Uses of Class
com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum

Packages that use Spectrum

Package	Description
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.io.mass_spectrometry	Classes for the handling of mass spectrometry files.
com.compomics.util.experiment.io.mass_spectrometry.apl	Classes for the handling of Andromeda peak list (apl) files.
com.compomics.util.experiment.io.mass_spectrometry.cms	Classes for the handling of Compomics mass spectrometry (cms) files.
com.compomics.util.experiment.io.mass_spectrometry.mgf	Classes for the handling of mgf files.
com.compomics.util.experiment.io.mass_spectrometry.ms2	Classes for the handling of ms2 files.
com.compomics.util.experiment.io.mass_spectrometry.mzml	Classes for the handling of mzml files.
com.compomics.util.experiment.mass_spectrometry	Experiment classes related to mass spectrometry.
com.compomics.util.experiment.mass_spectrometry.spectra	Experiment classes related to spectra.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Uses of Spectrum in com.compomics.util.experiment.identification.modification

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.
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.

Uses of Spectrum in com.compomics.util.experiment.identification.modification.scores

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, ModificationProvider modificationProvider)	Returns the PhosphoRS sequence probabilities for the modification possible locations.

Uses of Spectrum in com.compomics.util.experiment.identification.psm_scoring

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.
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.

Uses of Spectrum in com.compomics.util.experiment.identification.psm_scoring.psm_scores

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.
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.
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.

Uses of Spectrum in com.compomics.util.experiment.identification.spectrum_annotation

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.
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.

Uses of Spectrum in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

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.
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.

Uses of Spectrum in com.compomics.util.experiment.io.mass_spectrometry

Methods in com.compomics.util.experiment.io.mass_spectrometry that return Spectrum

Modifier and Type	Method	Description
Spectrum	MsFileHandler.getSpectrum(String fileNameWithoutExtension, String spectrumTitle)
Spectrum	MsFileIterator.getSpectrum()	Returns the spectrum corresponding to the title returned by the last call to the next() method.

Uses of Spectrum in com.compomics.util.experiment.io.mass_spectrometry.apl

Methods in com.compomics.util.experiment.io.mass_spectrometry.apl with parameters of type Spectrum

Modifier and Type	Method	Description
void	AplFileWriter.writeSpectrum(String spectrumTitle, Spectrum spectrum, FragmentationMethod fragmentationMethod, int charge)	Writes the given spectrum to the file.

Uses of Spectrum in com.compomics.util.experiment.io.mass_spectrometry.cms

Methods in com.compomics.util.experiment.io.mass_spectrometry.cms that return Spectrum

Modifier and Type	Method	Description
Spectrum	CmsFileIterator.getSpectrum()
Spectrum	CmsFileReader.getSpectrum(String spectrumTitle)	Returns the spectrum with the given title.
Spectrum	CmsFileReader.getSpectrum(String fileName, String spectrumTitle)

Methods in com.compomics.util.experiment.io.mass_spectrometry.cms with parameters of type Spectrum

Modifier and Type	Method	Description
void	CmsFileWriter.addSpectrum(String spectrumTitle, Spectrum spectrum)	Adds a spectrum to the file.

Uses of Spectrum in com.compomics.util.experiment.io.mass_spectrometry.mgf

Methods in com.compomics.util.experiment.io.mass_spectrometry.mgf that return Spectrum

Modifier and Type	Method	Description
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.
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.

Methods in com.compomics.util.experiment.io.mass_spectrometry.mgf with parameters of type Spectrum

Modifier and Type	Method	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.

Uses of Spectrum in com.compomics.util.experiment.io.mass_spectrometry.ms2

Methods in com.compomics.util.experiment.io.mass_spectrometry.ms2 with parameters of type Spectrum

Modifier and Type	Method	Description
void	Ms2Exporter.writeSpectrum(Spectrum spectrum, int scanNumber)	Writes the given spectrum in ms2 format.
void	Ms2FileWriter.writeSpectrum(Spectrum spectrum, int scanNumber)	Writes the given spectrum in ms2 format.

Uses of Spectrum in com.compomics.util.experiment.io.mass_spectrometry.mzml

Methods in com.compomics.util.experiment.io.mass_spectrometry.mzml that return Spectrum

Modifier and Type	Method	Description
Spectrum	MzmlFileIterator.getSpectrum()

Uses of Spectrum in com.compomics.util.experiment.mass_spectrometry

Methods in com.compomics.util.experiment.mass_spectrometry that return Spectrum

Modifier and Type	Method	Description
Spectrum	SpectrumProvider.getSpectrum(String fileNameWithoutExtension, String spectrumTitle)	Returns the spectrum with the given title in the given file.

Uses of Spectrum in com.compomics.util.experiment.mass_spectrometry.spectra

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).
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.

Uses of Spectrum in com.compomics.util.gui.spectrum

Constructors in com.compomics.util.gui.spectrum with parameters of type Spectrum

Modifier	Constructor	Description
	IntensityHistogram(IonMatch[] annotations, Spectrum currentSpectrum, double intensityThreshold, boolean lowResolution)	Creates an IntensityHistogram plot
	MassErrorPlot(IonMatch[] annotations, Spectrum currentSpectrum, double massTolerance, boolean lowResolution)	Creates a new MassErrorPlot.
	MassErrorPlot(IonMatch[] annotations, Spectrum currentSpectrum, double massTolerance, boolean useRelativeError, boolean lowResolution)	Creates a new MassErrorPlot.