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.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 that return types with arguments of type MSnSpectrum
static HashMap<Integer,MSnSpectrum> PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
          Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used.
 

Methods in com.compomics.util.experiment.identification with parameters of type MSnSpectrum
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, 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, double mzTolerance, double intensityLimit)
          Returns the ptm plot series in the jfreechert format for one psm.
static HashMap<Integer,MSnSpectrum> PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
          Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used.
 ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance)
          Returns the spectrum annotations of a spectrum in a list of IonMatches Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.
 

Uses of MSnSpectrum in com.compomics.util.experiment.io.massspectrometry
 

Methods in com.compomics.util.experiment.io.massspectrometry that return MSnSpectrum
static MSnSpectrum MgfReader.getSpectrum(RandomAccessFile randomAccessFile, long index, String fileName)
          Returns the next spectrum starting from the given index
 

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.gui.spectrum
 

Constructors in com.compomics.util.gui.spectrum with parameters of type MSnSpectrum
IntensityHistogram(ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, double intensityLevel, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates an IntensityHistogram plot
MassErrorPlot(ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates a new MassErrorPlot.
MassErrorPlot(ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean useRelativeError)
          Creates a new MassErrorPlot.
 

Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type MSnSpectrum
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.
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.
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.
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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