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

Packages that use MSnSpectrum
com.compomics.util.experiment.filters.massspectrometry   
com.compomics.util.experiment.filters.massspectrometry.spectrumfilters   
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.experiment.identification.ptm   
com.compomics.util.experiment.identification.scoring   
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.filters.massspectrometry
 

Methods in com.compomics.util.experiment.filters.massspectrometry with parameters of type MSnSpectrum
abstract  boolean SpectrumFilter.validateSpectrum(MSnSpectrum spectrum)
          Indicates whether a spectrum passed the filter.
 

Uses of MSnSpectrum in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
 

Methods in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters with parameters of type MSnSpectrum
 boolean PeakFilter.validateSpectrum(MSnSpectrum spectrum)
          Indicates whether a peak was found in the spectrum at the desired m/z in the given intensity quartile.
 boolean Or.validateSpectrum(MSnSpectrum spectrum)
          Returns a boolean indicating whether one of the implemented filters validated the spectrum.
 boolean MzFilter.validateSpectrum(MSnSpectrum spectrum)
          Indicates whether a peak was found in the spectrum at the desired m/z in the given intensity quartile.
 boolean FingerprintPattern.validateSpectrum(MSnSpectrum spectrum)
          Returns a boolean indicating whether the filter fingerprint was found in the spectrum.
 boolean CombFilter.validateSpectrum(MSnSpectrum spectrum)
          Returns a boolean indicating whether the filter m/z comb was found in the spectrum.
 boolean And.validateSpectrum(MSnSpectrum spectrum)
          Returns a boolean indicating whether all implemented filters validated the spectrum.
 

Uses of MSnSpectrum in com.compomics.util.experiment.identification
 

Methods in com.compomics.util.experiment.identification with parameters of type MSnSpectrum
 HashMap<Integer,ArrayList<IonMatch>> SpectrumAnnotator.getCoveredAminoAcids(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm)
          Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence.
 ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm)
          Returns the spectrum annotations of a spectrum in a list of IonMatches.
 

Uses of MSnSpectrum in com.compomics.util.experiment.identification.ptm
 

Methods in com.compomics.util.experiment.identification.ptm 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*m/z tolerance indexed by the depth used.
static HashMap<Integer,MSnSpectrum> PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance, int depthMax)
          Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.
 

Methods in com.compomics.util.experiment.identification.ptm with parameters of type MSnSpectrum
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location without accounting for neutral losses.
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location accounting for neutral losses.
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns the A-score for the best PTM location.
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> PTMLocationScores.getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, 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, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Get the PTM table content.
static HashMap<Integer,MSnSpectrum> PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
          Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.
static HashMap<Integer,MSnSpectrum> PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance, int depthMax)
          Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.
 

Uses of MSnSpectrum in com.compomics.util.experiment.identification.scoring
 

Methods in com.compomics.util.experiment.identification.scoring that return types with arguments of type MSnSpectrum
static HashMap<Integer,MSnSpectrum> PsmScores.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.
static HashMap<Integer,MSnSpectrum> PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance, int depthMax)
          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.scoring with parameters of type MSnSpectrum
static double PsmScores.getAScorePeptideScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns a PSM score like the peptide score calculated for the A-score.
static HashMap<Integer,MSnSpectrum> PsmScores.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.
static HashMap<Integer,MSnSpectrum> PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance, int depthMax)
          Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used.
 

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(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile, 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<Integer> currentFragmentIons, MSnSpectrum currentSpectrum, double intensityLevel, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates an IntensityHistogram plot //@TODO improve charge compatibility
MassErrorPlot(ArrayList<IonMatch> annotations, ArrayList<Integer> currentFragmentIons, MSnSpectrum currentSpectrum, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates a new MassErrorPlot.
MassErrorPlot(ArrayList<IonMatch> annotations, ArrayList<Integer> 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<Integer> 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<Integer> 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<Integer> 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<Integer> 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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