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.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.PeptideFragmentIonType in com.compomics.util.experiment.biology.ions
 

Methods in com.compomics.util.experiment.biology.ions that return PeptideFragmentIon.PeptideFragmentIonType
 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.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, int number, double mass, ArrayList<NeutralLoss> neutralLosses)
          Construction for a peptide fragment with neutral loss.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, String residue, double mass)
          Construction for a peptide fragment.
 

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

Method parameters in com.compomics.util.experiment.identification with type arguments of type PeptideFragmentIon.PeptideFragmentIonType
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, double mzTolerance)
          Returns the A-score for the best PTM location.
 ArrayList<IonMatch> SpectrumAnnotator.getCurrentAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges)
          Returns the currently matched ions with the given settings
 HashMap<Integer,ArrayList<PeptideFragmentIon>> SpectrumAnnotator.getExpectedIons(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, Peptide peptide, int precursorCharge)
          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.
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> PTMLocationScores.getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, double mzTolerance, double intensityLimit)
          Returns the ptm plot series in the jfreechert format for one psm.
 ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap 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, NeutralLossesMap neutralLosses, Peak peak, double massTolerance)
          This method matches the potential fragment ions of a given peptide with a given peak.
 

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

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, ArrayList<NeutralLoss> neutralLosses, 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<ArrayList<IonMatch>> allAnnotations, ArrayList<MSnSpectrum> allSpectra, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, NeutralLossesMap neutralLosses, 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, NeutralLossesMap neutralLosses, 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, double intensityLevel, 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.
 



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