Uses of Class
com.compomics.util.experiment.biology.ions.PeptideFragmentIon

Packages that use PeptideFragmentIon
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
 

Uses of PeptideFragmentIon in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology that return types with arguments of type PeptideFragmentIon
 Iterator<PeptideFragmentIon> Peptide.fragmentIterator()
          Method which returns an iterator on the fragment ions
 ArrayList<PeptideFragmentIon> FragmentFactory.getFragmentIons(Peptide peptide)
          This method returns the theoretic fragment ions expected from a peptide sequence.
 

Methods in com.compomics.util.experiment.biology with parameters of type PeptideFragmentIon
 void Peptide.addFragmentIon(PeptideFragmentIon fragment)
          method to add a fragmentIon
 

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

Methods in com.compomics.util.experiment.identification with parameters of type PeptideFragmentIon
 boolean SpectrumAnnotator.chargeValidated(PeptideFragmentIon fragmentIon, int charge)
          Returns a boolean indicating whether the given charge can be found on the given fragment ion
static String SpectrumAnnotator.getTheoreticFragmentKey(PeptideFragmentIon fragmentIon, int charge)
          Returns the key of a theoretic fragment
 boolean SpectrumAnnotator.isAccounted(HashMap<NeutralLoss,Integer> neutralLosses, NeutralLoss neutralLoss, PeptideFragmentIon fragmentIon, Peptide peptide)
          Returns a boolean indicating whether the neutral loss should be accounted for
 boolean SpectrumAnnotator.lossesValidated(HashMap<NeutralLoss,Integer> neutralLosses, PeptideFragmentIon fragmentIon, Peptide peptide)
          Returns a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map
 

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

Methods in com.compomics.util.gui.spectrum with parameters of type PeptideFragmentIon
static Color SpectrumPanel.determineFragmentIonColor(PeptideFragmentIon fragmentIon)
          Returns the peak color to be used for the given peak label.
 



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