Uses of Class
com.compomics.util.experiment.identification.matches.IonMatch
Package | Description |
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com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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com.compomics.util.experiment.identification.modification |
Modification mapping and localization.
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com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators |
This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
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com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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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, Integer 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 Constructor Description IntensityHistogram(IonMatch[] annotations, Spectrum currentSpectrum, double intensityThreshold)
Creates an IntensityHistogram plotMassErrorPlot(IonMatch[] annotations, Spectrum currentSpectrum, double massTolerance)
Creates a new MassErrorPlot.MassErrorPlot(IonMatch[] annotations, Spectrum currentSpectrum, double massTolerance, boolean useRelativeError)
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.