Uses of Class
fr.profi.mzdb.model.SpectrumHeader

Packages that use SpectrumHeader

Package	Description
fr.profi.mzdb
fr.profi.mzdb.io.reader.bb
fr.profi.mzdb.io.reader.cache
fr.profi.mzdb.io.reader.iterator
fr.profi.mzdb.io.writer
fr.profi.mzdb.io.writer.mgf
fr.profi.mzdb.model

Uses of SpectrumHeader in fr.profi.mzdb

Methods in fr.profi.mzdb that return SpectrumHeader

Modifier and Type	Method and Description
SpectrumHeader[]	MzDbReader.getMs1SpectrumHeaders() Gets the MS1 spectrum headers.
SpectrumHeader[]	MzDbReader.getMs2SpectrumHeaders() Gets the MS2 spectrum headers.
SpectrumHeader	MzDbReader.getSpectrumHeader(long id) Gets the spectrum header.
SpectrumHeader	MzDbReader.getSpectrumHeaderForTime(float time, int msLevel) Gets the spectrum header for time.
SpectrumHeader[]	MzDbReader.getSpectrumHeaders() Gets all spectrum headers.

Methods in fr.profi.mzdb that return types with arguments of type SpectrumHeader

Modifier and Type	Method and Description
Map<Long,SpectrumHeader>	MzDbReader.getMs1SpectrumHeaderById() Gets the MS1 spectrum header by id.
rx.Observable<Map<Long,SpectrumHeader>>	MzDbAsyncReader.getMs1SpectrumHeaderById() Gets the MS1 spectrum header by id.
Map<Long,SpectrumHeader>	MzDbReader.getMs2SpectrumHeaderById() Gets the MS2 spectrum header by id.
rx.Observable<Map<Long,SpectrumHeader>>	MzDbAsyncReader.getMs2SpectrumHeaderById() Gets the MS2 spectrum header by id.
rx.Observable<SpectrumHeader>	MzDbAsyncReader.getSpectrumHeader(long id) Gets the spectrum header.
Map<Long,SpectrumHeader>	MzDbReader.getSpectrumHeaderById() Gets each spectrum header mapped by its id.
rx.Observable<Map<Long,SpectrumHeader>>	MzDbAsyncReader.getSpectrumHeaderById() Gets each spectrum header mapped by its id.
rx.Observable<SpectrumHeader>	MzDbAsyncReader.getSpectrumHeaderForTime(float time, int msLevel) Gets the spectrum header for time.

Uses of SpectrumHeader in fr.profi.mzdb.io.reader.bb

Fields in fr.profi.mzdb.io.reader.bb with type parameters of type SpectrumHeader

Modifier and Type	Field and Description
protected Map<Long,SpectrumHeader>	AbstractBlobReader._spectrumHeaderById

Method parameters in fr.profi.mzdb.io.reader.bb with type arguments of type SpectrumHeader

Modifier and Type	Method and Description
static BoundingBox	BoundingBoxBuilder.buildBB(int bbId, byte[] bytes, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId)
static BoundingBox	BoundingBoxBuilder.buildBB(int bbId, InputStream stream, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId)
static BoundingBox	BoundingBoxBuilder.buildBB(int bbId, com.almworks.sqlite4java.SQLiteBlob blob, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId)

Constructor parameters in fr.profi.mzdb.io.reader.bb with type arguments of type SpectrumHeader

Constructor and Description
AbstractBlobReader(long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId) Abstract constructor
BytesReader(byte[] bytes, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId) Constructor
SQLiteBlobReader(com.almworks.sqlite4java.SQLiteBlob blob, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId) Constructor
StreamReader(InputStream inputStream, long firstSpectrumId, long lastSpectrumId, Map<Long,SpectrumHeader> spectrumHeaderById, Map<Long,DataEncoding> dataEncodingBySpectrumId)

