Modifier and Type | Method and 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.
|
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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
double |
HyperScore.getScore(Peptide peptide,
int charge,
Spectrum spectrum,
ArrayList<IonMatch> ionMatches)
Returns the hyperscore.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
ArrayList<IonMatch> ionMatchesList)
Returns the score.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.
|
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.
|
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.
|
Modifier and Type | Method and 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.
|
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.
|
static ArrayList<IonMatch> |
SpectrumAnnotator.matchReporterIon(Ion theoreticIon,
int charge,
Spectrum spectrum,
double massTolerance)
Convenience method to match a reporter ion in a spectrum.
|
protected void |
SpectrumAnnotator.setSpectrum(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
double intensityLimit)
Sets a new spectrum to annotate.
|
Modifier and Type | Method and 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[] |
TagSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
IonMatch[] |
PeptideSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
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.
|
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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
MsFileIterator.getSpectrum()
Returns the spectrum corresponding to the title returned by the last call
to the next() method.
|
Spectrum |
MsFileHandler.getSpectrum(String fileNameWithoutExtension,
String spectrumTitle) |
Modifier and Type | Method and Description |
---|---|
void |
AplFileWriter.writeSpectrum(String spectrumTitle,
Spectrum spectrum,
FragmentationMethod fragmentationMethod,
int charge)
Writes the given spectrum to the file.
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
CmsFileIterator.getSpectrum() |
Spectrum |
CmsFileReader.getSpectrum(String spectrumTitle)
Returns the spectrum with the given title.
|
Spectrum |
CmsFileReader.getSpectrum(String fileName,
String spectrumTitle) |
Modifier and Type | Method and Description |
---|---|
void |
CmsFileWriter.addSpectrum(String spectrumTitle,
Spectrum spectrum)
Adds a spectrum to the file.
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
MgfFileIterator.getSpectrum() |
static Spectrum |
MgfIndex.getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
long index)
Returns the next spectrum starting from the given index.
|
static Spectrum |
IndexedMgfReader.getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
long index,
String fileName)
Returns the next spectrum starting from the given index.
|
Modifier and Type | Method and Description |
---|---|
static String |
MgfFileWriter.asMgf(String spectrumTitle,
Spectrum spectrum)
Returns the spectrum as an mgf bloc.
|
static String |
MgfFileWriter.asMgf(String spectrumTitle,
Spectrum spectrum,
TreeMap<String,String> additionalTags)
Returns the spectrum as an mgf bloc.
|
void |
MgfFileWriter.writeSpectrum(String spectrumTitle,
Spectrum spectrum)
Writes the given spectrum to the file.
|
Modifier and Type | Method and Description |
---|---|
void |
Ms2FileWriter.writeSpectrum(Spectrum spectrum,
int scanNumber)
Writes the given spectrum in ms2 format.
|
void |
Ms2Exporter.writeSpectrum(Spectrum spectrum,
int scanNumber)
Writes the given spectrum in ms2 format.
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
MzmlFileIterator.getSpectrum() |
Modifier and Type | Method and Description |
---|---|
Spectrum |
SpectrumProvider.getSpectrum(String fileNameWithoutExtension,
String spectrumTitle)
Returns the spectrum with the given title in the given file.
|
Modifier and Type | Method and 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).
|
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).
|
boolean |
Spectrum.isSameAs(Spectrum otherSpectrum)
Returns a boolean indicating whether the spectrum is identical to the
other spectrum.
|
Constructor and Description |
---|
IntensityHistogram(IonMatch[] annotations,
Spectrum currentSpectrum,
double intensityThreshold)
Creates an IntensityHistogram plot
|
MassErrorPlot(IonMatch[] annotations,
Spectrum currentSpectrum,
double massTolerance)
Creates a new MassErrorPlot.
|
MassErrorPlot(IonMatch[] annotations,
Spectrum currentSpectrum,
double massTolerance,
boolean useRelativeError)
Creates a new MassErrorPlot.
|
Constructor and Description |
---|
FragmentIonTable(Peptide currentPeptide,
ArrayList<IonMatch[]> allAnnotations,
ArrayList<Spectrum> allSpectra,
HashSet<Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Creates a novel fragment ion table displaying bar charts with the
intensity of each fragment ion type.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<IonMatch[]> annotations,
ArrayList<Spectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<IonMatch[]> annotations,
ArrayList<Spectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<IonMatch[]> annotations,
ArrayList<Spectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
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