Uses of Class
com.compomics.util.experiment.identification.NeutralLossesMap

Packages that use NeutralLossesMap
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.experiment.identification.ptm   
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
 

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

Methods in com.compomics.util.experiment.identification that return NeutralLossesMap
static NeutralLossesMap SpectrumAnnotator.getDefaultLosses(Peptide peptide)
          Returns the possible neutral losses expected by default for a given peptide
 

Methods in com.compomics.util.experiment.identification with parameters of type NeutralLossesMap
 ArrayList<IonMatch> SpectrumAnnotator.getCurrentAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges)
          Returns the currently matched ions with the given settings
 HashMap<Integer,ArrayList<PeptideFragmentIon>> SpectrumAnnotator.getExpectedIons(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, Peptide peptide)
          Returns the expected ions in a map indexed by the possible charges Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.
 ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, 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.
 boolean SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, PeptideFragmentIon fragmentIon, Peptide peptide)
          Returns a boolean indicating whether the neutral loss should be accounted for
 boolean SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses, PeptideFragmentIon fragmentIon, Peptide peptide)
          Returns a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map
 ArrayList<IonMatch> SpectrumAnnotator.matchPeak(Peptide peptide, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> iontypes, ArrayList<Integer> charges, int precursorCharge, NeutralLossesMap neutralLosses, Peak peak, double massTolerance)
          This method matches the potential fragment ions of a given peptide with a given peak.
 

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

Methods in com.compomics.util.experiment.identification.ptm with parameters of type NeutralLossesMap
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, 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, 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, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
           
 

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

Constructors in com.compomics.util.gui.spectrum with parameters of type NeutralLossesMap
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.
FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges)
          Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
 



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