fr.profi.mzdb

Class MzDbReader

java.lang.Object

fr.profi.mzdb.AbstractMzDbReader

fr.profi.mzdb.MzDbReader

public class MzDbReader
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
MzDbReader(File dbLocation, boolean cacheEntities) Instantiates a new mzDB reader (secondary constructor).
MzDbReader(File dbLocation, MzDbEntityCache entityCache, boolean logConnections) Instantiates a new mzDB reader (primary constructor).
MzDbReader(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.
AcquisitionMode	getAcquisitionMode() Lazy loading of the acquisition mode, parameter
byte[]	getBoundingBoxData(int bbId) Gets the bounding box data.
int	getBoundingBoxesCount() Gets the bounding box count.
int	getBoundingBoxesCount(int runSliceId) Gets the bounding box count.
long	getBoundingBoxFirstSpectrumId(long spectrumId) Gets the bounding box first spectrum index.
Iterator<BoundingBox>	getBoundingBoxIterator(int msLevel)
float	getBoundingBoxMinMz(int bbId) Gets the bounding box min mz.
float	getBoundingBoxMinTime(int bbId) Gets the bounding box min time.
int	getBoundingBoxMsLevel(int bbId) Gets the bounding box ms level.
com.almworks.sqlite4java.SQLiteConnection	getConnection() Gets the connection.
int	getCyclesCount() Gets the cycle count.
DataEncoding	getDataEncoding(int id) Gets the data encoding.
Map<Long,DataEncoding>	getDataEncodingBySpectrumId() Gets the data encoding by spectrum id.
DataEncodingReader	getDataEncodingReader()
int	getDataEncodingsCount() Gets the data encoding count.
IsolationWindow[]	getDIAIsolationWindows() Get the DIA IsolationWindows
List<InstrumentConfiguration>	getInstrumentConfigurations()
float	getLastTime() Gets the last time.
Iterator<RunSlice>	getLcMsnRunSliceIterator(double minParentMz, double maxParentMz) Gets a DIA data RunSlice iterator
Iterator<RunSlice>	getLcMsnRunSliceIterator(double minParentMz, double maxParentMz, double minRunSliceMz, double maxRunSliceMz) Gets a DIA data RunSlice iterator for a given m/z range
Iterator<RunSlice>	getLcMsRunSliceIterator() Gets a RunSlice iterator.
Iterator<RunSlice>	getLcMsRunSliceIterator(double minRunSliceMz, double maxRunSliceMz) Gets a RunSlice iterator for a given m/z range
int	getMaxMsLevel() Gets the max ms level.
String	getModelVersion()
Map<Long,SpectrumHeader>	getMs1SpectrumHeaderById() Gets the MS1 spectrum header by id.
SpectrumHeader[]	getMs1SpectrumHeaders() Gets the MS1 spectrum headers.
Map<Long,SpectrumHeader>	getMs2SpectrumHeaderById() Gets the MS2 spectrum header by id.
SpectrumHeader[]	getMs2SpectrumHeaders() Gets the MS2 spectrum headers.
Peak[]	getMsnPeaksInMzRtRanges(double parentMz, double minFragMz, double maxFragMz, float minRt, float maxRt)
SpectrumSlice[]	getMsnSpectrumSlices(double parentMz, double minFragMz, double maxFragMz, float minRt, float maxRt)
Peak[]	getMsnXIC(double parentMz, double fragmentMz, double fragmentMzTolInDa, float minRt, float maxRt, XicMethod method)
Peak[]	getMsPeaksInMzRtRanges(double minMz, double maxMz, float minRt, float maxRt)
SpectrumSlice[]	getMsSpectrumSlices(double minMz, double maxMz, float minRt, float maxRt) Gets the spectrum slices.
Peak[]	getMsXic(double mz, double mzTolInDa, float minRt, float maxRt, int msLevel, XicMethod method)
Peak[]	getMsXicInMzRange(double minMz, double maxMz, XicMethod method) Gets the xic.
Peak[]	getMsXicInMzRtRanges(double minMz, double maxMz, float minRt, float maxRt, XicMethod method)
int[]	getMzRange(int msLevel) Gets the mz range.
String	getPwizMzDbVersion()
List<Run>	getRuns()
RunSliceData	getRunSliceData(int runSliceId) Gets the run slice data.
HashMap<Integer,RunSliceHeader>	getRunSliceHeaderById(int msLevel) Gets the run slice header by id.
RunSliceHeaderReader	getRunSliceHeaderReader()
RunSliceHeader[]	getRunSliceHeaders(int msLevel) Gets the run slices.
int	getRunSlicesCount() Gets the run slice count.
List<Sample>	getSamples()
List<Software>	getSoftwareList()
List<SourceFile>	getSourceFiles()
int	getSpectraCount() Gets the spectrum count.
int	getSpectraCount(int msLevel) Gets the spectrum count.
Spectrum	getSpectrum(long spectrumId) Gets the spectrum.
SpectrumData	getSpectrumData(long spectrumId) Gets the spectrum data.
DataEncoding	getSpectrumDataEncoding(long spectrumId) Gets the spectrum data encoding.
SpectrumHeader	getSpectrumHeader(long id) Gets the spectrum header.
Map<Long,SpectrumHeader>	getSpectrumHeaderById() Gets each spectrum header mapped by its id.
SpectrumHeader	getSpectrumHeaderForTime(float time, int msLevel) Gets the spectrum header for time.
SpectrumHeaderReader	getSpectrumHeaderReader()
SpectrumHeader[]	getSpectrumHeaders() Gets all spectrum headers.
Iterator<Spectrum>	getSpectrumIterator()
Iterator<Spectrum>	getSpectrumIterator(int msLevel) Gets the ms spectrum iterator.
Peak[]	getSpectrumPeaks(int spectrumId) Gets the spectrum peaks.
int	getTableRecordsCount(String tableName) Gets the table records count.

