Class Metrics
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
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Field Summary
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Constructor Summary
Constructors Constructor Description Metrics()
Constructor. -
Method Summary
Modifier and Type Method Description void
addFoundCharges(HashSet<Integer> foundCharges)
Adds a new charge to the list of found charges.void
clearFoundCharges()
Clears the found charges.int[]
getFoundCharges()
Returns the found charges.TreeSet<String>
getFoundModifications()
Returns the names of the variable modifications found in the dataset.HashMap<String,ArrayList<Long>>
getFractionPsmMatches()
Returns the list of fraction PSM matches.int
getMaxCharge()
Returns the maximal charge among found charges.Double
getMaxMW()
Returns the molecular weight of the fattest protein in the dataset.Integer
getMaxNPeptides()
Returns the maximal number of peptides among the proteins of the dataset.Integer
getMaxNPsms()
Returns the the maximal number of PSMs among the proteins of the dataset.double
getMaxPeptidePrecursorErrorDa()
Return the max peptide precursor mass error in Dalton.double
getMaxPeptidePrecursorErrorPpm()
Returns the max peptide precursor mass error in ppm.Integer
getMaxProteinAccessionLength()
Returns the max protein accession length.Double
getMaxProteinAveragePrecursorIntensity()
Returns the maximum protein average precursor intensity.Double
getMaxProteinSummedPrecursorIntensity()
Returns the maximum summed protein precursor intensity.Double
getMaxSpectrumCounting()
Returns the maximal spectrum counting value of the proteins of the dataset.double
getMaxTagPrecursorErrorDa()
Return the max tag precursor mass error in Dalton.double
getMaxTagPrecursorErrorPpm()
Returns the max tag precursor mass error in ppm.Integer
getMaxValidatedPeptidesPerFraction()
Returns the maximum validated peptides at the fraction level.Integer
getMaxValidatedSpectraPerFraction()
Returns the maximum validated spectra at the fraction level.Integer
getnConfidentProteins()
Returns the number of confident proteins.Integer
getnValidatedProteins()
Returns the number of validated proteins.HashMap<String,ArrayList<Double>>
getObservedFractionalMassesAll()
Returns the observed molecular masses in kDa for each fraction.NonSymmetricalNormalDistribution
getPeptideLengthDistribution()
Returns the distribution of validated peptide lengths.long[]
getProteinKeys()
Returns the list of ordered protein keys.HashMap<String,Integer>
getTotalPeptidesPerFraction()
Returns the total number of peptides per fraction.Double
getTotalSpectrumCounting()
Returns the total spectrum counting.Double
getTotalSpectrumCountingMass()
Returns the total spectrum counting masses.long[]
getValidatedTargetProteinKeys()
Returns the keys of the validated target protein matches.void
setFoundModifications(TreeSet<String> foundModifications)
Sets the list of variable modifications found in the dataset.void
setFractionPsmMatches(HashMap<String,ArrayList<Long>> fractionPsmMatches)
Set the fraction PSM matches.void
setMaxMW(Double maxMW)
Sets the molecular weight of the fattest protein in the dataset.void
setMaxNPeptides(Integer maxNPeptides)
Sets the maximal number of peptides among the proteins of the dataset.void
setMaxNPsms(Integer maxNSpectra)
Sets the the maximal amount of PSMs in the proteins of the dataset.void
setMaxPeptidePrecursorErrorDa(double maxPeptidePrecursorErrorDa)
Set the max peptide precursor mass error in Dalton.void
setMaxPeptidePrecursorErrorPpm(double maxPeptidePrecursorErrorPpm)
Set the max peptide precursor mass error in ppm.void
setMaxProteinAccessionLength(int maxProteinAccessionLength)
Sets the max protein accession length.void
setMaxProteinAveragePrecursorIntensity(Double maxProteinAveragePrecursorIntensity)
Set the maximum protein average precursor intensity.void
setMaxProteinSummedPrecursorIntensity(Double maxProteinSummedPrecursorIntensity)
Set the maximum summed protein precursor intensity.void
setMaxSpectrumCounting(Double maxSpectrumCounting)
Sets the maximal spectrum counting value of the proteins of the dataset.void
setMaxTagPrecursorErrorDa(double maxTagPrecursorErrorDa)
Set the max tag precursor mass error in Dalton.void
setMaxTagPrecursorErrorPpm(double maxTagPrecursorErrorPpm)
Set the max tag precursor mass error in ppm.void
setMaxValidatedPeptidesPerFraction(Integer maxValidatedPeptidesPerFraction)
Set the maximum validated peptides at the fraction level.void
setMaxValidatedSpectraPerFraction(Integer maxValidatedSpectraPerFraction)
Set the maximum validated spectra at the fraction level.void
setnConfidentProteins(int nConfidentProteins)
Sets the number of confident proteins.void
setnValidatedProteins(int nValidatedProteins)
Sets the number of validated proteins.void
setObservedFractionalMassesAll(HashMap<String,ArrayList<Double>> observedFractionalMassesAll)
Set the observed molecular masses for each fraction in kDa.void
setPeptideLengthDistribution(NonSymmetricalNormalDistribution peptideLengthDistribution)
Sets the distribution of validated peptide lengths.void
setProteinKeys(long[] proteinKeys)
Sets the list of ordered protein keys.void
