eu.isas.peptideshaker.followup

Class RecalibrationExporter

java.lang.Object

eu.isas.peptideshaker.followup.RecalibrationExporter

public class RecalibrationExporter
extends Object

This class exports recalibrated spectra.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static String	SUFFIX Suffix for the mgf file containing all recalibrated spectra.

Constructor Summary

Constructors

Constructor and Description
RecalibrationExporter()

Method Summary

Modifier and Type	Method and Description
static String	getRecalibratedFileName(String fileName) Returns the name of the recalibrated file.
static ArrayList<File>	writeRecalibratedSpectra(boolean recalibratePrecursors, boolean recalibrateFragmentIons, File folder, 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) Writes the recalibrated spectra in files named according to getRecalibratedFileName in the given folder.

Methods inherited from class java.lang.Object

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

Field Detail

SUFFIX

public static final String SUFFIX

Suffix for the mgf file containing all recalibrated spectra.

See Also:

Constant Field Values

Constructor Detail

RecalibrationExporter

public RecalibrationExporter()

Method Detail

writeRecalibratedSpectra

public static ArrayList<File> writeRecalibratedSpectra(boolean recalibratePrecursors,
                                                       boolean recalibrateFragmentIons,
                                                       File folder,
                                                       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)
                                                throws IOException

Writes the recalibrated spectra in files named according to getRecalibratedFileName in the given folder.

Parameters:

recalibratePrecursors - boolean indicating whether precursor ions shall be recalibrated

recalibrateFragmentIons - boolean indicating whether fragment ions shall be recalibrated

folder - folder where recalibrated files shall be written

identification - identification of the project

sequenceProvider - the sequence provider

spectrumProvider - the spectrum provider

identificationParameters - the identification parameters

waitingHandler - waiting handler displaying progress and used to cancel the process. Can be null. The method does not call RunFinished.

Returns:

ArrayList files containing recalibrated spectra

Throws:

IOException - exception thrown whenever an error occurred while writing the file

getRecalibratedFileName

public static String getRecalibratedFileName(String fileName)

Returns the name of the recalibrated file.

Parameters:

fileName - the original file name

Returns:

the name of the recalibrated file