fr.profi.mzdb

Class MzDbAsyncReader

java.lang.Object

fr.profi.mzdb.AbstractMzDbReader

fr.profi.mzdb.MzDbAsyncReader

public class MzDbAsyncReader
extends AbstractMzDbReader

Allows to manipulates data contained in the mzDB file.

Author:

David

Field Summary

Fields inherited from class fr.profi.mzdb.AbstractMzDbReader

_paramNameGetter, acquisitionMode, bbSizes, computationThreadPool, dbLocation, diaIsolationWindows, entityCache, instrumentConfigs, isNoLossMode, mzDbHeader, runs, rxCompScheduler, samples, softwareList, sourceFiles

Constructor Summary

Constructors

Constructor and Description
MzDbAsyncReader(File dbLocation, boolean cacheEntities) Instantiates a new mzDB reader (secondary constructor).
MzDbAsyncReader(File dbLocation, MzDbEntityCache entityCache, boolean logConnections) Instantiates a new mzDB reader (primary constructor).
MzDbAsyncReader(String dbPath, boolean cacheEntities) Instantiates a new mzDB reader (secondary constructor).

Method Summary

Modifier and Type	Method and Description
void	close() close the connection to avoid memory leaks.
protected com.almworks.sqlite4java.SQLiteConnection	createBlockingSQLiteConnection()
rx.Observable<AcquisitionMode>	getAcquisitionMode() Lazy loading of the acquisition mode, parameter
rx.Observable<byte[]>	getBoundingBoxData(int bbId) Gets the bounding box data.
rx.Observable<Integer>	getBoundingBoxesCount() Gets the bounding box count.
rx.Observable<Integer>	getBoundingBoxesCount(int runSliceId) Gets the bounding box count.
rx.Observable<Long>	getBoundingBoxFirstSpectrumId(long spectrumId) Gets the bounding box first spectrum index.
rx.Observable<Float>	getBoundingBoxMinMz(int bbId) Gets the bounding box min mz.
rx.Observable<Float>	getBoundingBoxMinTime(int bbId) Gets the bounding box min time.
rx.Observable<Integer>	getBoundingBoxMsLevel(int bbId) Gets the bounding box ms level.
rx.Observable<BoundingBox>	getBoundingBoxStream(int msLevel) Gets the bounding box iterator.
rx.Observable<Integer>	getCyclesCount() Gets the cycle count.
rx.Observable<DataEncoding>	getDataEncoding(int id) Gets the data encoding.
rx.Observable<Map<Long,DataEncoding>>	getDataEncodingBySpectrumId() Gets the data encoding by spectrum id.
DataEncodingAsyncReader	getDataEncodingReader()
rx.Observable<Integer>	getDataEncodingsCount() Gets the data encoding count.
rx.Observable<IsolationWindow[]>	getDIAIsolationWindows() ImmutablePair can not be wrapped into an array
List<InstrumentConfiguration>	getInstrumentConfigurations()
rx.Observable<Float>	getLastTime() Gets the last time.
rx.Observable<RunSlice>	getLcMsnRunSliceStream(double minParentMz, double maxParentMz) Gets a DIA data RunSlice iterator
rx.Observable<RunSlice>	getLcMsnRunSliceStream(double minParentMz, double maxParentMz, double minRunSliceMz, double maxRunSliceMz) Gets a DIA data RunSlice iterator for a given m/z range
rx.Observable<RunSlice>	getLcMsRunSliceStream() Gets a RunSlice iterator.
rx.Observable<RunSlice>	getLcMsRunSliceStream(double minRunSliceMz, double maxRunSliceMz) Gets a RunSlice iterator for a given m/z range
rx.Observable<Integer>	getMaxMsLevel() Gets the max ms level.
rx.Observable<String>	getModelVersion()
rx.Observable<Map<Long,SpectrumHeader>>	getMs1SpectrumHeaderById() Gets the MS1 spectrum header by id.
rx.Observable<SpectrumHeader[]>	getMs1SpectrumHeaders() Gets the MS1 spectrum headers.
rx.Observable<Map<Long,SpectrumHeader>>	getMs2SpectrumHeaderById() Gets the MS2 spectrum header by id.
rx.Observable<SpectrumHeader[]>	getMs2SpectrumHeaders() Gets the MS2 spectrum headers.
rx.Observable<Peak[]>	getMsnPeaksInMzRtRanges(double parentMz, double minFragMz, double maxFragMz, float minRt, float maxRt)