Uses of SpectrumHeader in fr.profi.mzdb.io.reader.cache

Fields in fr.profi.mzdb.io.reader.cache declared as SpectrumHeader

Modifier and Type	Field and Description
protected SpectrumHeader[]	MzDbEntityCache.ms1SpectrumHeaders
protected SpectrumHeader[]	MzDbEntityCache.ms2SpectrumHeaders
protected SpectrumHeader[]	MzDbEntityCache.ms3SpectrumHeaders
protected SpectrumHeader[]	MzDbEntityCache.spectrumHeaders

Fields in fr.profi.mzdb.io.reader.cache with type parameters of type SpectrumHeader

Modifier and Type	Field and Description
protected Map<Long,SpectrumHeader>	MzDbEntityCache.ms1SpectrumHeaderById
protected Map<Long,SpectrumHeader>	MzDbEntityCache.ms2SpectrumHeaderById
protected Map<Long,SpectrumHeader>	MzDbEntityCache.ms3SpectrumHeaderById
protected Map<Long,SpectrumHeader>	MzDbEntityCache.spectrumHeaderById

Methods in fr.profi.mzdb.io.reader.cache that return SpectrumHeader

Modifier and Type	Method and Description
SpectrumHeader[]	SpectrumHeaderReader.getMs1SpectrumHeaders() Gets the MS1 spectrum headers.
SpectrumHeader[]	MzDbEntityCache.getMs1SpectrumHeaders()
protected SpectrumHeader[]	AbstractSpectrumHeaderReader.getMs1SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS1 spectrum headers.
SpectrumHeader[]	SpectrumHeaderReader.getMs2SpectrumHeaders() Gets the MS2 spectrum headers.
SpectrumHeader[]	MzDbEntityCache.getMs2SpectrumHeaders()
protected SpectrumHeader[]	AbstractSpectrumHeaderReader.getMs2SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum headers.
protected SpectrumHeader[]	AbstractSpectrumHeaderReader.getMs3SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum headers.
SpectrumHeader	SpectrumHeaderReader.getSpectrumHeader(long id) /** Gets the spectrum header.
SpectrumHeader	AbstractSpectrumHeaderReader.getSpectrumHeader(long id, com.almworks.sqlite4java.SQLiteConnection connection) /** Gets the spectrum header.
SpectrumHeader	SpectrumHeaderReader.getSpectrumHeaderForTime(float time, int msLevel) Gets the spectrum header for time.
protected SpectrumHeader	AbstractSpectrumHeaderReader.getSpectrumHeaderForTime(float time, int msLevel, com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum header for time.
SpectrumHeader[]	SpectrumHeaderReader.getSpectrumHeaders() Gets the spectrum headers.
protected SpectrumHeader[]	AbstractSpectrumHeaderReader.getSpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum headers.

Methods in fr.profi.mzdb.io.reader.cache that return types with arguments of type SpectrumHeader

Modifier and Type	Method and Description
Map<Long,SpectrumHeader>	SpectrumHeaderReader.getMs1SpectrumHeaderById() Gets the MS1 spectrum header by id.
rx.Observable<Map<Long,SpectrumHeader>>	SpectrumHeaderAsyncReader.getMs1SpectrumHeaderById() Gets the MS1 spectrum header by id.
Map<Long,SpectrumHeader>	MzDbEntityCache.getMs1SpectrumHeaderById()
Map<Long,SpectrumHeader>	AbstractSpectrumHeaderReader.getMs1SpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS1 spectrum header by id.
Map<Long,SpectrumHeader>	SpectrumHeaderReader.getMs2SpectrumHeaderById() Gets the MS2 spectrum header by id.
rx.Observable<Map<Long,SpectrumHeader>>	SpectrumHeaderAsyncReader.getMs2SpectrumHeaderById() Gets the MS2 spectrum header by id.
Map<Long,SpectrumHeader>	MzDbEntityCache.getMs2SpectrumHeaderById()
Map<Long,SpectrumHeader>	AbstractSpectrumHeaderReader.getMs2SpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum header by id.
Map<Long,SpectrumHeader>	AbstractSpectrumHeaderReader.getMs3SpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum header by id.
rx.Observable<SpectrumHeader>	SpectrumHeaderAsyncReader.getSpectrumHeader(long id) /** Gets the spectrum header.
Map<Long,SpectrumHeader>	SpectrumHeaderReader.getSpectrumHeaderById() Gets the spectrum headers by id.
rx.Observable<Map<Long,SpectrumHeader>>	SpectrumHeaderAsyncReader.getSpectrumHeaderById() Gets the spectrum headers by id.
Map<Long,SpectrumHeader>	AbstractSpectrumHeaderReader.getSpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum headers by id.
rx.Observable<SpectrumHeader>	SpectrumHeaderAsyncReader.getSpectrumHeaderForTime(float time, int msLevel) Gets the spectrum header for time.

