java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.peptide_shaker.Metrics
All Implemented Interfaces:
Serializable

public class Metrics
extends ExperimentObject
This class contains metrics gathered during the creation of a PeptideShaker project.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form
  • Constructor Details

    • Metrics

      public Metrics()
      Constructor.
  • Method Details

    • getFoundCharges

      public int[] getFoundCharges()
      Returns the found charges.
      Returns:
      the found charges.
    • clearFoundCharges

      public void clearFoundCharges()
      Clears the found charges.
    • addFoundCharges

      public void addFoundCharges​(HashSet<Integer> foundCharges)
      Adds a new charge to the list of found charges.
      Parameters:
      foundCharges - the new charge to add
    • getMaxCharge

      public int getMaxCharge()
      Returns the maximal charge among found charges.
      Returns:
      the maximal charge
    • getMaxPeptidePrecursorErrorDa

      public double getMaxPeptidePrecursorErrorDa()
      Return the max peptide precursor mass error in Dalton.
      Returns:
      the max peptide precursor mass error in Dalton
    • setMaxPeptidePrecursorErrorDa

      public void setMaxPeptidePrecursorErrorDa​(double maxPeptidePrecursorErrorDa)
      Set the max peptide precursor mass error in Dalton.
      Parameters:
      maxPeptidePrecursorErrorDa - the mass error to set
    • getMaxPeptidePrecursorErrorPpm

      public double getMaxPeptidePrecursorErrorPpm()
      Returns the max peptide precursor mass error in ppm.
      Returns:
      the max peptide precursor mass error in ppm
    • setMaxPeptidePrecursorErrorPpm

      public void setMaxPeptidePrecursorErrorPpm​(double maxPeptidePrecursorErrorPpm)
      Set the max peptide precursor mass error in ppm.
      Parameters:
      maxPeptidePrecursorErrorPpm - the max peptide precursor mass error in ppm
    • getMaxTagPrecursorErrorDa

      public double getMaxTagPrecursorErrorDa()
      Return the max tag precursor mass error in Dalton.
      Returns:
      the max tag precursor mass error in Dalton
    • setMaxTagPrecursorErrorDa

      public void setMaxTagPrecursorErrorDa​(double maxTagPrecursorErrorDa)
      Set the max tag precursor mass error in Dalton.
      Parameters:
      maxTagPrecursorErrorDa - the mass error to set
    • getMaxTagPrecursorErrorPpm

      public double getMaxTagPrecursorErrorPpm()
      Returns the max tag precursor mass error in ppm.
      Returns:
      the max tag precursor mass error in ppm
    • setMaxTagPrecursorErrorPpm

      public void setMaxTagPrecursorErrorPpm​(double maxTagPrecursorErrorPpm)
      Set the max tag precursor mass error in ppm.
      Parameters:
      maxTagPrecursorErrorPpm - the max tag precursor mass error in ppm
    • getMaxMW

      public Double getMaxMW()
      Returns the molecular weight of the fattest protein in the dataset.
      Returns:
      the molecular weight of the fattest protein in the dataset
    • setMaxMW

      public void setMaxMW​(Double maxMW)
      Sets the molecular weight of the fattest protein in the dataset.
      Parameters:
      maxMW - the molecular weight of the fattest protein in the dataset
    • getMaxNPeptides

      public Integer getMaxNPeptides()
      Returns the maximal number of peptides among the proteins of the dataset.
      Returns:
      the maximal number of peptides among the proteins of the dataset
    • setMaxNPeptides

      public void setMaxNPeptides​(Integer maxNPeptides)
      Sets the maximal number of peptides among the proteins of the dataset.
      Parameters:
      maxNPeptides - the maximal number of peptides among the proteins of the dataset
    • getMaxNPsms

      public Integer getMaxNPsms()
      Returns the the maximal number of PSMs among the proteins of the dataset.
      Returns:
      the the maximal number of PSMs among the proteins of the dataset
    • setMaxNPsms

      public void setMaxNPsms​(Integer maxNSpectra)
      Sets the the maximal amount of PSMs in the proteins of the dataset.
      Parameters:
      maxNSpectra - the the maximal amount of PSMs in the proteins of the dataset
    • getMaxSpectrumCounting