rx.Observable<SpectrumSlice[]>	getMsnSpectrumSlices(double parentMz, double minFragMz, double maxFragMz, float minRt, float maxRt)
rx.Observable<Peak[]>	getMsnXic(double parentMz, double fragmentMz, double fragmentMzTolInDa, float minRt, float maxRt, XicMethod method)
rx.Observable<Peak[]>	getMsPeaksInMzRtRanges(double minMz, double maxMz, float minRt, float maxRt)
rx.Observable<SpectrumSlice[]>	getMsSpectrumSlices(double minMz, double maxMz, float minRt, float maxRt) Gets the spectrum slices.
rx.Observable<Peak[]>	getMsXic(double mz, double mzTolInDa, float minRt, float maxRt, XicMethod method)
rx.Observable<Peak[]>	getMsXicInMzRange(double minMz, double maxMz, XicMethod method)
rx.Observable<Peak[]>	getMsXicInMzRtRanges(double minMz, double maxMz, float minRt, float maxRt, XicMethod method)
rx.Observable<int[]>	getMzRange(int msLevel) Gets the mz range.
rx.Observable<String>	getPwizMzDbVersion()
List<Run>	getRuns()
rx.Observable<RunSliceData>	getRunSliceData(int runSliceId) Gets the run slice data.
rx.Observable<HashMap<Integer,RunSliceHeader>>	getRunSliceHeaderById(int msLevel) Gets the run slice header by id.
RunSliceHeaderAsyncReader	getRunSliceHeaderReader()
rx.Observable<RunSliceHeader[]>	getRunSliceHeaders(int msLevel) Gets the run slices.
rx.Observable<Integer>	getRunSlicesCount() Gets the run slice count.
List<Sample>	getSamples()
List<Software>	getSoftwareList()
List<SourceFile>	getSourceFiles()
rx.Observable<Integer>	getSpectraCount() Gets the spectrum count.
rx.Observable<Integer>	getSpectraCount(int msLevel) Gets the spectrum count.
rx.Observable<Spectrum>	getSpectrum(long spectrumId) Gets the spectrum.
rx.Observable<SpectrumData>	getSpectrumData(long spectrumId) Gets the spectrum data.
rx.Observable<DataEncoding>	getSpectrumDataEncoding(long spectrumId) Gets the spectrum data encoding.
rx.Observable<SpectrumHeader>	getSpectrumHeader(long id) Gets the spectrum header.
rx.Observable<Map<Long,SpectrumHeader>>	getSpectrumHeaderById() Gets each spectrum header mapped by its id.
rx.Observable<SpectrumHeader>	getSpectrumHeaderForTime(float time, int msLevel) Gets the spectrum header for time.
SpectrumHeaderAsyncReader	getSpectrumHeaderReader()
rx.Observable<SpectrumHeader[]>	getSpectrumHeaders() Gets all spectrum headers.
rx.Observable<Peak[]>	getSpectrumPeaks(int spectrumId) Gets the spectrum peaks.
rx.Observable<Spectrum>	getSpectrumStream()
rx.Observable<Spectrum>	getSpectrumStream(int msLevel) Gets the ms spectrum iterator.
rx.Observable<Integer>	getTableRecordsCount(String tableName) Gets the table records count.
<T> SQLiteObservableJob<T>	observeJobExecution(ISQLiteConnectionFunction<T> sqliteConnFunction)
void	waitForQueries() Waits for the reader to stop execution of queries.

Methods inherited from class fr.profi.mzdb.AbstractMzDbReader

_setBBSizes, enableParamTreeLoading, enablePrecursorListLoading, enableScanListLoading, getAcquisitionMode, getBBSizes, getDbLocation, getDIAIsolationWindows, getEntityCache, getFirstSourceFileName, getMsnPeaksInMzRtRanges, getMsnSpectrumSlices, getMsnXic, getMsPeaksInMzRtRanges, getMsSpectrumSlices, getMsXic, getMsXicInMzRange, getMsXicInMzRtRanges, getMzDbHeader, getRunSliceData, getSpectrum, getSpectrumData, getSpectrumPeaks, isNoLossMode, isParamTreeLoadingEnabled, isPrecursorListLoadingEnabled, isScanListLoadingEnabled

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDbAsyncReader

public MzDbAsyncReader(File dbLocation,
                       MzDbEntityCache entityCache,
                       boolean logConnections)
                throws ClassNotFoundException,
                       FileNotFoundException,
                       com.almworks.sqlite4java.SQLiteException

Instantiates a new mzDB reader (primary constructor). Builds a SQLite connection.