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

MzDbReader

public MzDbReader(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

MzDbReader

public MzDbReader(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

MzDbReader

public MzDbReader(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

getConnection

public com.almworks.sqlite4java.SQLiteConnection getConnection()

Gets the connection.

Returns:

the connection

close

public void close()

close the connection to avoid memory leaks.

Specified by:

close in class AbstractMzDbReader

getDataEncodingReader

public DataEncodingReader getDataEncodingReader()

Specified by:

getDataEncodingReader in class AbstractMzDbReader

getSpectrumHeaderReader

public SpectrumHeaderReader getSpectrumHeaderReader()

Specified by:

getSpectrumHeaderReader in class AbstractMzDbReader

getRunSliceHeaderReader

public RunSliceHeaderReader getRunSliceHeaderReader()

Specified by:

getRunSliceHeaderReader in class AbstractMzDbReader

getModelVersion

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

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

getPwizMzDbVersion

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

Throws:

com.almworks.sqlite4java.SQLiteException

getLastTime

public float getLastTime()
                  throws com.almworks.sqlite4java.SQLiteException

Gets the last time.

Returns:

float the rt of the last spectrum

Throws:

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

getMaxMsLevel

public int getMaxMsLevel()
                  throws com.almworks.sqlite4java.SQLiteException

Gets the max ms level.

Returns:

the max ms level

Throws:

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

getMzRange

public int[] getMzRange(int msLevel)
                 throws com.almworks.sqlite4java.SQLiteException

Gets the mz range.

Parameters:

msLevel - the ms level

Returns:

runSlice min mz and runSlice max mz

Throws:

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

getBoundingBoxesCount

public int getBoundingBoxesCount()
                          throws com.almworks.sqlite4java.SQLiteException

Gets the bounding box count.

Returns:

int, the number of bounding box

Throws:

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

getBoundingBoxesCount

public int getBoundingBoxesCount(int runSliceId)
                          throws com.almworks.sqlite4java.SQLiteException

Gets the bounding box count.

Parameters:

runSliceId - the run slice id

Returns:

the number of bounding box contained in the specified runSliceId

Throws:

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

getCyclesCount

public int getCyclesCount()
                   throws com.almworks.sqlite4java.SQLiteException

Gets the cycle count.

Returns:

the cycle count

Throws:

com.almworks.sqlite4java.SQLiteException

getDataEncodingsCount

public int getDataEncodingsCount()
                          throws com.almworks.sqlite4java.SQLiteException

Gets the data encoding count.

Returns:

the data encoding count

Throws:

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

getSpectraCount

public int getSpectraCount()
                    throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum count.

Returns:

int the number of spectra

Throws:

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

getSpectraCount

public int getSpectraCount(int msLevel)
                    throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum count.

Returns:

int the number of spectra

Throws:

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

getRunSlicesCount

public int getRunSlicesCount()
                      throws com.almworks.sqlite4java.SQLiteException

Gets the run slice count.

