public class Metrics extends Object implements Serializable
Constructor and Description |
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Metrics()
Constructor.
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Modifier and Type | Method and Description |
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void |
addFoundCharges(HashSet<Integer> foundCharges)
Adds a new charge to the list of found charges.
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void |
clearFoundCharges()
Clears the found charges.
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int[] |
getFoundCharges()
Returns the found charges.
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TreeSet<String> |
getFoundModifications()
Returns the names of the variable modifications found in the dataset.
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HashMap<String,ArrayList<Long>> |
getFractionPsmMatches()
Returns the list of fraction PSM matches.
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int |
getMaxCharge()
Returns the maximal charge among found charges.
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Double |
getMaxMW()
Returns the molecular weight of the fattest protein in the dataset.
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Integer |
getMaxNPeptides()
Returns the maximal amount of peptides in the proteins of the dataset.
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Integer |
getMaxNSpectra()
Returns the the maximal amount of PSMs in the proteins of the dataset.
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double |
getMaxPeptidePrecursorErrorDa()
Return the max peptide precursor mass error in Dalton.
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double |
getMaxPeptidePrecursorErrorPpm()
Returns the max peptide precursor mass error in ppm.
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Double |
getMaxProteinAveragePrecursorIntensity()
Returns the maximum protein average precursor intensity.
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Integer |
getMaxProteinKeyLength()
Returns the max protein key length.
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Double |
getMaxProteinSummedPrecursorIntensity()
Returns the maximum summed protein precursor intensity.
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Double |
getMaxSpectrumCounting()
Returns the maximal spectrum counting value of the proteins of the
dataset.
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double |
getMaxTagPrecursorErrorDa()
Return the max tag precursor mass error in Dalton.
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double |
getMaxTagPrecursorErrorPpm()
Returns the max tag precursor mass error in ppm.
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Integer |
getMaxValidatedPeptidesPerFraction()
Returns the maximum validated peptides at the fraction level.
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Integer |
getMaxValidatedSpectraPerFraction()
Returns the maximum validated spectra at the fraction level.
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Integer |
getnConfidentProteins()
Returns the number of confident proteins.
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Integer |
getnValidatedProteins()
Returns the number of validated proteins.
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HashMap<String,ArrayList<Double>> |
getObservedFractionalMassesAll()
Returns the observed molecular masses in kDa for each fraction.
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NonSymmetricalNormalDistribution |
getPeptideLengthDistribution()
Returns the distribution of validated peptide lengths.
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long[] |
getProteinKeys()
Returns the list of ordered protein keys.
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HashMap<String,Integer> |
getTotalPeptidesPerFraction()
Returns the total number of peptides per fraction.
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Double |
getTotalSpectrumCounting()
Returns the total spectrum counting.
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Double |
getTotalSpectrumCountingMass()
Returns the total spectrum counting masses.
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long[] |
getValidatedTargetProteinKeys()
Returns the keys of the validated target protein matches.
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void |
setFoundModifications(TreeSet<String> foundModifications)
Sets the list of variable modifications found in the dataset.
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void |
setFractionPsmMatches(HashMap<String,ArrayList<Long>> fractionPsmMatches)
Set the fraction PSM matches.
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void |
setMaxMW(Double maxMW)
Sets the molecular weight of the fattest protein in the dataset.
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void |
setMaxNPeptides(Integer maxNPeptides)
Sets the maximal amount of peptides in the proteins of the dataset.
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void |
setMaxNSpectra(Integer maxNSpectra)
Sets the the maximal amount of PSMs in the proteins of the dataset.
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void |
setMaxPeptidePrecursorErrorDa(double maxPeptidePrecursorErrorDa)
Set the max peptide precursor mass error in Dalton.
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void |
setMaxPeptidePrecursorErrorPpm(double maxPeptidePrecursorErrorPpm)
Set the max peptide precursor mass error in ppm.
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void |
setMaxProteinAveragePrecursorIntensity(Double maxProteinAveragePrecursorIntensity)
Set the maximum protein average precursor intensity.
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void |
setMaxProteinKeyLength(Integer maxProteinKeyLength)
Sets the max protein key length.
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void |
setMaxProteinSummedPrecursorIntensity(Double maxProteinSummedPrecursorIntensity)
Set the maximum summed protein precursor intensity.
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void |
setMaxSpectrumCounting(Double maxSpectrumCounting)
Sets the maximal spectrum counting value of the proteins of the dataset.
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void |
setMaxTagPrecursorErrorDa(double maxTagPrecursorErrorDa)
Set the max tag precursor mass error in Dalton.
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void |
setMaxTagPrecursorErrorPpm(double maxTagPrecursorErrorPpm)
Set the max tag precursor mass error in ppm.
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void |
setMaxValidatedPeptidesPerFraction(Integer maxValidatedPeptidesPerFraction)
Set the maximum validated peptides at the fraction level.
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void |
setMaxValidatedSpectraPerFraction(Integer maxValidatedSpectraPerFraction)
Set the maximum validated spectra at the fraction level.
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void |
setnConfidentProteins(int nConfidentProteins)
Sets the number of confident proteins.
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void |
setnValidatedProteins(int nValidatedProteins)
Sets the number of validated proteins.
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void |
setObservedFractionalMassesAll(HashMap<String,ArrayList<Double>> observedFractionalMassesAll)
Set the observed molecular masses for each fraction in kDa.
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void |
setPeptideLengthDistribution(NonSymmetricalNormalDistribution peptideLengthDistribution)
Sets the distribution of validated peptide lengths.
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void |
setProteinKeys(long[] proteinKeys)
Sets the list of ordered protein keys.
