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

Packages that use PeptideFragmentIon.PeptideFragmentIonType
com.compomics.util.experiment.biology.ions This package contains experiment classes related to ions. 
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
 

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

Methods in com.compomics.util.experiment.biology.ions that return PeptideFragmentIon.PeptideFragmentIonType
static PeptideFragmentIon.PeptideFragmentIonType PeptideFragmentIon.getImmoniumIon(String aminoAcidResidue)
          Converts a given amino acid residue to the given immonium ion.
 PeptideFragmentIon.PeptideFragmentIonType PeptideFragmentIon.getType()
          Getter for the ion type
static PeptideFragmentIon.PeptideFragmentIonType PeptideFragmentIon.PeptideFragmentIonType.valueOf(String name)
          Returns the enum constant of this type with the specified name.
static PeptideFragmentIon.PeptideFragmentIonType[] PeptideFragmentIon.PeptideFragmentIonType.values()
          Returns an array containing the constants of this enum type, in the order they are declared.
 

Constructors in com.compomics.util.experiment.biology.ions with parameters of type PeptideFragmentIon.PeptideFragmentIonType
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, double mass)
          Construction for a peptide fragment.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, int number, double mass)
          Construction for a peptide fragment.
 

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

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

Method parameters in com.compomics.util.gui.spectrum with type arguments of type PeptideFragmentIon.PeptideFragmentIonType
static Vector<DefaultSpectrumAnnotation> SpectrumPanel.filterAnnotations(Vector<DefaultSpectrumAnnotation> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> fragmentIonTypes, boolean h2oLossSelected, boolean nh3LossSelected, boolean singleChargeSelected, boolean doubleChargeSelected, boolean moreThanTwoChargesSelected)
          Filters the annotations and returns the annotations matching the currently selected types.
 

Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type PeptideFragmentIon.PeptideFragmentIonType
FragmentIonTable(Peptide currentPeptide, ArrayList<SpectrumAnnotator.SpectrumAnnotationMap> 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, SpectrumAnnotator.SpectrumAnnotationMap 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(SpectrumAnnotator.SpectrumAnnotationMap annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, boolean annotateMostIntensePeaks, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates an IntensityHistogram plot
MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<SpectrumAnnotator.SpectrumAnnotationMap> 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<SpectrumAnnotator.SpectrumAnnotationMap> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, int bubbleScale, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers)
          Creates a new MassErrorBubblePlot.
MassErrorPlot(SpectrumAnnotator.SpectrumAnnotationMap annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates a new MassErrorPlot.
 



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