Uses of Class
com.compomics.util.experiment.identification.matches.IonMatch

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

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

Methods in com.compomics.util.experiment.identification that return IonMatch
 IonMatch PeptideAssumption.getPrecursorMatch(Peak precursorPeak)
          Returns the ion match.
 

Methods in com.compomics.util.experiment.identification that return types with arguments of type IonMatch
 ArrayList<IonMatch> SpectrumAnnotator.getCurrentAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges)
          Returns the currently matched ions with the given settings.
 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.
 ArrayList<IonMatch> SpectrumAnnotator.matchPeak(Peptide peptide, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, NeutralLossesMap neutralLosses, Peak peak)
          This method matches the potential fragment ions of a given peptide with a given peak.
 

Method parameters in com.compomics.util.experiment.identification with type arguments of type IonMatch
static Vector<DefaultSpectrumAnnotation> SpectrumAnnotator.getSpectrumAnnotation(ArrayList<IonMatch> ionMatches)
          Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel.
 

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

Methods in com.compomics.util.experiment.identification.ptm that return types with arguments of type IonMatch
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.
 

Uses of IonMatch in com.compomics.util.experiment.quantification.matches
 

Methods in com.compomics.util.experiment.quantification.matches that return types with arguments of type IonMatch
 HashMap<Integer,IonMatch> PsmQuantification.getReporterMatches()
          Getter for the reporter matches
 

Methods in com.compomics.util.experiment.quantification.matches with parameters of type IonMatch
 void PsmQuantification.addIonMatch(int reporterIndex, IonMatch match)
          Method to add a match between a peak and a reporter ion
 

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

Method parameters in com.compomics.util.gui.spectrum with type arguments of type IonMatch
 void SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aReverseIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags)
          Add reference areas annotating the de novo tags.
 

Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type IonMatch
FragmentIonTable(Peptide currentPeptide, ArrayList<ArrayList<IonMatch>> allAnnotations, ArrayList<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges)
          Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
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.
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
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.
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.
SequenceFragmentationPanel(String aSequence, ArrayList<IonMatch> aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationProfile modificationProfile)
          Deprecated. use the panel with ion selection instead
SequenceFragmentationPanel(String aSequence, ArrayList<IonMatch> aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationProfile modificationProfile, int forwardIon, int rewindIon)
          Creates a new SequenceFragmentationPanel working with B and Y ions.
SequenceFragmentationPanel(String taggedModifiedSequence, ArrayList<IonMatch> aIonMatches, boolean aHighlightModifications, ModificationProfile modificationProfile, int forwardIon, int rewindIon)
          Creates a new SequenceFragmentationPanel working with B and Y ions.
 



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