      public Double getMaxSpectrumCounting()
      Returns the maximal spectrum counting value of the proteins of the dataset.
      Returns:
      the maximal spectrum counting value of the proteins of the dataset
    • setMaxSpectrumCounting

      public void setMaxSpectrumCounting​(Double maxSpectrumCounting)
      Sets the maximal spectrum counting value of the proteins of the dataset.
      Parameters:
      maxSpectrumCounting - the maximal spectrum counting value of the proteins of the dataset
    • getProteinKeys

      public long[] getProteinKeys()
      Returns the list of ordered protein keys.
      Returns:
      the list of ordered protein keys
    • setProteinKeys

      public void setProteinKeys​(long[] proteinKeys)
      Sets the list of ordered protein keys.
      Parameters:
      proteinKeys - the list of ordered protein keys
    • setMaxProteinAccessionLength

      public void setMaxProteinAccessionLength​(int maxProteinAccessionLength)
      Sets the max protein accession length.
      Parameters:
      maxProteinAccessionLength - the length to set
    • getMaxProteinAccessionLength

      public Integer getMaxProteinAccessionLength()
      Returns the max protein accession length.
      Returns:
      the max protein accession length
    • getnValidatedProteins

      public Integer getnValidatedProteins()
      Returns the number of validated proteins.
      Returns:
      the number of validated proteins
    • setnValidatedProteins

      public void setnValidatedProteins​(int nValidatedProteins)
      Sets the number of validated proteins.
      Parameters:
      nValidatedProteins - the number of validated proteins
    • getnConfidentProteins

      public Integer getnConfidentProteins()
      Returns the number of confident proteins.
      Returns:
      the number of confident proteins
    • setnConfidentProteins

      public void setnConfidentProteins​(int nConfidentProteins)
      Sets the number of confident proteins.
      Parameters:
      nConfidentProteins - the number of confident proteins
    • getFoundModifications

      public TreeSet<String> getFoundModifications()
      Returns the names of the variable modifications found in the dataset.
      Returns:
      the names of the variable modifications found in the dataset
    • setFoundModifications

      public void setFoundModifications​(TreeSet<String> foundModifications)
      Sets the list of variable modifications found in the dataset.
      Parameters:
      foundModifications - the list of variable modifications found in the dataset
    • setFractionPsmMatches

      public void setFractionPsmMatches​(HashMap<String,​ArrayList<Long>> fractionPsmMatches)
      Set the fraction PSM matches. Key: 'fraction name'_'peptide key'. Values: arraylist of spectrum keys.
      Parameters:
      fractionPsmMatches - the fraction PSM matches
    • getFractionPsmMatches

      public HashMap<String,​ArrayList<Long>> getFractionPsmMatches()
      Returns the list of fraction PSM matches. Key: 'fraction name'_'peptide key'. Values: arraylist of spectrum keys.
      Returns:
      he list of fraction PSM matches
    • setTotalPeptidesPerFraction

      public void setTotalPeptidesPerFraction​(HashMap<String,​Integer> totalPeptidesPerFractions)
      Set the total number of peptides per fraction.
      Parameters:
      totalPeptidesPerFractions - the total number of peptides per fraction map
    • getTotalPeptidesPerFraction

      public HashMap<String,​Integer> getTotalPeptidesPerFraction()
      Returns the total number of peptides per fraction. Null if the values have not been set.
      Returns:
      the total number of peptides per fraction, null if the values have not been set
    • getObservedFractionalMassesAll

      public HashMap<String,​ArrayList<Double>> getObservedFractionalMassesAll()
      Returns the observed molecular masses in kDa for each fraction. The key is the file path of the fraction.
      Returns:
      the observed average molecular masses for each fraction
    • setObservedFractionalMassesAll

      public void setObservedFractionalMassesAll​(HashMap<String,​ArrayList<Double>> observedFractionalMassesAll)
      Set the observed molecular masses for each fraction in kDa. The key is the file path of the fraction.
      Parameters:
      observedFractionalMassesAll - the observedFractionalMasses to set
    • getMaxValidatedPeptidesPerFraction

