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Packages that use IonMatch | |
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com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.quantification.reporterion.quantification | This package contains experiment classes related to quantification by reporter ions. |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of IonMatch in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return types with arguments of type IonMatch | |
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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. |
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. |
Method parameters in com.compomics.util.experiment.identification with type arguments of type IonMatch | |
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static Vector<DefaultSpectrumAnnotation> |
SpectrumAnnotator.getSpectrumAnnotation(ArrayList<IonMatch> ionMatches)
Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel. |
Uses of IonMatch 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 IonMatch | |
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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 IonMatch in com.compomics.util.experiment.quantification.reporterion.quantification |
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Methods in com.compomics.util.experiment.quantification.reporterion.quantification that return types with arguments of type IonMatch | |
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HashMap<Integer,IonMatch> |
PsmQuantification.getReporterMatches()
Getter for the reporter matches |
Methods in com.compomics.util.experiment.quantification.reporterion.quantification with parameters of type IonMatch | |
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void |
PsmQuantification.addIonMatch(int reporterIndex,
IonMatch match)
Method to add a match between a peak and a reporter ion |
Uses of IonMatch in com.compomics.util.gui.spectrum |
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Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type IonMatch | |
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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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SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
HashMap<String,Color> aModificationColors,
HashMap<String,String> aModificationNames)
Creates a new SequenceFragmentationPanel. |
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