Package eu.isas.reporter.calculation

Class QuantificationFilter

java.lang.Object
eu.isas.reporter.calculation.QuantificationFilter
public class QuantificationFilter extends Object
This class indicates whether identification features or ratios are valid according to the user settings.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    QuantificationFilter()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static boolean
    isPeptideValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch)
    Filters the peptide to be used for quantification according to the user quantification preferences.
    static boolean
    isProteinValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, long matchKey)
    Filters the protein to be used for quantification according to the user quantification preferences.
    static boolean
    isPsmValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, long matchKey)
    Filters the PSMs to be used for quantification according to the user quantification preferences.
    static boolean
    isRatioValid(RatioEstimationSettings ratioEstimationSettings, Double ratio)
    Filters out NaN and 0 ratios.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • QuantificationFilter

      public QuantificationFilter()

  • Method Details

    • isRatioValid

      public static boolean isRatioValid(RatioEstimationSettings ratioEstimationSettings, Double ratio)
      Filters out NaN and 0 ratios.
      Parameters:
      ratioEstimationSettings - the ratio estimation settings
      ratio - the ratio of interest
      Returns:
      true if the ratio is not NaN and should be accounted for according to the user settings

    • isPsmValid

      public static boolean isPsmValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, long matchKey)
      Filters the PSMs to be used for quantification according to the user quantification preferences.
      Parameters:
      ratioEstimationSettings - the ratio estimation settings
      identification - the identification where to get the information from
      matchKey - the key of the match of interest
      Returns:
      true if the PSM can be used for quantification

    • isPeptideValid

      public static boolean isPeptideValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch)
      Filters the peptide to be used for quantification according to the user quantification preferences.
      Parameters:
      ratioEstimationSettings - the ratio estimation settings
      identification - the identification where to get the information from
      searchParameters - the identification parameters
      peptideMatch - the match of interest
      Returns:
      true if the PSM can be used for quantification

    • isProteinValid

      public static boolean isProteinValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, long matchKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
      Filters the protein to be used for quantification according to the user quantification preferences.
      Parameters:
      ratioEstimationSettings - the ratio estimation settings
      identification - the identification where to get the information from
      matchKey - the key of the match of interest
      Returns:
      true if the PSM can be used for quantification
      Throws:
      SQLException - thrown if an SQLException occurs
      IOException - thrown if an IOException
      ClassNotFoundException - thrown if a ClassNotFoundException
      InterruptedException - thrown if an InterruptedException