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.experiment.identification.ptm   
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
 ArrayList<PeptideFragmentIon> FragmentFactory.getFragmentIons(Peptide peptide)
          This method returns the theoretic fragment ions expected from a peptide sequence
 

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

Methods in com.compomics.util.experiment.identification that return types with arguments of type PeptideFragmentIon
 HashMap<Integer,ArrayList<PeptideFragmentIon>> SpectrumAnnotator.getExpectedIons(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, Peptide peptide)
          Returns the expected ions in a map indexed by the possible charges Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.
 

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(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, PeptideFragmentIon fragmentIon, Peptide peptide)
          Returns a boolean indicating whether the neutral loss should be accounted for
 boolean SpectrumAnnotator.lossesValidated(NeutralLossesMap 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.experiment.identification.ptm
 

Methods in com.compomics.util.experiment.identification.ptm that return types with arguments of type PeptideFragmentIon
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> PTMLocationScores.getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Returns the ptm plot series in the jfreechart format for one psm.
 

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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