Package eu.isas.reporter.calculation

Class QuantificationFeaturesGenerator

java.lang.Object
eu.isas.reporter.calculation.QuantificationFeaturesGenerator
public class QuantificationFeaturesGenerator extends Object
The quantification features generator provides various quantification features.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Details

    • QuantificationFeaturesGenerator

      public QuantificationFeaturesGenerator(QuantificationFeaturesCache quantificationFeaturesCache, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, ReporterSettings reporterSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters)
      Constructor.
      Parameters:
      quantificationFeaturesCache - the cache to use to store quantification results
      identification - the identification object containing all identification results
      identificationFeaturesGenerator - the identification features generator
      reporterSettings - the reporter settings
      reporterIonQuantification - the reporter ion quantification settings
      searchParameters - the identification parameters used for the identification of spectra
      sequenceMatchingParameters - the sequence matching preferences

  • Method Details

    • getProteinMatchQuantificationDetails

      public ProteinQuantificationDetails getProteinMatchQuantificationDetails(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, long matchKey, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Returns the quantification details of a protein match.
      Parameters:
      spectrumProvider - the spectrum provider
      matchKey - the key of the match of interest
      waitingHandler - the waiting handler
      Returns:
      the quantification details of the match

    • getPTMQuantificationDetails

      public ProteinPtmQuantificationDetails getPTMQuantificationDetails(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, String ptmName, long matchKey, int site, com.compomics.util.waiting.WaitingHandler waitingHandler) throws SQLException, IOException, ClassNotFoundException, InterruptedException
      Returns the quantification details of a PTM.
      Parameters:
      spectrumProvider - the spectrum provider
      ptmName - the name of the PTM
      matchKey - the key of the match of interest
      site - the site on the protein sequence
      waitingHandler - the waiting handler
      Returns:
      the quantification details of the match
      Throws:
      SQLException - thrown if an SQLException occurs
      IOException - thrown if an IOException
      ClassNotFoundException - thrown if a ClassNotFoundException
      InterruptedException - thrown if an InterruptedException

    • getPeptideMatchQuantificationDetails

      public PeptideQuantificationDetails getPeptideMatchQuantificationDetails(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Returns the quantification details of a peptide match.
      Parameters:
      spectrumProvider - the spectrum provider
      peptideMatch - the peptide match
      waitingHandler - the waiting handler
      Returns:
      the quantification details of the match

    • getPSMQuantificationDetails

      public PsmQuantificationDetails getPSMQuantificationDetails(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, Long matchKey)
      Returns the quantification details of a PSM.
      Parameters:
      spectrumProvider - the spectrum provider
      matchKey - the key of the match of interest
      Returns:
      the quantification details of the match

    • getSpectrumQuantificationDetails

      public SpectrumQuantificationDetails getSpectrumQuantificationDetails(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterIonSelectionSettings reporterIonSelectionSettings, com.compomics.util.experiment.identification.matches.SpectrumMatch aSpectrumMatch)
      Returns the quantification details of a spectrum.
      Parameters:
      spectrumProvider - the spectrum provider
      reporterIonQuantification - the quantification object
      reporterIonSelectionSettings - the reporter ion selection settings
      aSpectrumMatch - the spectrum match of interest
      Returns:
      the quantification details of the match

    • getDeisotoper

      public Deisotoper getDeisotoper(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, double reporterIonMassAccuracy)
      Returns the deisotoper corresponding to the given method.
      Parameters:
      reporterMethod - the reporter method
      reporterIonMassAccuracy - the mass accuracy in the reporter ion region
      Returns:
      the deisotoper corresponding to the given method

    • getQuantificationFeaturesCache

      public QuantificationFeaturesCache getQuantificationFeaturesCache()
      Returns the quantification features cache.
      Returns:
      the quantification features cache

    • setQuantificationFeaturesCache

      public void setQuantificationFeaturesCache(QuantificationFeaturesCache quantificationFeaturesCache)
      Sets the quantification features cache.
      Parameters:
      quantificationFeaturesCache - the quantification features cache