Returns:

int the number of runSlice

Throws:

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

getTableRecordsCount

public int getTableRecordsCount(String tableName)
                         throws com.almworks.sqlite4java.SQLiteException

Gets the table records count.

Parameters:

tableName - the table name

Returns:

the int

Throws:

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

getDataEncoding

public DataEncoding getDataEncoding(int id)
                             throws com.almworks.sqlite4java.SQLiteException

Gets the data encoding.

Parameters:

id - the id

Returns:

the data encoding

Throws:

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

getDataEncodingBySpectrumId

public Map<Long,DataEncoding> getDataEncodingBySpectrumId()
                                                   throws com.almworks.sqlite4java.SQLiteException

Gets the data encoding by spectrum id.

Returns:

the data encoding by spectrum id

Throws:

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

getSpectrumDataEncoding

public DataEncoding getSpectrumDataEncoding(long spectrumId)
                                     throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum data encoding.

Parameters:

spectrumId - the spectrum id

Returns:

the spectrum data encoding

Throws:

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

getRunSliceHeaders

public RunSliceHeader[] getRunSliceHeaders(int msLevel)
                                    throws com.almworks.sqlite4java.SQLiteException

Gets the run slices.

Returns:

array of runSlice instance without data associated

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLite exception

getRunSliceHeaderById

public HashMap<Integer,RunSliceHeader> getRunSliceHeaderById(int msLevel)
                                                      throws com.almworks.sqlite4java.SQLiteException

Gets the run slice header by id.

Parameters:

msLevel - the ms level

Returns:

the run slice header by id

Throws:

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

getRunSliceData

public RunSliceData getRunSliceData(int runSliceId)
                             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

getBoundingBoxData

public byte[] getBoundingBoxData(int bbId)
                          throws com.almworks.sqlite4java.SQLiteException

Gets the bounding box data.

Parameters:

bbId - the bb id

Returns:

the bounding box data

Throws:

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

getBoundingBoxFirstSpectrumId

public long getBoundingBoxFirstSpectrumId(long spectrumId)
                                   throws com.almworks.sqlite4java.SQLiteException

Gets the bounding box first spectrum index.

Parameters:

spectrumId - the spectrum id

Returns:

the bounding box first spectrum index

Throws:

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

getBoundingBoxMinMz

public float getBoundingBoxMinMz(int bbId)
                          throws com.almworks.sqlite4java.SQLiteException

Gets the bounding box min mz.

Parameters:

bbId - the bb id

Returns:

the bounding box min mz

Throws:

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

getBoundingBoxMinTime

public float getBoundingBoxMinTime(int bbId)
                            throws com.almworks.sqlite4java.SQLiteException

Gets the bounding box min time.

Parameters:

bbId - the bb id

Returns:

the bounding box min time

Throws:

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

getBoundingBoxMsLevel

public int getBoundingBoxMsLevel(int bbId)
                          throws com.almworks.sqlite4java.SQLiteException

Gets the bounding box ms level.

Parameters:

bbId - the bb id

Returns:

the bounding box ms level

Throws:

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

getMs1SpectrumHeaders

public SpectrumHeader[] getMs1SpectrumHeaders()
                                       throws com.almworks.sqlite4java.SQLiteException

Gets the MS1 spectrum headers.

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLiteException

getMs1SpectrumHeaderById

public Map<Long,SpectrumHeader> getMs1SpectrumHeaderById()
                                                  throws com.almworks.sqlite4java.SQLiteException

Gets the MS1 spectrum header by id.

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLiteException

getMs2SpectrumHeaders

public SpectrumHeader[] getMs2SpectrumHeaders()
                                       throws com.almworks.sqlite4java.SQLiteException

Gets the MS2 spectrum headers.

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLiteException

getMs2SpectrumHeaderById

public Map<Long,SpectrumHeader> getMs2SpectrumHeaderById()
                                                  throws com.almworks.sqlite4java.SQLiteException

Gets the MS2 spectrum header by id.

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLiteException

getSpectrumHeaders

public SpectrumHeader[] getSpectrumHeaders()
                                    throws com.almworks.sqlite4java.SQLiteException

Gets all spectrum headers.

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLiteException

getSpectrumHeaderById

public Map<Long,SpectrumHeader> getSpectrumHeaderById()
                                               throws com.almworks.sqlite4java.SQLiteException

Gets each spectrum header mapped by its id.

