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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.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.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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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. |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
int number,
double mass,
ArrayList<NeutralLoss> neutralLosses)
Construction for a peptide fragment with neutral loss. |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
String residue,
double mass)
Construction for a peptide fragment. |
Uses of PeptideFragmentIon.PeptideFragmentIonType in com.compomics.util.experiment.identification |
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Method parameters in com.compomics.util.experiment.identification with type arguments of type PeptideFragmentIon.PeptideFragmentIonType | |
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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,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges. |
ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance)
Returns the spectrum annotations of a spectrum in a list of IonMatches. |
ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
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.experiment.identification.ptm |
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Methods in com.compomics.util.experiment.identification.ptm that return types with arguments of type PeptideFragmentIon.PeptideFragmentIonType | |
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HashMap<Integer,HashMap<PeptideFragmentIon.PeptideFragmentIonType,HashMap<Integer,ArrayList<Double>>>> |
PtmtableContent.getMap()
Get the map. |
Methods in com.compomics.util.experiment.identification.ptm with parameters of type PeptideFragmentIon.PeptideFragmentIonType | |
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void |
PtmtableContent.addIntensity(int nMod,
PeptideFragmentIon.PeptideFragmentIonType peptideFragmentIonType,
int aa,
double intensity)
Add intensity. |
int[] |
PtmtableContent.getHistogram(int nMod,
PeptideFragmentIon.PeptideFragmentIonType peptideFragmentIonType,
int aa,
int bins)
Get histogram. |
ArrayList<Double> |
PtmtableContent.getIntensities(int nMod,
PeptideFragmentIon.PeptideFragmentIonType peptideFragmentIonType,
int aa)
Get intensity. |
Double |
PtmtableContent.getQuantile(int nMod,
PeptideFragmentIon.PeptideFragmentIonType peptideFragmentIonType,
int aa,
double quantile)
Get the quantile. |
Method parameters in com.compomics.util.experiment.identification.ptm with type arguments of type PeptideFragmentIon.PeptideFragmentIonType | |
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static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location. |
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. |
static PtmtableContent |
PTMLocationScores.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content. |
Uses of PeptideFragmentIon.PeptideFragmentIonType in com.compomics.util.gui.spectrum |
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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,
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 | |
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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. |
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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. |
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IntensityHistogram(ArrayList<IonMatch> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
MSnSpectrum currentSpectrum,
double intensityLevel,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates an IntensityHistogram plot |
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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. |
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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. |
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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. |
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MassErrorPlot(ArrayList<IonMatch> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates a new MassErrorPlot. |
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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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