setTotalPeptidesPerFraction(HashMap<String,Integer> totalPeptidesPerFractions)
Set the total number of peptides per fraction.void
setTotalSpectrumCounting(Double totalSpectrumCountingIndexes)
Sets the total spectrum counting.void
setTotalSpectrumCountingMass(double totalSpectrumCountingMass)
Sets the total spectrum counting value.void
setValidatedTargetProteinKeys(long[] validatedTargetProteinKeys)
Sets the keys of the validated target protein matches.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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Metrics
public Metrics()Constructor.
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Method Details
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getFoundCharges
public int[] getFoundCharges()Returns the found charges.- Returns:
- the found charges.
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clearFoundCharges
public void clearFoundCharges()Clears the found charges. -
addFoundCharges
Adds a new charge to the list of found charges.- Parameters:
foundCharges
- the new charge to add
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getMaxCharge
public int getMaxCharge()Returns the maximal charge among found charges.- Returns:
- the maximal charge
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getMaxPeptidePrecursorErrorDa
public double getMaxPeptidePrecursorErrorDa()Return the max peptide precursor mass error in Dalton.- Returns:
- the max peptide precursor mass error in Dalton
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setMaxPeptidePrecursorErrorDa
public void setMaxPeptidePrecursorErrorDa(double maxPeptidePrecursorErrorDa)Set the max peptide precursor mass error in Dalton.- Parameters:
maxPeptidePrecursorErrorDa
- the mass error to set
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getMaxPeptidePrecursorErrorPpm
public double getMaxPeptidePrecursorErrorPpm()Returns the max peptide precursor mass error in ppm.- Returns:
- the max peptide precursor mass error in ppm
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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
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getMaxTagPrecursorErrorDa
public double getMaxTagPrecursorErrorDa()Return the max tag precursor mass error in Dalton.- Returns:
- the max tag precursor mass error in Dalton
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setMaxTagPrecursorErrorDa
public void setMaxTagPrecursorErrorDa(double maxTagPrecursorErrorDa)Set the max tag precursor mass error in Dalton.- Parameters:
maxTagPrecursorErrorDa
- the mass error to set
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getMaxTagPrecursorErrorPpm
public double getMaxTagPrecursorErrorPpm()Returns the max tag precursor mass error in ppm.- Returns:
- the max tag precursor mass error in ppm
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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
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getMaxMW
Returns the molecular weight of the fattest protein in the dataset.- Returns:
- the molecular weight of the fattest protein in the dataset
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setMaxMW
Sets the molecular weight of the fattest protein in the dataset.- Parameters:
maxMW
- the molecular weight of the fattest protein in the dataset
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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
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setMaxNPeptides
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
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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
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setMaxNPsms
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
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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
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setMaxSpectrumCounting
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
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getProteinKeys
public long[] getProteinKeys()Returns the list of ordered protein keys.- Returns:
- the list of ordered protein keys
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setProteinKeys
public void setProteinKeys(long[] proteinKeys)Sets the list of ordered protein keys.- Parameters:
proteinKeys
- the list of ordered protein keys
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setMaxProteinAccessionLength
public void setMaxProteinAccessionLength(int maxProteinAccessionLength)Sets the max protein accession length.- Parameters:
maxProteinAccessionLength
- the length to set
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getMaxProteinAccessionLength
Returns the max protein accession length.- Returns:
- the max protein accession length
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getnValidatedProteins
Returns the number of validated proteins.- Returns:
- the number of validated proteins
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setnValidatedProteins
public void setnValidatedProteins(int nValidatedProteins)Sets the number of validated proteins.- Parameters:
nValidatedProteins
- the number of validated proteins
