eu.isas.peptideshaker.recalibration

Class SpectrumRecalibrator

java.lang.Object

eu.isas.peptideshaker.recalibration.SpectrumRecalibrator

public class SpectrumRecalibrator
extends Object

This class recalibrates spectra.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
SpectrumRecalibrator() Constructor.

Method Summary

Modifier and Type	Method and Description
void	clearErrors(String spectrumFileName) Clears the loaded error statistics for the given file name in order to save memory.
void	estimateErrors(String spectrumFileNameWithoutExtension, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) Estimates the file m/z errors and displays the progress in a waiting handler.
RunMzDeviation	getRunMzDeviations(String spectrumFileName) Returns the mz deviation statistics class for the spectrum file of interest.
com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum	recalibrateSpectrum(String fileName, String spectrumTitle, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, boolean recalibratePrecursor, boolean recalibrateFragmentIons) Recalibrates a spectrum.

Methods inherited from class java.lang.Object

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

Constructor Detail

SpectrumRecalibrator

public SpectrumRecalibrator()

Constructor.

Method Detail

clearErrors

public void clearErrors(String spectrumFileName)

Clears the loaded error statistics for the given file name in order to save memory.

Parameters:

spectrumFileName - the spectrum file name

getRunMzDeviations

public RunMzDeviation getRunMzDeviations(String spectrumFileName)

Returns the mz deviation statistics class for the spectrum file of interest. Null if not estimated.

Parameters:

spectrumFileName - name of the spectrum file

Returns:

the mz deviation statistics

estimateErrors

public void estimateErrors(String spectrumFileNameWithoutExtension,
                           com.compomics.util.experiment.identification.Identification identification,
                           com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                           com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                           com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                           com.compomics.util.waiting.WaitingHandler waitingHandler)

Estimates the file m/z errors and displays the progress in a waiting handler. Shall be done before calibration. The information generated can be cleared from the mapping using clearErrors(String spectrumFileName). The progress will only be updated, max value is the number of spectra

Parameters:

spectrumFileNameWithoutExtension - the name of the file of the run

identification - the corresponding identification

sequenceProvider - the sequence provider

spectrumProvider - the spectrum provider

identificationParameters - the identification parameters

waitingHandler - a waiting handler displaying the progress and allowing the user to cancel the process. Can be null

recalibrateSpectrum

public com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum recalibrateSpectrum(String fileName,
                                                                                            String spectrumTitle,
                                                                                            com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                                                            boolean recalibratePrecursor,
                                                                                            boolean recalibrateFragmentIons)

Recalibrates a spectrum.

Parameters:

fileName - the name of the file where to find the spectrum

spectrumTitle - the title of the spectrum

spectrumProvider - the spectrum provider

recalibratePrecursor - boolean indicating whether precursors shall be recalibrated

recalibrateFragmentIons - boolean indicating whether fragment ions shall be recalibrated

Returns:

a recalibrated spectrum