Parameters:

dbLocation - the db location

cacheEntities - the cache entities

logConnections - the log connections

Throws:

ClassNotFoundException - the class not found exception

FileNotFoundException - the file not found exception

com.almworks.sqlite4java.SQLiteException - the SQLite exception

MzDbAsyncReader

public MzDbAsyncReader(File dbLocation,
                       boolean cacheEntities)
                throws ClassNotFoundException,
                       FileNotFoundException,
                       com.almworks.sqlite4java.SQLiteException

Instantiates a new mzDB reader (secondary constructor).

Parameters:

dbLocation - the db location

cacheEntities - the cache entities

Throws:

ClassNotFoundException - the class not found exception

FileNotFoundException - the file not found exception

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

MzDbAsyncReader

public MzDbAsyncReader(String dbPath,
                       boolean cacheEntities)
                throws ClassNotFoundException,
                       FileNotFoundException,
                       com.almworks.sqlite4java.SQLiteException

Instantiates a new mzDB reader (secondary constructor).

Parameters:

dbPath - the db path

cacheEntities - the cache entities

Throws:

ClassNotFoundException - the class not found exception

FileNotFoundException - the file not found exception

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

Method Detail

close

public void close()

close the connection to avoid memory leaks.

Specified by:

close in class AbstractMzDbReader

Throws:

InterruptedException

getDataEncodingReader

public DataEncodingAsyncReader getDataEncodingReader()

Specified by:

getDataEncodingReader in class AbstractMzDbReader

getSpectrumHeaderReader

public SpectrumHeaderAsyncReader getSpectrumHeaderReader()

Specified by:

getSpectrumHeaderReader in class AbstractMzDbReader

getRunSliceHeaderReader

public RunSliceHeaderAsyncReader getRunSliceHeaderReader()

Specified by:

getRunSliceHeaderReader in class AbstractMzDbReader

waitForQueries

public void waitForQueries()
                    throws InterruptedException

Waits for the reader to stop execution of queries.

Throws:

InterruptedException

createBlockingSQLiteConnection

protected com.almworks.sqlite4java.SQLiteConnection createBlockingSQLiteConnection()
                                                                            throws com.almworks.sqlite4java.SQLiteException

Returns:

the _blockingMzDbReader

Throws:

com.almworks.sqlite4java.SQLiteException

FileNotFoundException

ClassNotFoundException

observeJobExecution

public <T> SQLiteObservableJob<T> observeJobExecution(ISQLiteConnectionFunction<T> sqliteConnFunction)

getModelVersion

public rx.Observable<String> getModelVersion()

getPwizMzDbVersion

public rx.Observable<String> getPwizMzDbVersion()

getLastTime

public rx.Observable<Float> getLastTime()

Gets the last time.

Returns:

float the rt of the last spectrum

getMaxMsLevel

public rx.Observable<Integer> getMaxMsLevel()

Gets the max ms level.

Returns:

the max ms level

getMzRange

public rx.Observable<int[]> getMzRange(int msLevel)

Gets the mz range.

Parameters:

msLevel - the ms level

Returns:

runSlice min mz and runSlice max mz

getBoundingBoxesCount

public rx.Observable<Integer> getBoundingBoxesCount()

Gets the bounding box count.

Returns:

int, the number of bounding box

getBoundingBoxesCount

public rx.Observable<Integer> getBoundingBoxesCount(int runSliceId)

Gets the bounding box count.

Parameters:

runSliceId - the run slice id

Returns:

the number of bounding box contained in the specified runSliceId

getCyclesCount

public rx.Observable<Integer> getCyclesCount()

Gets the cycle count.

Returns:

the cycle count

getDataEncodingsCount

public rx.Observable<Integer> getDataEncodingsCount()

Gets the data encoding count.

Returns:

the data encoding count

getSpectraCount

public rx.Observable<Integer> getSpectraCount()

Gets the spectrum count.

Returns:

int the number of spectra

getSpectraCount

public rx.Observable<Integer> getSpectraCount(int msLevel)

Gets the spectrum count.

Returns:

int the number of spectra

getRunSlicesCount

public rx.Observable<Integer> getRunSlicesCount()

Gets the run slice count.

Returns:

int the number of runSlice

getTableRecordsCount

public rx.Observable<Integer> getTableRecordsCount(String tableName)

Gets the table records count.

