameGetter _paramNameGetter

isNoLossMode

protected Boolean isNoLossMode

The is no loss mode. If no loss mode is enabled, all data points will be encoded as highres, i.e. 64 bits mz and 64 bits int. No peak picking and not fitting will be performed on profile data.

acquisitionMode

protected AcquisitionMode acquisitionMode

Define some lazy fields

diaIsolationWindows

protected IsolationWindow[] diaIsolationWindows

instrumentConfigs

protected List<InstrumentConfiguration> instrumentConfigs

runs

protected List<Run> runs

samples

protected List<Sample> samples

softwareList

protected List<Software> softwareList

sourceFiles

protected List<SourceFile> sourceFiles

Constructor Detail

AbstractMzDbReader

public AbstractMzDbReader()

Method Detail

close

public abstract void close()

Close the file to avoid memory leaks. Method to be implemented in child classes.

getDataEncodingReader

public abstract AbstractDataEncodingReader getDataEncodingReader()

getSpectrumHeaderReader

public abstract AbstractSpectrumHeaderReader getSpectrumHeaderReader()

getRunSliceHeaderReader

public abstract AbstractRunSliceHeaderReader getRunSliceHeaderReader()

isParamTreeLoadingEnabled

public boolean isParamTreeLoadingEnabled()

enableParamTreeLoading

public void enableParamTreeLoading()

isScanListLoadingEnabled

public boolean isScanListLoadingEnabled()

enableScanListLoading

public void enableScanListLoading()

isPrecursorListLoadingEnabled

public boolean isPrecursorListLoadingEnabled()

enablePrecursorListLoading

public void enablePrecursorListLoading()

getEntityCache

public MzDbEntityCache getEntityCache()

Gets the entity cache.

Returns:

the entity cache

getDbLocation

public String getDbLocation()

getMzDbHeader

public MzDbHeader getMzDbHeader()
                         throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

isNoLossMode

public boolean isNoLossMode()
                     throws com.almworks.sqlite4java.SQLiteException

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

getBBSizes

public BBSizes getBBSizes()
                   throws com.almworks.sqlite4java.SQLiteException

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

_setBBSizes

protected void _setBBSizes(IMzDBParamNameGetter paramNameGetter)

Parameters:

bbSizes -

paramNameGetter -

header -

getRunSliceData

protected RunSliceData getRunSliceData(int runSliceId,
                                       com.almworks.sqlite4java.SQLiteConnection connection)
                                throws com.almworks.sqlite4java.SQLiteException,
                                       StreamCorruptedException

Gets the run slice data.

Parameters:

runSliceId - the run slice id

Returns:

the run slice data

Throws:

com.almworks.sqlite4java.SQLiteException - the sQ lite exception

StreamCorruptedException

getSpectrumData

protected SpectrumData getSpectrumData(long spectrumId,
                                       com.almworks.sqlite4java.SQLiteConnection connection)
                                throws com.almworks.sqlite4java.SQLiteException,
                                       StreamCorruptedException

Gets the spectrum data.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum data

Throws:

com.almworks.sqlite4java.SQLiteException - the sQ lite exception

StreamCorruptedException

getSpectrum

protected Spectrum getSpectrum(long spectrumId,
                               com.almworks.sqlite4java.SQLiteConnection connection)
                        throws com.almworks.sqlite4java.SQLiteException,
                               StreamCorruptedException

Gets the spectrum.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum

Throws:

com.almworks.sqlite4java.SQLiteException - the SQlite exception

StreamCorruptedException

getSpectrumPeaks

protected Peak[] getSpectrumPeaks(int spectrumId,
                                  com.almworks.sqlite4java.SQLiteConnection connection)
                           throws com.almworks.sqlite4java.SQLiteException,
                                  StreamCorruptedException

Gets the spectrum peaks.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum peaks

Throws:

com.almworks.sqlite4java.SQLiteException - the sQ lite exception

StreamCorruptedException

getMsSpectrumSlices

protected SpectrumSlice[] getMsSpectrumSlices(double minMz,
                                              double maxMz,
                                              float minRt,
                                              float maxRt,
                                              com.almworks.sqlite4java.SQLiteConnection connection)
                                       throws com.almworks.sqlite4java.SQLiteException,
                                              StreamCorruptedException

Gets the spectrum slices. Each returned spectrum slice corresponds to a single spectrum.

