public class HyperScore extends Object
Constructor and Description |
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HyperScore()
Constructor using a uniform fragmentation.
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HyperScore(PeptideFragmentationModel peptideFragmentationModel)
Constructor.
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Modifier and Type | Method and Description |
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HashMap<Double,Integer> |
getAs()
Returns a histogram of the as found in the previously interpolated
scores.
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HashMap<Double,Integer> |
getBs()
Returns a histogram of the bs found in the previously interpolated
scores.
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HashMap<Double,Double> |
getEValueMap(ArrayList<Double> hyperScores)
Returns the e-value corresponding to a list of scores in a map.
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HashMap<Double,Double> |
getEValueMap(ArrayList<Double> hyperScores,
boolean useCache)
Returns the e-value corresponding to a list of scores in a map.
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HashMap<Double,Double> |
getInterpolation(ArrayList<Double> hyperScores,
Double a,
Double b)
Returns the interpolation of a list of hyperscores using a linear
interpolation of the form result = a * log(score) + b.
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static double |
getInterpolation(double logScore,
double a,
double b)
Returns the interpolated value for a given score in log.
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double[] |
getInterpolationValues(HashMap<Integer,Integer> scoreHistogram,
boolean useCache)
Returns the interpolation values for the given score histogram in the
form {a, b}.
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double[] |
getInterpolationValues(int[] scores,
boolean useCache)
Returns the interpolation values for the given scores in the form {a, b}.
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Double |
getMendianA()
Returns the rounded median of the as found in the previously interpolated
scores.
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Double |
getMendianB()
Returns the rounded median of the bs found in the previously interpolated
scores.
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double |
getScore(Peptide peptide,
int charge,
Spectrum spectrum,
ArrayList<IonMatch> ionMatches)
Returns the hyperscore.
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double |
getScore(Peptide peptide,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the hyperscore.
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public HyperScore(PeptideFragmentationModel peptideFragmentationModel)
peptideFragmentationModel
- the peptide fragmentation model to usepublic HyperScore()
public double getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
peptide
- the peptide of interestspectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumspectrum
- the spectrumannotationSettings
- the general spectrum annotation settingsspecificAnnotationSettings
- the annotation settings specific to
this PSMpeptideSpectrumAnnotator
- the spectrum annotator to usemodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching
preferences for modification to peptide mappingpublic double getScore(Peptide peptide, int charge, Spectrum spectrum, ArrayList<IonMatch> ionMatches)
peptide
- the peptide of interestcharge
- the chargespectrum
- the spectrum of interestionMatches
- the ion matches obtained from spectrum annotationpublic HashMap<Double,Double> getEValueMap(ArrayList<Double> hyperScores)
hyperScores
- the different scorespublic HashMap<Double,Double> getEValueMap(ArrayList<Double> hyperScores, boolean useCache)
hyperScores
- the different scoresuseCache
- if true the interpolation values will be stored in the
histograms in cachepublic double[] getInterpolationValues(int[] scores, boolean useCache)
scores
- the scoresuseCache
- if true the interpolation values will be stored in the
histograms in cachepublic double[] getInterpolationValues(HashMap<Integer,Integer> scoreHistogram, boolean useCache)
scoreHistogram
- the score histogramuseCache
- if true the interpolation values will be stored in the
histograms in cachepublic HashMap<Double,Double> getInterpolation(ArrayList<Double> hyperScores, Double a, Double b)
hyperScores
- a list of hyperscoresa
- the slope of the interpolationb
- the offset of the interpolationpublic static double getInterpolation(double logScore, double a, double b)
logScore
- the log of the scorea
- the slope of the interpolationb
- the offset of the interpolationpublic Double getMendianA()
public Double getMendianB()
public HashMap<Double,Integer> getAs()
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