Parameters:

tableName - the table name

Returns:

the int

getDataEncoding

public rx.Observable<DataEncoding> getDataEncoding(int id)

Gets the data encoding.

Parameters:

id - the id

Returns:

the data encoding

getDataEncodingBySpectrumId

public rx.Observable<Map<Long,DataEncoding>> getDataEncodingBySpectrumId()

Gets the data encoding by spectrum id.

Returns:

the data encoding by spectrum id

getSpectrumDataEncoding

public rx.Observable<DataEncoding> getSpectrumDataEncoding(long spectrumId)

Gets the spectrum data encoding.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum data encoding

getRunSliceHeaders

public rx.Observable<RunSliceHeader[]> getRunSliceHeaders(int msLevel)

Gets the run slices.

Returns:

array of runSlice instance without data associated

getRunSliceHeaderById

public rx.Observable<HashMap<Integer,RunSliceHeader>> getRunSliceHeaderById(int msLevel)

Gets the run slice header by id.

Parameters:

msLevel - the ms level

Returns:

the run slice header by id

getRunSliceData

public rx.Observable<RunSliceData> getRunSliceData(int runSliceId)

Gets the run slice data.

Parameters:

runSliceId - the run slice id

Returns:

the run slice data

getBoundingBoxData

public rx.Observable<byte[]> getBoundingBoxData(int bbId)

Gets the bounding box data.

Parameters:

bbId - the bb id

Returns:

the bounding box data

getBoundingBoxFirstSpectrumId

public rx.Observable<Long> getBoundingBoxFirstSpectrumId(long spectrumId)

Gets the bounding box first spectrum index.

Parameters:

spectrumId - the spectrum id

Returns:

the bounding box first spectrum index

getBoundingBoxMinMz

public rx.Observable<Float> getBoundingBoxMinMz(int bbId)

Gets the bounding box min mz.

Parameters:

bbId - the bb id

Returns:

the bounding box min mz

getBoundingBoxMinTime

public rx.Observable<Float> getBoundingBoxMinTime(int bbId)

Gets the bounding box min time.

Parameters:

bbId - the bb id

Returns:

the bounding box min time

getBoundingBoxMsLevel

public rx.Observable<Integer> getBoundingBoxMsLevel(int bbId)

Gets the bounding box ms level.

Parameters:

bbId - the bb id

Returns:

the bounding box ms level

getMs1SpectrumHeaders

public rx.Observable<SpectrumHeader[]> getMs1SpectrumHeaders()

Gets the MS1 spectrum headers.

Returns:

the spectrum headers

getMs1SpectrumHeaderById

public rx.Observable<Map<Long,SpectrumHeader>> getMs1SpectrumHeaderById()

Gets the MS1 spectrum header by id.

Returns:

the spectrum header by id

getMs2SpectrumHeaders

public rx.Observable<SpectrumHeader[]> getMs2SpectrumHeaders()

Gets the MS2 spectrum headers.

Returns:

the spectrum headers

getMs2SpectrumHeaderById

public rx.Observable<Map<Long,SpectrumHeader>> getMs2SpectrumHeaderById()

Gets the MS2 spectrum header by id.

Returns:

the spectrum header by id

getSpectrumHeaders

public rx.Observable<SpectrumHeader[]> getSpectrumHeaders()

Gets all spectrum headers.

Returns:

the spectrum headers

getSpectrumHeaderById

public rx.Observable<Map<Long,SpectrumHeader>> getSpectrumHeaderById()

Gets each spectrum header mapped by its id.

Returns:

the spectrum header by id

getSpectrumHeader

public rx.Observable<SpectrumHeader> getSpectrumHeader(long id)

Gets the spectrum header.

Parameters:

id - the id

Returns:

the spectrum header

getSpectrumHeaderForTime

public rx.Observable<SpectrumHeader> getSpectrumHeaderForTime(float time,
                                                              int msLevel)

Gets the spectrum header for time.

Parameters:

time - the time

msLevel - the ms level

Returns:

spectrumheader the closest to the time input parameter

getSpectrumData

public rx.Observable<SpectrumData> getSpectrumData(long spectrumId)

Gets the spectrum data.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum data

getSpectrum

public rx.Observable<Spectrum> getSpectrum(long spectrumId)

Gets the spectrum.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum

getSpectrumPeaks

public rx.Observable<Peak[]> getSpectrumPeaks(int spectrumId)

Gets the spectrum peaks.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum peaks

getMsSpectrumSlices

public rx.Observable<SpectrumSlice[]> getMsSpectrumSlices(double minMz,
                                                          double maxMz,
                                                          float minRt,
                                                          float maxRt)

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

getMsnSpectrumSlices

public rx.Observable<SpectrumSlice[]> getMsnSpectrumSlices(double parentMz,
                                                           double minFragMz,
                                                           double maxFragMz,
                                                           float minRt,
                                                           float maxRt)

getBoundingBoxStream

public rx.Observable<BoundingBox> getBoundingBoxStream(int msLevel)

Gets the bounding box iterator.

