fr.profi.mzdb.io.writer.mgf

Class DefaultPrecursorComputer

java.lang.Object

fr.profi.mzdb.io.writer.mgf.DefaultPrecursorComputer

All Implemented Interfaces:

IPrecursorComputation

public class DefaultPrecursorComputer
extends Object
implements IPrecursorComputation

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	DefaultPrecursorComputer(float mzTolPPM)
	DefaultPrecursorComputer(PrecursorMzComputationEnum precComp, float mzTolPPM)

Method Summary

Modifier and Type	Method and Description
protected double	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
String	getParamName()
int	getPrecursorCharge(MzDbReader mzDbReader, SpectrumHeader spectrumHeader) Returns the precursor m/z value of the specified SpectrumHeader.
double	getPrecursorMz(MzDbReader mzDbReader, SpectrumHeader spectrumHeader) Returns the precursor m/z value of the specified SpectrumHeader.
protected Double	refinePrecMz(MzDbReader mzDbReader, Precursor precursor, double precMz, double mzTolPPM, float time, float timeTol) Refines the provided target m/z value by looking at the nearest value in the survey.

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultPrecursorComputer

protected DefaultPrecursorComputer(float mzTolPPM)

DefaultPrecursorComputer

public DefaultPrecursorComputer(PrecursorMzComputationEnum precComp,
                                float mzTolPPM)

Method Detail

getParamName

public String getParamName()

Specified by:

getParamName in interface IPrecursorComputation

getPrecursorCharge

public int getPrecursorCharge(MzDbReader mzDbReader,
                              SpectrumHeader spectrumHeader)
                       throws com.almworks.sqlite4java.SQLiteException

Description copied from interface: IPrecursorComputation

Returns the precursor m/z value of the specified SpectrumHeader.

Specified by:

getPrecursorCharge in interface IPrecursorComputation

Returns:

the precursor m/z value of the specified SpectrumHeader

Throws:

com.almworks.sqlite4java.SQLiteException

getPrecursorMz

public double getPrecursorMz(MzDbReader mzDbReader,
                             SpectrumHeader spectrumHeader)
                      throws com.almworks.sqlite4java.SQLiteException

Description copied from interface: IPrecursorComputation

Returns the precursor m/z value of the specified SpectrumHeader.

Specified by:

getPrecursorMz in interface IPrecursorComputation

Returns:

the precursor m/z value of the specified SpectrumHeader

Throws:

com.almworks.sqlite4java.SQLiteException

extractPrecMz

protected double extractPrecMz(MzDbReader mzDbReader,
                               Precursor precursor,
                               double precMz,
                               SpectrumHeader spectrumHeader,
                               float timeTol)
                        throws StreamCorruptedException,
                               com.almworks.sqlite4java.SQLiteException

Detects isotopic pattern in the survey and return the most probable mono-isotopic m/z value

Parameters:

centerMz - the m/z value at the center of the isolation window

Returns:

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException

refinePrecMz

protected Double refinePrecMz(MzDbReader mzDbReader,
                              Precursor precursor,
                              double precMz,
                              double mzTolPPM,
                              float time,
                              float timeTol)
                       throws StreamCorruptedException,
                              com.almworks.sqlite4java.SQLiteException

Refines the provided target m/z value by looking at the nearest value in the survey.

Parameters:

precMz - the precursor m/z value to refine

Returns:

the refined precursor m/z value

Throws:

com.almworks.sqlite4java.SQLiteException

StreamCorruptedException