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

Packages that use MSnSpectrum
com.compomics.angrypeptide.bijection   
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.angrypeptide.bijection
 

Methods in com.compomics.angrypeptide.bijection with parameters of type MSnSpectrum
 Targets BoringToFun.getTargets(MSnSpectrum spectrum, int precursorCharge)
          Returns the targets corresponding to a given spectrum
 

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
 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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