Package eu.isas.peptideshaker.followup

Class PeaksIntensitiesExport

java.lang.Object
eu.isas.peptideshaker.followup.PeaksIntensitiesExport
public class PeaksIntensitiesExport extends Object
Export for peak intensities.
Author:
Dafni Skiadopoulou

  • Constructor Summary

    Constructors
    Constructor
    Description
    PeaksIntensitiesExport()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    peaksIntensitiesExport(File peaksIntensitiesFile, File ms2pipFile, File psmIDsFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Export the peak intensities.
    static void
    peaksIntensitiesExport(File peaksIntensitiesFile, HashMap<String,ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>> fragmentationPrediction, ArrayList<String> psmIDs, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Export the peak intensities.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PeaksIntensitiesExport

      public PeaksIntensitiesExport()

  • Method Details

    • peaksIntensitiesExport

      public static void peaksIntensitiesExport(File peaksIntensitiesFile, File ms2pipFile, File psmIDsFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Export the peak intensities.
      Parameters:
      peaksIntensitiesFile - The file to write the export.
      ms2pipFile - The file with ms2pip results.
      psmIDsFile - The file with the PSM ids.
      identification - the identification
      sequenceMatchingParameters - The sequence matching parameters.
      annotationParameters - The spectrum annotation parameters.
      modificationLocalizationParameters - The modification localization parameters.
      modificationParameters - The modification parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.

    • peaksIntensitiesExport

      public static void peaksIntensitiesExport(File peaksIntensitiesFile, HashMap<String,ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>> fragmentationPrediction, ArrayList<String> psmIDs, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Export the peak intensities.
      Parameters:
      peaksIntensitiesFile - The file to write the export.
      fragmentationPrediction - the map of predicted spectrum key to fragmentation predictions.
      psmIDs - the list of PSM ids to be used for the export.
      identification - the identification
      modificationParameters - The modification parameters.
      sequenceProvider - The sequence provider.
      sequenceMatchingParameters - The sequence matching parameters.
      annotationParameters - The spectrum annotation parameters.
      modificationLocalizationParameters - The modification localization parameters.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.