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLiteException

getSpectrumHeader

public SpectrumHeader getSpectrumHeader(long id)
                                 throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum header.

Parameters:

id - the id

Returns:

the spectrum header

Throws:

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

getSpectrumHeaderForTime

public SpectrumHeader getSpectrumHeaderForTime(float time,
                                               int msLevel)
                                        throws Exception

Gets the spectrum header for time.

Parameters:

time - the time

msLevel - the ms level

Returns:

spectrumheader the closest to the time input parameter

Throws:

Exception

getSpectrumData

public SpectrumData getSpectrumData(long spectrumId)
                             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

public Spectrum getSpectrum(long spectrumId)
                     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

public Peak[] getSpectrumPeaks(int spectrumId)
                        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

public SpectrumSlice[] getMsSpectrumSlices(double minMz,
                                           double maxMz,
                                           float minRt,
                                           float maxRt)
                                    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

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

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getBoundingBoxIterator

public Iterator<BoundingBox> getBoundingBoxIterator(int msLevel)
                                             throws com.almworks.sqlite4java.SQLiteException,
                                                    StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getSpectrumIterator

public Iterator<Spectrum> getSpectrumIterator()
                                       throws com.almworks.sqlite4java.SQLiteException,
                                              StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getSpectrumIterator

public Iterator<Spectrum> getSpectrumIterator(int msLevel)
                                       throws com.almworks.sqlite4java.SQLiteException,
                                              StreamCorruptedException

Gets the ms spectrum iterator.

Parameters:

msLevel - the ms level

Returns:

the ms spectrum iterator

Throws:

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

StreamCorruptedException

getLcMsRunSliceIterator

public Iterator<RunSlice> getLcMsRunSliceIterator()
                                           throws com.almworks.sqlite4java.SQLiteException,
                                                  StreamCorruptedException

Gets a RunSlice iterator.

Returns:

the RunSlice iterator

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getLcMsRunSliceIterator

public Iterator<RunSlice> getLcMsRunSliceIterator(double minRunSliceMz,
                                                  double maxRunSliceMz)
                                           throws com.almworks.sqlite4java.SQLiteException,
                                                  StreamCorruptedException

Gets a RunSlice iterator for a given m/z range

Parameters:

minRunSliceMz -

minRunSliceMz -

Returns:

the RunSlice iterator

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getLcMsnRunSliceIterator

public Iterator<RunSlice> getLcMsnRunSliceIterator(double minParentMz,
                                                   double maxParentMz)
                                            throws com.almworks.sqlite4java.SQLiteException,
                                                   StreamCorruptedException

Gets a DIA data RunSlice iterator

Parameters:

minParentMz -

maxParentMz -

Returns:

the RunSlice iterator

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getLcMsnRunSliceIterator

public Iterator<RunSlice> getLcMsnRunSliceIterator(double minParentMz,
                                                   double maxParentMz,
                                                   double minRunSliceMz,
                                                   double maxRunSliceMz)
                                            throws com.almworks.sqlite4java.SQLiteException,
                                                   StreamCorruptedException

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

Parameters:

msLevel -

minParentMz -

maxParentMz -

Returns:

the RunSlice iterator

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getAcquisitionMode

public AcquisitionMode getAcquisitionMode()
                                   throws com.almworks.sqlite4java.SQLiteException

Lazy loading of the acquisition mode, parameter

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

getDIAIsolationWindows

public IsolationWindow[] getDIAIsolationWindows()
                                         throws com.almworks.sqlite4java.SQLiteException

Get the DIA IsolationWindows

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

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 Peak[] getMsXicInMzRange(double minMz,
                                double maxMz,
                                XicMethod method)
                         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

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

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getMsXic

public Peak[] getMsXic(double mz,
                       double mzTolInDa,
                       float minRt,
                       float maxRt,
                       int msLevel,
                       XicMethod method)
                throws com.almworks.sqlite4java.SQLiteException,
                       StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getMsnXIC

public Peak[] getMsnXIC(double parentMz,
                        double fragmentMz,
                        double fragmentMzTolInDa,
                        float minRt,
                        float maxRt,
                        XicMethod method)
                 throws com.almworks.sqlite4java.SQLiteException,
                        StreamCorruptedException

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getMsPeaksInMzRtRanges

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

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

getMsnPeaksInMzRtRanges

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

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException