Uses of Class
com.compomics.util.experiment.identification.matches.IonMatch

Packages that use IonMatch

Package	Description
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
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.simple_annotators	This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
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.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Uses of IonMatch in com.compomics.util.experiment.identification

Methods in com.compomics.util.experiment.identification that return IonMatch

Modifier and Type	Method	Description
IonMatch	SpectrumIdentificationAssumption.getPrecursorMatch(double precursorMz, double precursorIntensity)	Returns the ion match.

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

Methods in com.compomics.util.experiment.identification.modification that return types with arguments of type IonMatch

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.

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

Method parameters in com.compomics.util.experiment.identification.psm_scoring.psm_scores with type arguments of type IonMatch

Modifier and Type	Method	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.

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

Methods in com.compomics.util.experiment.identification.spectrum_annotation that return IonMatch

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.
protected IonMatch	SpectrumAnnotator.matchInSpectrum(double[] spectrumMz, double[] spectrumIntensity, Ion theoreticIon, int inspectedCharge)	Matches a theoretic ion in the spectrum.
protected IonMatch	SpectrumAnnotator.setBestPeak(double[] spectrumMz, double[] spectrumIntensity, int[] matchedPeaksIndexes, IonMatch ionMatch)	Returns the peak to retain of the matched peaks according to the ties resolution setting.

Methods in com.compomics.util.experiment.identification.spectrum_annotation that return types with arguments of type IonMatch

Modifier and Type	Method	Description
protected ArrayList<IonMatch>	SpectrumAnnotator.matchPeak(SpecificAnnotationParameters specificAnnotationSettings, double peakMz, double peakIntensity)	This method matches the potential fragment ions of a given peptide with a given peak.
static ArrayList<IonMatch>	SpectrumAnnotator.matchReporterIon(Ion theoreticIon, int charge, Spectrum spectrum, double massTolerance)	Convenience method to match a reporter ion in a spectrum.

Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type IonMatch

Modifier and Type	Method	Description
static Vector<SpectrumAnnotation>	SpectrumAnnotator.getSpectrumAnnotation(IonMatch[] ionMatches)	Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel.
protected IonMatch	SpectrumAnnotator.setBestPeak(double[] spectrumMz, double[] spectrumIntensity, int[] matchedPeaksIndexes, IonMatch ionMatch)	Returns the peak to retain of the matched peaks according to the ties resolution setting.

Uses of IonMatch in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators

Methods in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators that return types with arguments of type IonMatch

Modifier and Type	Method	Description
ArrayList<IonMatch>	FragmentAnnotator.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge)	Returns the ions matched in the given spectrum at the given charge.
ArrayList<IonMatch>	FragmentAnnotatorNL.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge)	Returns the ions matched in the given spectrum at the given charge.
ArrayList<IonMatch>	ImmoniumIonAnnotator.getIonMatches(SpectrumIndex spectrumIndex)	Returns the ions matched in the given spectrum.
ArrayList<IonMatch>	PrecursorAnnotator.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int isotopeMax)	Returns the ions matched in the given spectrum at the given charge.
ArrayList<IonMatch>	ReporterIonAnnotator.getIonMatches(SpectrumIndex spectrumIndex)	Returns the ions matched in the given spectrum.

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

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators that return IonMatch

Modifier and Type	Method	Description
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.

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators that return types with arguments of type IonMatch

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.
ArrayList<IonMatch>	SimplePeptideAnnotator.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int precursorIsotopeMax)	Returns the ion matches for the given spectrum.
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.
ArrayList<IonMatch>	PeptideSpectrumAnnotator.matchPeak(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, double peakMz, double peakIntensity)	This method matches the potential fragment ions of a given peptide with a given peak according to the annotation settings.

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

Methods in com.compomics.util.gui.spectrum with parameters of type IonMatch

Modifier and Type	Method	Description
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored)	Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored)	Add reference areas annotating the de novo tags.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SequenceFragmentationPanel.setIonMatches(IonMatch[] lIonMatches)	Set the ArrayList with FragmentIon matches.

Method parameters in com.compomics.util.gui.spectrum with type arguments of type IonMatch

Modifier and Type	Method	Description
static void	MassErrorBubblePlot.addFragmentIonTypeMarkers(HashMap<IonMatch,ArrayList<XYZDataPoint>> data, org.jfree.chart.JFreeChart chart, boolean showMarkers)	Adds interval markers for all the fragment ion types.
org.jfree.data.xy.DefaultXYZDataset	MassErrorBubblePlot.addXYZDataSeries(HashMap<IonMatch,ArrayList<XYZDataPoint>> data)	Adds the provided data series to an XYZ data set.

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

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.
	SequenceFragmentationPanel(String aSequence, IonMatch[] aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon)	Creates a new SequenceFragmentationPanel working with B and Y ions.
	SequenceFragmentationPanel(String taggedModifiedSequence, IonMatch[] aIonMatches, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon)	Creates a new SequenceFragmentationPanel working with B and Y ions.