      public Integer getMaxValidatedPeptidesPerFraction()
      Returns the maximum validated peptides at the fraction level.
      Returns:
      the maxValidatedPeptidesPerFraction
    • setMaxValidatedPeptidesPerFraction

      public void setMaxValidatedPeptidesPerFraction​(Integer maxValidatedPeptidesPerFraction)
      Set the maximum validated peptides at the fraction level.
      Parameters:
      maxValidatedPeptidesPerFraction - the maxValidatedPeptidesPerFraction to set
    • getMaxValidatedSpectraPerFraction

      public Integer getMaxValidatedSpectraPerFraction()
      Returns the maximum validated spectra at the fraction level.
      Returns:
      the maxValidatedSpectraPerFraction
    • setMaxValidatedSpectraPerFraction

      public void setMaxValidatedSpectraPerFraction​(Integer maxValidatedSpectraPerFraction)
      Set the maximum validated spectra at the fraction level.
      Parameters:
      maxValidatedSpectraPerFraction - the maxValidatedSpectraPerFraction to set
    • getMaxProteinAveragePrecursorIntensity

      public Double getMaxProteinAveragePrecursorIntensity()
      Returns the maximum protein average precursor intensity.
      Returns:
      the maxProteinAveragePrecursorIntensity
    • setMaxProteinAveragePrecursorIntensity

      public void setMaxProteinAveragePrecursorIntensity​(Double maxProteinAveragePrecursorIntensity)
      Set the maximum protein average precursor intensity.
      Parameters:
      maxProteinAveragePrecursorIntensity - the maxProteinAveragePrecursorIntensity to set
    • getMaxProteinSummedPrecursorIntensity

      public Double getMaxProteinSummedPrecursorIntensity()
      Returns the maximum summed protein precursor intensity.
      Returns:
      the maxProteinSummedPrecursorIntensity
    • setMaxProteinSummedPrecursorIntensity

      public void setMaxProteinSummedPrecursorIntensity​(Double maxProteinSummedPrecursorIntensity)
      Set the maximum summed protein precursor intensity.
      Parameters:
      maxProteinSummedPrecursorIntensity - the maxProteinSummedPrecursorIntensity to set
    • getPeptideLengthDistribution

      public NonSymmetricalNormalDistribution getPeptideLengthDistribution()
      Returns the distribution of validated peptide lengths. Null if not set.
      Returns:
      the distribution of validated peptide lengths
    • setPeptideLengthDistribution

      public void setPeptideLengthDistribution​(NonSymmetricalNormalDistribution peptideLengthDistribution)
      Sets the distribution of validated peptide lengths.
      Parameters:
      peptideLengthDistribution - the distribution of validated peptide lengths
    • getTotalSpectrumCountingMass

      public Double getTotalSpectrumCountingMass()
      Returns the total spectrum counting masses.
      Returns:
      the total spectrum counting masses
    • setTotalSpectrumCountingMass

      public void setTotalSpectrumCountingMass​(double totalSpectrumCountingMass)
      Sets the total spectrum counting value.
      Parameters:
      totalSpectrumCountingMass - the total spectrum counting masses
    • getTotalSpectrumCounting

      public Double getTotalSpectrumCounting()
      Returns the total spectrum counting.
      Returns:
      the total spectrum counting
    • setTotalSpectrumCounting

      public void setTotalSpectrumCounting​(Double totalSpectrumCountingIndexes)
      Sets the total spectrum counting.
      Parameters:
      totalSpectrumCountingIndexes - the total spectrum counting
    • getValidatedTargetProteinKeys

      public long[] getValidatedTargetProteinKeys()
      Returns the keys of the validated target protein matches.
      Returns:
      the keys of the validated target protein matches
    • setValidatedTargetProteinKeys

      public void setValidatedTargetProteinKeys​(long[] validatedTargetProteinKeys)
      Sets the keys of the validated target protein matches.
      Parameters:
      validatedTargetProteinKeys - the keys of the validated target protein matches