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void |
setTotalPeptidesPerFraction(HashMap<String,Integer> totalPeptidesPerFractions)
Set the total number of peptides per fraction.
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void |
setTotalSpectrumCounting(Double totalSpectrumCountingIndexes)
Sets the total spectrum counting.
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void |
setTotalSpectrumCountingMass(double totalSpectrumCountingMass)
Sets the total spectrum counting value.
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void |
setValidatedTargetProteinKeys(long[] validatedTargetProteinKeys)
Sets the keys of the validated target protein matches.
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public int[] getFoundCharges()
public void clearFoundCharges()
public void addFoundCharges(HashSet<Integer> foundCharges)
foundCharges
- the new charge to addpublic int getMaxCharge()
public double getMaxPeptidePrecursorErrorDa()
public void setMaxPeptidePrecursorErrorDa(double maxPeptidePrecursorErrorDa)
maxPeptidePrecursorErrorDa
- the mass error to setpublic double getMaxPeptidePrecursorErrorPpm()
public void setMaxPeptidePrecursorErrorPpm(double maxPeptidePrecursorErrorPpm)
maxPeptidePrecursorErrorPpm
- the max peptide precursor mass error
in ppmpublic double getMaxTagPrecursorErrorDa()
public void setMaxTagPrecursorErrorDa(double maxTagPrecursorErrorDa)
maxTagPrecursorErrorDa
- the mass error to setpublic double getMaxTagPrecursorErrorPpm()
public void setMaxTagPrecursorErrorPpm(double maxTagPrecursorErrorPpm)
maxTagPrecursorErrorPpm
- the max tag precursor mass error in ppmpublic Double getMaxMW()
public void setMaxMW(Double maxMW)
maxMW
- the molecular weight of the fattest protein in the datasetpublic Integer getMaxNPeptides()
public void setMaxNPeptides(Integer maxNPeptides)
maxNPeptides
- the maximal amount of peptides in the proteins of the
datasetpublic Integer getMaxNSpectra()
public void setMaxNSpectra(Integer maxNSpectra)
maxNSpectra
- the the maximal amount of PSMs in the proteins of the
datasetpublic Double getMaxSpectrumCounting()
public void setMaxSpectrumCounting(Double maxSpectrumCounting)
maxSpectrumCounting
- the maximal spectrum counting value of the
proteins of the datasetpublic long[] getProteinKeys()
public void setProteinKeys(long[] proteinKeys)
proteinKeys
- the list of ordered protein keyspublic void setMaxProteinKeyLength(Integer maxProteinKeyLength)
maxProteinKeyLength
- the length to setpublic Integer getMaxProteinKeyLength()
public Integer getnValidatedProteins()
public void setnValidatedProteins(int nValidatedProteins)
nValidatedProteins
- the number of validated proteinspublic Integer getnConfidentProteins()
public void setnConfidentProteins(int nConfidentProteins)
nConfidentProteins
- the number of confident proteinspublic TreeSet<String> getFoundModifications()
public void setFoundModifications(TreeSet<String> foundModifications)
foundModifications
- the list of variable modifications found in the
datasetpublic void setFractionPsmMatches(HashMap<String,ArrayList<Long>> fractionPsmMatches)
fractionPsmMatches
- the fraction PSM matchespublic HashMap<String,ArrayList<Long>> getFractionPsmMatches()
public void setTotalPeptidesPerFraction(HashMap<String,Integer> totalPeptidesPerFractions)
totalPeptidesPerFractions
- the total number of peptides per
fraction mappublic HashMap<String,Integer> getTotalPeptidesPerFraction()
public HashMap<String,ArrayList<Double>> getObservedFractionalMassesAll()
public void setObservedFractionalMassesAll(HashMap<String,ArrayList<Double>> observedFractionalMassesAll)
observedFractionalMassesAll
- the observedFractionalMasses to setpublic Integer getMaxValidatedPeptidesPerFraction()
public void setMaxValidatedPeptidesPerFraction(Integer maxValidatedPeptidesPerFraction)
maxValidatedPeptidesPerFraction
- the
maxValidatedPeptidesPerFraction to setpublic Integer getMaxValidatedSpectraPerFraction()
public void setMaxValidatedSpectraPerFraction(Integer maxValidatedSpectraPerFraction)
maxValidatedSpectraPerFraction
- the maxValidatedSpectraPerFraction
to setpublic Double getMaxProteinAveragePrecursorIntensity()
public void setMaxProteinAveragePrecursorIntensity(Double maxProteinAveragePrecursorIntensity)
maxProteinAveragePrecursorIntensity
- the
maxProteinAveragePrecursorIntensity to setpublic Double getMaxProteinSummedPrecursorIntensity()
public void setMaxProteinSummedPrecursorIntensity(Double maxProteinSummedPrecursorIntensity)
maxProteinSummedPrecursorIntensity
- the
maxProteinSummedPrecursorIntensity to setpublic NonSymmetricalNormalDistribution getPeptideLengthDistribution()
public void setPeptideLengthDistribution(NonSymmetricalNormalDistribution peptideLengthDistribution)
peptideLengthDistribution
- the distribution of validated peptide
lengthspublic Double getTotalSpectrumCountingMass()
public void setTotalSpectrumCountingMass(double totalSpectrumCountingMass)
totalSpectrumCountingMass
- the total spectrum counting massespublic Double getTotalSpectrumCounting()
public void setTotalSpectrumCounting(Double totalSpectrumCountingIndexes)
totalSpectrumCountingIndexes
- the total spectrum countingpublic long[] getValidatedTargetProteinKeys()
public void setValidatedTargetProteinKeys(long[] validatedTargetProteinKeys)
validatedTargetProteinKeys
- the keys of the validated target protein matchesCopyright © 2018. All rights reserved.