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Packages that use MSnSpectrum | |
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com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.io.massspectrometry | |
com.compomics.util.experiment.massspectrometry | This package contains experiment classes related to spectra. |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of MSnSpectrum in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification with parameters of type MSnSpectrum | |
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SpectrumAnnotator.SpectrumAnnotationMap |
SpectrumAnnotator.annotateSpectrum(Peptide peptide,
MSnSpectrum spectrum,
double massTolerance,
double intensityLimit)
Annotates a spectrum and returns a map containing the annotations: ion type -> charge -> Ion match |
Vector<DefaultSpectrumAnnotation> |
SpectrumAnnotator.getSpectrumAnnotations(Peptide peptide,
MSnSpectrum spectrum,
double massTolerance,
double intensityLimit)
Annotates a spectrum and returns the annotations as a vector of DefaultSpectrumAnnotation that can be added to a SpectrumPanel. |
Uses of MSnSpectrum in com.compomics.util.experiment.io.massspectrometry |
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Methods in com.compomics.util.experiment.io.massspectrometry that return types with arguments of type MSnSpectrum | |
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ArrayList<MSnSpectrum> |
MgfReader.getSpectra(File aFile)
Reads an mgf file and retrieves a list of spectra. |
Uses of MSnSpectrum in com.compomics.util.experiment.massspectrometry |
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Methods in com.compomics.util.experiment.massspectrometry with parameters of type MSnSpectrum | |
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void |
SpectrumCollection.addSpectrum(MSnSpectrum spectrum)
Adds a spectrum to the collection |
Uses of MSnSpectrum in com.compomics.util.gui.spectrum |
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Constructors in com.compomics.util.gui.spectrum with parameters of type MSnSpectrum | |
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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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MassErrorPlot(SpectrumAnnotator.SpectrumAnnotationMap annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates a new MassErrorPlot. |
Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type MSnSpectrum | |
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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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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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