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Methods in com.compomics.util.experiment.identification.modification with parameters of type Spectrum
Modifier and Type |
Method |
Description |
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters) |
Returns the modification plot series in the JFreechart format for one
PSM.
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static ModificationtableContent |
ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption,
Modification modification,
int nMod,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters) |
Get the table content.
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Methods in com.compomics.util.experiment.identification.modification.scores with parameters of type Spectrum
Modifier and Type |
Method |
Description |
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
ModificationParameters modificationParameters,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationParameters,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator spectrumAnnotator) |
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
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Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type Spectrum
Modifier and Type |
Method |
Description |
double |
PsmScoresEstimator.getDecreasingScore(Peptide peptide,
int peptideCharge,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex) |
Scores the match between the given peptide and spectrum using the given
score.
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double |
PsmScoresEstimator.getScore(Peptide peptide,
int peptideCharge,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex) |
Scores the match between the given peptide and spectrum using the given
score.
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double |
PsmScoresEstimator.getScore(Peptide peptide,
int peptideCharge,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
PsmScore psmScore) |
Scores the match between the given peptide and spectrum using the given
score.
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Methods in com.compomics.util.experiment.identification.psm_scoring.psm_scores with parameters of type Spectrum
Modifier and Type |
Method |
Description |
double |
HyperScore.getScore(Peptide peptide,
int charge,
Spectrum spectrum,
ArrayList<IonMatch> ionMatches) |
Returns the hyperscore.
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double |
HyperScore.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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double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
ArrayList<IonMatch> ionMatchesList) |
Returns the score.
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double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches) |
Returns the score.
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double |
SnrScore.getScore(Peptide peptide,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters) |
Returns the score.
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Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type Spectrum
Modifier and Type |
Method |
Description |
IonMatch[] |
SpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters) |
Returns the currently matched ions with the given settings using the
intensity filter.
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abstract IonMatch[] |
SpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
Returns the currently matched ions with the given settings.
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static ArrayList<IonMatch> |
SpectrumAnnotator.matchReporterIon(Ion theoreticIon,
int charge,
Spectrum spectrum,
double massTolerance) |
Convenience method to match a reporter ion in a spectrum.
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protected void |
SpectrumAnnotator.setSpectrum(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
double intensityLimit) |
Sets a new spectrum to annotate.
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Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type Spectrum
Modifier and Type |
Method |
Description |
Map<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
IonMatch[] |
PeptideSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
|
IonMatch[] |
TagSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters) |
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter) |
Returns the spectrum annotations of a spectrum in an array of IonMatches.
|
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag) |
Returns the spectrum annotations of a spectrum in a list of IonMatches
using an intensity filter.
|
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter) |
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters) |
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
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java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter) |
Returns the spectrum annotations of a spectrum in a stream of IonMatches.
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Methods in com.compomics.util.experiment.mass_spectrometry.spectra with parameters of type Spectrum
Modifier and Type |
Method |
Description |
static double |
SpectrumUtil.getIntensityLimit(Spectrum spectrum,
AnnotationParameters.IntensityThresholdType intensityThresholdType,
double thresholdValue) |
Returns the limit in intensity according to the given threshold.
|
static int |
SpectrumUtil.getNPeaksAboveThreshold(Spectrum spectrum,
int startIndex,
int endIndex,
double intensityThreshold) |
Returns the number of peaks between the start index (inclusive) and the end index (exclusive) above the intensity threshold (inclusive).
|
static double[][] |
SpectrumUtil.getPeaksAboveIntensityThreshold(Spectrum spectrum,
AnnotationParameters.IntensityThresholdType intensityThresholdType,
double thresholdValue) |
Returns the peaks above intensity threshold as an array of double (mz,
intensity).
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static int[] |
SpectrumUtil.getWindowIndexes(Spectrum spectrum,
double mzMin,
double mzMax) |
Returns the start (inclusive) and end (exclusive) indexes of the peaks between mzMin (inclusive) and mzMax (exclusive).
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boolean |
Spectrum.isSameAs(Spectrum otherSpectrum) |
Returns a boolean indicating whether the spectrum is identical to the
other spectrum.
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