Package eu.isas.reporter.settings

Class RatioEstimationSettings

java.lang.Object
eu.isas.reporter.settings.RatioEstimationSettings
All Implemented Interfaces:
Serializable
public class RatioEstimationSettings extends Object implements Serializable
Settings for the estimation of a peptide or protein ratio.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Summary

    Constructors
    Constructor
    Description
    RatioEstimationSettings()
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addExcludingPtm(String ptmName)
    Adds an excluding PTM.
    RatioEstimationSettings
    clone()
     
    void
    emptyPTMList()
    Empty the list of ignored PTMs.
    HashSet<String>
    getExcludingPtms()
    Returns the list of PTMs to ignore.
    int
    getMinUnique()
    Returns the minimal number of unique peptides required for a protein, ignored if negative.
    com.compomics.util.experiment.identification.validation.MatchValidationLevel
    getPeptideValidationLevel()
    Indicates the validation level to require for peptide quantification.
    double
    getPercentile()
    Returns the share in percent of ratios considered to set the width of the maximum likelihood estimators.
    com.compomics.util.experiment.identification.validation.MatchValidationLevel
    getProteinValidationLevel()
    Indicates the validation level to require for protein quantification.
    com.compomics.util.experiment.identification.validation.MatchValidationLevel
    getPsmValidationLevel()
    Indicates the validation level to require for PSM quantification.
    double
    getRatioResolution()
    Returns the ratio resolution.
    boolean
    isIgnoreMissedCleavages()
    Returns a boolean indicating whether miscleaved peptides should be ignored.
    boolean
    isIgnoreNullIntensities()
    Returns a boolean indicating whether null intensities should be ignored.
    boolean
    isSameAs(RatioEstimationSettings anotherSetting)
    Indicates whether another setting is the same as this one.
    void
    setIgnoreMissedCleavages(boolean ignoreMissedCleavages)
    Sets whether miscleaved peptides should be ignored.
    void
    setIgnoreNullIntensities(boolean ignoreNullIntensities)
    Sets whether null intensities should be ignored.
    void
    setMinUnique(int minUnique)
    Sets the minimal number of unique peptides required for a protein, ignored if negative.
    void
    setPeptideValidationLevel(com.compomics.util.experiment.identification.validation.MatchValidationLevel matchValidationLevel)
    Sets the validation level to require for quantification.
    void
    setPercentile(double percentile)
    Sets the share in percent of ratios considered to set the width of the maximum likelihood estimators.
    void
    setProteinValidationLevel(com.compomics.util.experiment.identification.validation.MatchValidationLevel matchValidationLevel)
    Sets the validation level to require for quantification.
    void
    setPsmValidationLevel(com.compomics.util.experiment.identification.validation.MatchValidationLevel matchValidationLevel)
    Sets the validation level to require for quantification.
    void
    setRatioResolution(double ratioResolution)
    Sets the ratio resolution.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • RatioEstimationSettings

      public RatioEstimationSettings()
      Constructor.

  • Method Details

    • clone

      public RatioEstimationSettings clone()
      Overrides:
      clone in class Object

    • isSameAs

      public boolean isSameAs(RatioEstimationSettings anotherSetting)
      Indicates whether another setting is the same as this one.
      Parameters:
      anotherSetting - another setting
      Returns:
      a boolean indicating whether another setting is the same as this one

    • isIgnoreMissedCleavages

      public boolean isIgnoreMissedCleavages()
      Returns a boolean indicating whether miscleaved peptides should be ignored.
      Returns:
      a boolean indicating whether miscleaved peptides should be ignored

    • setIgnoreMissedCleavages

      public void setIgnoreMissedCleavages(boolean ignoreMissedCleavages)
      Sets whether miscleaved peptides should be ignored.
      Parameters:
      ignoreMissedCleavages - a boolean indicating whether miscleaved peptides should be ignored

    • isIgnoreNullIntensities

      public boolean isIgnoreNullIntensities()
      Returns a boolean indicating whether null intensities should be ignored.
      Returns:
      a boolean indicating whether null intensities should be ignored

    • setIgnoreNullIntensities

      public void setIgnoreNullIntensities(boolean ignoreNullIntensities)
      Sets whether null intensities should be ignored.
      Parameters:
      ignoreNullIntensities - a boolean indicating whether null intensities should be ignored

    • getPercentile

      public double getPercentile()
      Returns the share in percent of ratios considered to set the width of the maximum likelihood estimators.
      Returns:
      the share in percent of ratios considered to set the width of the maximum likelihood estimators

    • setPercentile

      public void setPercentile(double percentile)
      Sets the share in percent of ratios considered to set the width of the maximum likelihood estimators.
      Parameters:
      percentile - the share in percent of ratios considered to set the width of the maximum likelihood estimators

    • getRatioResolution

      public double getRatioResolution()
      Returns the ratio resolution.
      Returns:
      the ratio resolution

    • setRatioResolution

      public void setRatioResolution(double ratioResolution)
      Sets the ratio resolution.
      Parameters:
      ratioResolution - the ratio resolution

    • getExcludingPtms

      public HashSet<String> getExcludingPtms()
      Returns the list of PTMs to ignore.
      Returns:
      the list of PTMs to ignore

    • addExcludingPtm

      public void addExcludingPtm(String ptmName)
      Adds an excluding PTM.
      Parameters:
      ptmName - the name of the excluding PTM

    • emptyPTMList

      public void emptyPTMList()
      Empty the list of ignored PTMs.

    • getProteinValidationLevel

      public com.compomics.util.experiment.identification.validation.MatchValidationLevel getProteinValidationLevel()
      Indicates the validation level to require for protein quantification.
      Returns:
      the minimal validation level for a protein to be accounted for

    • setProteinValidationLevel

      public void setProteinValidationLevel(com.compomics.util.experiment.identification.validation.MatchValidationLevel matchValidationLevel)
      Sets the validation level to require for quantification.
      Parameters:
      matchValidationLevel - the minimal validation level for a protein to be accounted for

    • getPeptideValidationLevel

      public com.compomics.util.experiment.identification.validation.MatchValidationLevel getPeptideValidationLevel()
      Indicates the validation level to require for peptide quantification.
      Returns:
      the minimal validation level for a protein to be accounted for

    • setPeptideValidationLevel

      public void setPeptideValidationLevel(com.compomics.util.experiment.identification.validation.MatchValidationLevel matchValidationLevel)
      Sets the validation level to require for quantification.
      Parameters:
      matchValidationLevel - the minimal validation level for a peptide to be accounted for

    • getPsmValidationLevel

      public com.compomics.util.experiment.identification.validation.MatchValidationLevel getPsmValidationLevel()
      Indicates the validation level to require for PSM quantification.
      Returns:
      the minimal validation level for a protein to be accounted for

    • setPsmValidationLevel

      public void setPsmValidationLevel(com.compomics.util.experiment.identification.validation.MatchValidationLevel matchValidationLevel)
      Sets the validation level to require for quantification.
      Parameters:
      matchValidationLevel - the minimal validation level for a PSM to be accounted for

    • getMinUnique

      public int getMinUnique()
      Returns the minimal number of unique peptides required for a protein, ignored if negative.
      Returns:
      the minimal number of unique peptides required for a protein

    • setMinUnique

      public void setMinUnique(int minUnique)
      Sets the minimal number of unique peptides required for a protein, ignored if negative.
      Parameters:
      minUnique - the minimal number of unique peptides required for a protein