Parameters:

msLevel - the ms level

Returns:

the bounding box iterator

getSpectrumStream

public rx.Observable<Spectrum> getSpectrumStream()

getSpectrumStream

public rx.Observable<Spectrum> getSpectrumStream(int msLevel)

Gets the ms spectrum iterator.

Parameters:

msLevel - the ms level

Returns:

the ms spectrum iterator

getLcMsRunSliceStream

public rx.Observable<RunSlice> getLcMsRunSliceStream()

Gets a RunSlice iterator.

Returns:

the RunSlice iterator

getLcMsRunSliceStream

public rx.Observable<RunSlice> getLcMsRunSliceStream(double minRunSliceMz,
                                                     double maxRunSliceMz)

Gets a RunSlice iterator for a given m/z range

Parameters:

minRunSliceMz -

minRunSliceMz -

Returns:

the RunSlice iterator

getLcMsnRunSliceStream

public rx.Observable<RunSlice> getLcMsnRunSliceStream(double minParentMz,
                                                      double maxParentMz)

Gets a DIA data RunSlice iterator

Parameters:

minParentMz -

maxParentMz -

Returns:

the RunSlice iterator

getLcMsnRunSliceStream

public rx.Observable<RunSlice> getLcMsnRunSliceStream(double minParentMz,
                                                      double maxParentMz,
                                                      double minRunSliceMz,
                                                      double maxRunSliceMz)

Gets a DIA data RunSlice iterator for a given m/z range

Parameters:

msLevel -

minParentMz -

maxParentMz -

Returns:

the RunSlice iterator

getAcquisitionMode

public rx.Observable<AcquisitionMode> getAcquisitionMode()

Lazy loading of the acquisition mode, parameter

Returns:

getDIAIsolationWindows

public rx.Observable<IsolationWindow[]> getDIAIsolationWindows()

ImmutablePair can not be wrapped into an array

Returns:

getInstrumentConfigurations

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

Specified by:

getInstrumentConfigurations in class AbstractMzDbReader

Throws:

com.almworks.sqlite4java.SQLiteException

getRuns

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

Specified by:

getRuns in class AbstractMzDbReader

Throws:

com.almworks.sqlite4java.SQLiteException

getSamples

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

Specified by:

getSamples in class AbstractMzDbReader

Throws:

com.almworks.sqlite4java.SQLiteException

getSoftwareList

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

Specified by:

getSoftwareList in class AbstractMzDbReader

Throws:

com.almworks.sqlite4java.SQLiteException

getSourceFiles

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

Specified by:

getSourceFiles in class AbstractMzDbReader

Throws:

com.almworks.sqlite4java.SQLiteException

getMsXicInMzRange

public rx.Observable<Peak[]> getMsXicInMzRange(double minMz,
                                               double maxMz,
                                               XicMethod method)

getMsXicInMzRtRanges

public rx.Observable<Peak[]> getMsXicInMzRtRanges(double minMz,
                                                  double maxMz,
                                                  float minRt,
                                                  float maxRt,
                                                  XicMethod method)

getMsXic

public rx.Observable<Peak[]> getMsXic(double mz,
                                      double mzTolInDa,
                                      float minRt,
                                      float maxRt,
                                      XicMethod method)

getMsnXic

public rx.Observable<Peak[]> getMsnXic(double parentMz,
                                       double fragmentMz,
                                       double fragmentMzTolInDa,
                                       float minRt,
                                       float maxRt,
                                       XicMethod method)

getMsPeaksInMzRtRanges

public rx.Observable<Peak[]> getMsPeaksInMzRtRanges(double minMz,
                                                    double maxMz,
                                                    float minRt,
                                                    float maxRt)

getMsnPeaksInMzRtRanges

public rx.Observable<Peak[]> getMsnPeaksInMzRtRanges(double parentMz,
                                                     double minFragMz,
                                                     double maxFragMz,
                                                     float minRt,
                                                     float maxRt)