Uses of Class
com.compomics.util.experiment.identification.SpectrumAnnotator.SpectrumAnnotationMap

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

Uses of SpectrumAnnotator.SpectrumAnnotationMap in com.compomics.util.experiment.identification
 

Methods in com.compomics.util.experiment.identification that return SpectrumAnnotator.SpectrumAnnotationMap
 SpectrumAnnotator.SpectrumAnnotationMap SpectrumAnnotator.annotateSpectrum(Peptide peptide, MSnSpectrum spectrum, double massTolerance, double intensityLimit)
          Annotates a spectrum and returns a map containing the annotations: ion type -> charge -> Ion match
 

Methods in com.compomics.util.experiment.identification with parameters of type SpectrumAnnotator.SpectrumAnnotationMap
 Vector<DefaultSpectrumAnnotation> SpectrumAnnotator.getSpectrumAnnotations(SpectrumAnnotator.SpectrumAnnotationMap annotations)
          Annotates a spectrum and returns the annotations as a vector of DefaultSpectrumAnnotation that can be added to a SpectrumPanel.
 

Uses of SpectrumAnnotator.SpectrumAnnotationMap in com.compomics.util.gui.spectrum
 

Constructors in com.compomics.util.gui.spectrum with parameters of type SpectrumAnnotator.SpectrumAnnotationMap
FragmentIonTable(Peptide currentPeptide, SpectrumAnnotator.SpectrumAnnotationMap annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, boolean singleCharge, boolean twoCharges)
          Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
IntensityHistogram(SpectrumAnnotator.SpectrumAnnotationMap annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, boolean annotateMostIntensePeaks, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates an IntensityHistogram plot
MassErrorPlot(SpectrumAnnotator.SpectrumAnnotationMap annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, MSnSpectrum currentSpectrum, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges)
          Creates a new MassErrorPlot.
SequenceFragmentationPanel(String aSequence, SpectrumAnnotator.SpectrumAnnotationMap annotations, boolean boolModifiedSequence)
          Creates a new SequenceFragmentationPanel.
 

Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type SpectrumAnnotator.SpectrumAnnotationMap
FragmentIonTable(Peptide currentPeptide, ArrayList<SpectrumAnnotator.SpectrumAnnotationMap> allAnnotations, ArrayList<MSnSpectrum> allSpectra, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, 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<SpectrumAnnotator.SpectrumAnnotationMap> 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<SpectrumAnnotator.SpectrumAnnotationMap> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, int bubbleScale, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers)
          Creates a new MassErrorBubblePlot.
 



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