Parameters:

minmz - the minMz

maxmz - the maxMz

minrt - the minRt

maxrt - the maxRt

msLevel - the ms level

Returns:

the spectrum slices

Throws:

com.almworks.sqlite4java.SQLiteException - the sQ lite exception

StreamCorruptedException

getMsnSpectrumSlices

protected SpectrumSlice[] getMsnSpectrumSlices(double parentMz,
                                               double minFragMz,
                                               double maxFragMz,
                                               float minRt,
                                               float maxRt,
                                               com.almworks.sqlite4java.SQLiteConnection connection)
                                        throws com.almworks.sqlite4java.SQLiteException,
                                               StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getAcquisitionMode

protected AcquisitionMode getAcquisitionMode(com.almworks.sqlite4java.SQLiteConnection connection)
                                      throws com.almworks.sqlite4java.SQLiteException

Lazy loading of the acquisition mode, parameter

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

getDIAIsolationWindows

protected IsolationWindow[] getDIAIsolationWindows(com.almworks.sqlite4java.SQLiteConnection connection)
                                            throws com.almworks.sqlite4java.SQLiteException

Get the DIA IsolationWindows

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

getInstrumentConfigurations

public abstract List<InstrumentConfiguration> getInstrumentConfigurations()
                                                                   throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

getRuns

public abstract List<Run> getRuns()
                           throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

getSamples

public abstract List<Sample> getSamples()
                                 throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

getSoftwareList

public abstract List<Software> getSoftwareList()
                                        throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

getSourceFiles

public abstract List<SourceFile> getSourceFiles()
                                         throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

getFirstSourceFileName

public String getFirstSourceFileName()
                              throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

getMsXicInMzRange

protected Peak[] getMsXicInMzRange(double minMz,
                                   double maxMz,
                                   XicMethod method,
                                   com.almworks.sqlite4java.SQLiteConnection connection)
                            throws com.almworks.sqlite4java.SQLiteException,
                                   StreamCorruptedException

Gets the xic.

Parameters:

minMz - the min mz

maxMz - the max mz

msLevel - the ms level

Returns:

the xic

Throws:

com.almworks.sqlite4java.SQLiteException - the sQ lite exception

StreamCorruptedException

getMsXicInMzRtRanges

protected Peak[] getMsXicInMzRtRanges(double minMz,
                                      double maxMz,
                                      float minRt,
                                      float maxRt,
                                      XicMethod method,
                                      com.almworks.sqlite4java.SQLiteConnection connection)
                               throws com.almworks.sqlite4java.SQLiteException,
                                      StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getMsXic

protected Peak[] getMsXic(double mz,
                          double mzTolInDa,
                          float minRt,
                          float maxRt,
                          XicMethod method,
                          com.almworks.sqlite4java.SQLiteConnection connection)
                   throws com.almworks.sqlite4java.SQLiteException,
                          StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getMsnXic

protected Peak[] getMsnXic(double parentMz,
                           double fragmentMz,
                           double fragmentMzTolInDa,
                           float minRt,
                           float maxRt,
                           XicMethod method,
                           com.almworks.sqlite4java.SQLiteConnection connection)
                    throws com.almworks.sqlite4java.SQLiteException,
                           StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getMsPeaksInMzRtRanges

protected Peak[] getMsPeaksInMzRtRanges(double minMz,
                                        double maxMz,
                                        float minRt,
                                        float maxRt,
                                        com.almworks.sqlite4java.SQLiteConnection connection)
                                 throws com.almworks.sqlite4java.SQLiteException,
                                        StreamCorruptedException

Gets the peaks.

Parameters:

minmz - the minmz

maxmz - the maxmz

minrt - the minrt

maxrt - the maxrt

msLevel - the ms level

Returns:

the peaks

Throws:

com.almworks.sqlite4java.SQLiteException - the sQ lite exception

StreamCorruptedException

getMsnPeaksInMzRtRanges

protected Peak[] getMsnPeaksInMzRtRanges(double parentMz,
                                         double minFragMz,
                                         double maxFragMz,
                                         float minRt,
                                         float maxRt,
                                         com.almworks.sqlite4java.SQLiteConnection connection)
                                  throws com.almworks.sqlite4java.SQLiteException,
                                         StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException