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Packages that use PeptideFragmentIon.PeptideFragmentIonType | |
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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 |
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Methods in com.compomics.util.experiment.biology.ions that return PeptideFragmentIon.PeptideFragmentIonType | |
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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 | |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
double mass)
Construction for a peptide fragment. |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
int number,
double mass)
Construction for a peptide fragment. |
Uses of PeptideFragmentIon.PeptideFragmentIonType in com.compomics.util.gui.spectrum |
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Methods in com.compomics.util.gui.spectrum with parameters of type PeptideFragmentIon.PeptideFragmentIonType | |
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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 | |
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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 | |
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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. |
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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. |
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IntensityHistogram(SpectrumAnnotator.SpectrumAnnotationMap annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
MSnSpectrum currentSpectrum,
boolean annotateMostIntensePeaks,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates an IntensityHistogram plot |
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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. |
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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. |
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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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