Package 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
    Description
    static final String
    SUFFIX
    Suffix for the mgf file containing all recalibrated spectra.

  • Constructor Summary

    Constructors
    Constructor
    Description
    RecalibrationExporter()
     

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • SUFFIX

      public static final String SUFFIX
      Suffix for the mgf file containing all recalibrated spectra.
      See Also:

  • Constructor Details

    • RecalibrationExporter

      public RecalibrationExporter()

  • Method Details

    • 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