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
 HashMap<String,HashMap<Integer,IonMatch>> SpectrumAnnotator.SpectrumAnnotationMap.getAnnotations()
          Returns the actual annotations "hidden" inside the SpectrumAnnotationMap object.
 HashSet<IonMatch> PeptideAssumption.getAnnotations()
          retrieves all fragment ion annotation
 ArrayList<IonMatch> SpectrumAnnotator.matchPeak(Peptide peptide, Peak peak, double massTolerance, Charge charge)
          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
 

Constructor parameters in com.compomics.util.experiment.identification with type arguments of type IonMatch
SpectrumAnnotator.SpectrumAnnotationMap(HashMap<String,HashMap<Integer,IonMatch>> annotations)
          Create a new SpectrumAnnotationMap.
 

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
SequenceFragmentationPanel(String aSequence, ArrayList<IonMatch> aIonMatches, boolean boolModifiedSequence)
          Creates a new SequenceFragmentationPanel.
 



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