Uses of Class
com.compomics.util.experiment.massspectrometry.MSnSpectrum

Packages that use MSnSpectrum
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
 

Methods in com.compomics.util.experiment.identification with parameters of type MSnSpectrum
 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
 

Methods in com.compomics.util.experiment.io.massspectrometry that return types with arguments of type MSnSpectrum
 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
 

Methods in com.compomics.util.experiment.massspectrometry with parameters of type MSnSpectrum
 void SpectrumCollection.addSpectrum(MSnSpectrum spectrum)
          Adds a spectrum to the collection
 

Uses of MSnSpectrum in com.compomics.util.gui.spectrum
 

Constructors in com.compomics.util.gui.spectrum with parameters of type MSnSpectrum
IntensityHistogram(SpectrumAnnotator.SpectrumAnnotationMap annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, boolean annotateMostIntensePeaks, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates an IntensityHistogram plot
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
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.
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.
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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