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

Packages that use IonMatch
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.experiment.quantification.reporterion.quantification This package contains experiment classes related to quantification by reporter ions. 
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
 

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

Methods in com.compomics.util.experiment.identification that return types with arguments of type IonMatch
 HashSet<IonMatch> PeptideAssumption.getAnnotations()
          retrieves all fragment ion annotation
 ArrayList<IonMatch> SpectrumAnnotator.getCurrentAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, HashMap<NeutralLoss,Integer> neutralLosses, ArrayList<Integer> charges)
          Returns the currently matched ions with the given settings
 ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, HashMap<NeutralLoss,Integer> neutralLosses, ArrayList<Integer> charges, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance)
          Returns the spectrum annotations of a spectrum in a list of IonMatches Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.
 ArrayList<IonMatch> SpectrumAnnotator.matchPeak(Peptide peptide, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> iontypes, ArrayList<Integer> charges, HashMap<NeutralLoss,Integer> neutralLosses, Peak peak, double massTolerance)
          This method matches the potential fragment ions of a given peptide with a given peak.
 

Methods in com.compomics.util.experiment.identification with parameters of type IonMatch
 void PeptideAssumption.addAnnotation(IonMatch ionMatch)
          add a fragment ion annotation
 

Method parameters in com.compomics.util.experiment.identification with type arguments of type IonMatch
static Vector<DefaultSpectrumAnnotation> SpectrumAnnotator.getSpectrumAnnotation(ArrayList<IonMatch> ionMatches)
          Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPAnel
 

Uses of IonMatch in com.compomics.util.experiment.quantification.reporterion.quantification
 

Methods in com.compomics.util.experiment.quantification.reporterion.quantification that return types with arguments of type IonMatch
 HashMap<Integer,IonMatch> PsmQuantification.getReporterMatches()
          Getter for the reporter matches
 

Methods in com.compomics.util.experiment.quantification.reporterion.quantification with parameters of type IonMatch
 void PsmQuantification.addIonMatch(int reporterIndex, IonMatch match)
          Method to add a match between a peak and a reporter ion
 

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

Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type IonMatch
FragmentIonTable(Peptide currentPeptide, ArrayList<ArrayList<IonMatch>> allAnnotations, ArrayList<MSnSpectrum> allSpectra, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, boolean singleCharge, boolean twoCharges)
          Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type.
FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, boolean singleCharge, boolean twoCharges)
          Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
IntensityHistogram(ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, boolean annotateMostIntensePeaks, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates an IntensityHistogram plot
MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<ArrayList<IonMatch>> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers)
          Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<ArrayList<IonMatch>> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
          Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<ArrayList<IonMatch>> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, double bubbleScale, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
          Creates a new MassErrorBubblePlot.
MassErrorPlot(ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates a new MassErrorPlot.
MassErrorPlot(ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean useRelativeError)
          Creates a new MassErrorPlot.
SequenceFragmentationPanel(String aSequence, ArrayList<IonMatch> aIonMatches, boolean boolModifiedSequence)
          Creates a new SequenceFragmentationPanel.
 



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