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getnConfidentProteins
Returns the number of confident proteins.- Returns:
- the number of confident proteins
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setnConfidentProteins
public void setnConfidentProteins(int nConfidentProteins)Sets the number of confident proteins.- Parameters:
nConfidentProteins
- the number of confident proteins
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getFoundModifications
Returns the names of the variable modifications found in the dataset.- Returns:
- the names of the variable modifications found in the dataset
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setFoundModifications
Sets the list of variable modifications found in the dataset.- Parameters:
foundModifications
- the list of variable modifications found in the dataset
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setFractionPsmMatches
Set the fraction PSM matches. Key: 'fraction name'_'peptide key'. Values: arraylist of spectrum keys.- Parameters:
fractionPsmMatches
- the fraction PSM matches
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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
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setTotalPeptidesPerFraction
Set the total number of peptides per fraction.- Parameters:
totalPeptidesPerFractions
- the total number of peptides per fraction map
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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
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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
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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
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getMaxValidatedPeptidesPerFraction
Returns the maximum validated peptides at the fraction level.- Returns:
- the maxValidatedPeptidesPerFraction
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setMaxValidatedPeptidesPerFraction
Set the maximum validated peptides at the fraction level.- Parameters:
maxValidatedPeptidesPerFraction
- the maxValidatedPeptidesPerFraction to set
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getMaxValidatedSpectraPerFraction
Returns the maximum validated spectra at the fraction level.- Returns:
- the maxValidatedSpectraPerFraction
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setMaxValidatedSpectraPerFraction
Set the maximum validated spectra at the fraction level.- Parameters:
maxValidatedSpectraPerFraction
- the maxValidatedSpectraPerFraction to set
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getMaxProteinAveragePrecursorIntensity
Returns the maximum protein average precursor intensity.- Returns:
- the maxProteinAveragePrecursorIntensity
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setMaxProteinAveragePrecursorIntensity
Set the maximum protein average precursor intensity.- Parameters:
maxProteinAveragePrecursorIntensity
- the maxProteinAveragePrecursorIntensity to set
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getMaxProteinSummedPrecursorIntensity
Returns the maximum summed protein precursor intensity.- Returns:
- the maxProteinSummedPrecursorIntensity
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setMaxProteinSummedPrecursorIntensity
Set the maximum summed protein precursor intensity.- Parameters:
maxProteinSummedPrecursorIntensity
- the maxProteinSummedPrecursorIntensity to set
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getPeptideLengthDistribution
Returns the distribution of validated peptide lengths. Null if not set.- Returns:
- the distribution of validated peptide lengths
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setPeptideLengthDistribution
public void setPeptideLengthDistribution(NonSymmetricalNormalDistribution peptideLengthDistribution)Sets the distribution of validated peptide lengths.- Parameters:
peptideLengthDistribution
- the distribution of validated peptide lengths
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getTotalSpectrumCountingMass
Returns the total spectrum counting masses.- Returns:
- the total spectrum counting masses
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setTotalSpectrumCountingMass
public void setTotalSpectrumCountingMass(double totalSpectrumCountingMass)Sets the total spectrum counting value.- Parameters:
totalSpectrumCountingMass
- the total spectrum counting masses
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getTotalSpectrumCounting
Returns the total spectrum counting.- Returns:
- the total spectrum counting
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setTotalSpectrumCounting
Sets the total spectrum counting.- Parameters:
totalSpectrumCountingIndexes
- the total spectrum counting
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getValidatedTargetProteinKeys
public long[] getValidatedTargetProteinKeys()Returns the keys of the validated target protein matches.- Returns:
- the keys of the validated target protein matches
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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
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