Package eu.isas.reporter

Class Reporter

java.lang.Object
eu.isas.reporter.Reporter
public class Reporter extends Object
Reporter performs reporter ion based quantification on MS2/MS3 spectra.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    Reporter()
    Empty constructor for instantiation purposes.

  • Method Summary

    Modifier and Type
    Method
    Description
    static PeptideQuantificationDetails
    estimatePeptideMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the quantification details of a peptide match.
    static ProteinQuantificationDetails
    estimateProteinMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the quantification details of a protein match.
    static PsmQuantificationDetails
    estimatePSMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, ReporterIonSelectionSettings reporterIonSelectionSettings, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, Long matchKey)
    Returns the quantification details of a PSM.
    static ProteinPtmQuantificationDetails
    estimatePTMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, String ptmName, long matchKey, int site, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the quantification details of a PTM on a protein.//@TODO: discriminate peptides according to the neighboring sites?
    static SpectrumQuantificationDetails
    estimateSpectrumQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, 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.
    static com.compomics.util.experiment.identification.matches.IonMatch
    getBestReporterIonMatch(com.compomics.util.experiment.biology.ions.impl.ReporterIon reporterIon, int charge, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum spectrum, double mzTolerance, boolean mostAccurate)
    Returns the best reporter ion match based on mass accuracy.
    static File
    getConfigFolder()
    Returns the folder where the configuration files are stored.
    static File
    getEnzymesFile()
    Returns the enzymes file.
    static String
    getJarFilePath()
    Returns the path to the jar file.
    static File
    getMatchesFolder()
    Returns the file containing the database.
    static File
    getMethodsFile()
    Returns the default methods file.
    static String
    getTempFolderPath(File configFolder)
    Returns the folder to use for temporary files.
    static void
    setPathConfiguration()
    Sets the path configuration.
    static void
    setTempFolderPath(String tempFolderPath)
    Sets the folder to use for temporary files.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • Reporter

      public Reporter()
      Empty constructor for instantiation purposes.

  • Method Details

    • estimateProteinMatchQuantificationDetails

      public static ProteinQuantificationDetails estimateProteinMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Returns the quantification details of a protein match.
      Parameters:
      identification - the identification containing identification details
      spectrumProvider - the spectrum provider
      identificationFeaturesGenerator - the identification features generator used to store and retrieve identification details
      quantificationFeaturesGenerator - the quantification features generator used to store and retrieve quantification details
      ratioEstimationSettings - the ratio estimation settings
      reporterIonQuantification - the reporter quantification settings
      searchParameters - the identification parameters
      proteinMatch - the protein match
      waitingHandler - waiting handler displaying progress to the user and allowing canceling the process
      Returns:
      the quantification details of the match

    • estimatePTMQuantificationDetails

      public static ProteinPtmQuantificationDetails estimatePTMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, String ptmName, long matchKey, int site, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException
      Returns the quantification details of a PTM on a protein.//@TODO: discriminate peptides according to the neighboring sites?
      Parameters:
      identification - the identification containing identification details
      spectrumProvider - the spectrum provider
      quantificationFeaturesGenerator - the quantification features generator used to store and retrieve quantification details
      ratioEstimationSettings - the ratio estimation settings
      reporterIonQuantification - the reporter quantification settings
      searchParameters - the identification settings used
      sequenceMatchingParameters - the sequence matching preferences
      ptmName - the name of the PTM
      matchKey - the key of the match of interest
      site - the site of the PTM on the protein sequence
      waitingHandler - waiting handler displaying progress to the user and allowing canceling the process
      Returns:
      the quantification details of the match
      Throws:
      SQLException - exception thrown whenever an error occurred while interacting with the database
      IOException - exception thrown whenever an error occurred while interacting with a file
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object
      InterruptedException - exception thrown whenever a threading error occurred
      IllegalArgumentException

    • estimatePeptideMatchQuantificationDetails

      public static PeptideQuantificationDetails estimatePeptideMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Returns the quantification details of a peptide match.
      Parameters:
      identification - the identification containing identification details
      spectrumProvider - the spectrum provider
      quantificationFeaturesGenerator - the quantification features generator used to store and retrieve quantification details
      ratioEstimationSettings - the ratio estimation settings
      reporterIonQuantification - the reporter quantification settings
      peptideMatch - the peptide match
      waitingHandler - waiting handler displaying progress to the user and allowing canceling the process
      Returns:
      the quantification details of the match

    • estimatePSMQuantificationDetails

      public static PsmQuantificationDetails estimatePSMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, ReporterIonSelectionSettings reporterIonSelectionSettings, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, Long matchKey)
      Returns the quantification details of a PSM.
      Parameters:
      identification - the identification containing identification details
      spectrumProvider - the spectrum provider
      quantificationFeaturesGenerator - the quantification features generator used to store and retrieve quantification details
      reporterIonSelectionSettings - the reporter ion selection settings
      ratioEstimationSettings - the ratio estimation settings
      reporterIonQuantification - the reporter quantification settings
      matchKey - the key of the match of interest
      Returns:
      the quantification details of the match

    • estimateSpectrumQuantificationDetails

      public static SpectrumQuantificationDetails estimateSpectrumQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, 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:
      identification - the identification containing identification details
      spectrumProvider - the spectrum provider
      quantificationFeaturesGenerator - the quantification features generator used to store and retrieve quantification details
      reporterIonQuantification - the reporter ion quantification details
      reporterIonSelectionSettings - the reporter ion selection settings
      aSpectrumMatch - the spectrum match of interest
      Returns:
      the quantification details of the spectrum

    • getBestReporterIonMatch

      public static com.compomics.util.experiment.identification.matches.IonMatch getBestReporterIonMatch(com.compomics.util.experiment.biology.ions.impl.ReporterIon reporterIon, int charge, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum spectrum, double mzTolerance, boolean mostAccurate)
      Returns the best reporter ion match based on mass accuracy. It is possible to select the most accurate or the most intense ion, as set by the mostAccurate boolean. Null if none found
      Parameters:
      reporterIon - the reporter ion to match
      charge - the expected charge
      spectrum - the spectrum inspected
      mzTolerance - the m/z tolerance
      mostAccurate - boolean indicating whether the most accurate ion should be selected
      Returns:
      the best ion match

    • getJarFilePath

      public static String getJarFilePath()
      Returns the path to the jar file.
      Returns:
      the path to the jar file

    • getConfigFolder

      public static File getConfigFolder()
      Returns the folder where the configuration files are stored.
      Returns:
      the folder where the configuration files are stored

    • setTempFolderPath

      public static void setTempFolderPath(String tempFolderPath)
      Sets the folder to use for temporary files.
      Parameters:
      tempFolderPath - the folder to use for temporary files

    • getTempFolderPath

      public static String getTempFolderPath(File configFolder)
      Returns the folder to use for temporary files. By default the resources folder is used.
      Parameters:
      configFolder - the path to the jar file
      Returns:
      the folder to use for temporary files

    • getMatchesFolder

      public static File getMatchesFolder()
      Returns the file containing the database.
      Returns:
      the file containing the database

    • setPathConfiguration

      public static void setPathConfiguration() throws IOException
      Sets the path configuration.
      Throws:
      IOException - exception thrown whenever an error occurs while reading or writing the paths configuration file

    • getEnzymesFile

      public static File getEnzymesFile()
      Returns the enzymes file.
      Returns:
      the enzymes file

    • getMethodsFile

      public static File getMethodsFile()
      Returns the default methods file.
      Returns:
      the default methods file