Uses of SpectrumHeader in fr.profi.mzdb.io.reader.iterator

Fields in fr.profi.mzdb.io.reader.iterator with type parameters of type SpectrumHeader

Modifier and Type	Field and Description
protected Map<Long,SpectrumHeader>	BoundingBoxIterator.spectrumHeaderById

Uses of SpectrumHeader in fr.profi.mzdb.io.writer

Methods in fr.profi.mzdb.io.writer with parameters of type SpectrumHeader

Modifier and Type	Method and Description
static void	MsSpectrumTSVWriter.writeRun(SpectrumHeader[] spectra, Integer runId, File outFile)

Uses of SpectrumHeader in fr.profi.mzdb.io.writer.mgf

Methods in fr.profi.mzdb.io.writer.mgf with parameters of type SpectrumHeader

Modifier and Type	Method and Description
protected double	DefaultPrecursorComputer.extractPrecMz(MzDbReader mzDbReader, Precursor precursor, double precMz, SpectrumHeader spectrumHeader, float timeTol) Detects isotopic pattern in the survey and return the most probable mono-isotopic m/z value
int	IPrecursorComputation.getPrecursorCharge(MzDbReader mzDbReader, SpectrumHeader spectrumHeader) Returns the precursor m/z value of the specified SpectrumHeader.
int	DefaultPrecursorComputer.getPrecursorCharge(MzDbReader mzDbReader, SpectrumHeader spectrumHeader)
double	IPrecursorComputation.getPrecursorMz(MzDbReader mzDbReader, SpectrumHeader spectrumHeader) Returns the precursor m/z value of the specified SpectrumHeader.
double	DefaultPrecursorComputer.getPrecursorMz(MzDbReader mzDbReader, SpectrumHeader spectrumHeader)

Uses of SpectrumHeader in fr.profi.mzdb.model

Fields in fr.profi.mzdb.model declared as SpectrumHeader

Modifier and Type	Field and Description
protected SpectrumHeader	Spectrum.header The header.

Fields in fr.profi.mzdb.model with type parameters of type SpectrumHeader

Modifier and Type	Field and Description
static Comparator<SpectrumHeader>	SpectrumHeader.rtComp The rt comp.

Methods in fr.profi.mzdb.model that return SpectrumHeader

Modifier and Type	Method and Description
SpectrumHeader	Spectrum.getHeader() Gets the header.
SpectrumHeader	Peak.getSpectrumHeader() Gets the SpectrumHeader.

Methods in fr.profi.mzdb.model with parameters of type SpectrumHeader

Modifier and Type	Method and Description
static void	SpectrumHeader.loadParamTrees(SpectrumHeader[] spectrumHeaders, com.almworks.sqlite4java.SQLiteConnection mzDbConnection)

Constructors in fr.profi.mzdb.model with parameters of type SpectrumHeader

Constructor and Description
Spectrum(SpectrumHeader header, SpectrumData spectrumData) Instantiates a new spectrum.
SpectrumSlice(SpectrumHeader header, SpectrumData spectrumData) Instantiates a new spectrum slice.