Uses of Class
com.compomics.util.experiment.biology.Peptide

Packages that use Peptide
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.experiment.identification.matches This package contains experiment classes releated to matches. e.g., pepties, proteins, modifications and spectra. 
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
 

Uses of Peptide in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology with parameters of type Peptide
 ArrayList<PeptideFragmentIon> FragmentFactory.getFragmentIons(Peptide peptide)
          This method returns the theoretic fragment ions expected from a peptide sequence.
 boolean Peptide.isSameAs(Peptide anOtherPeptide)
          a method which compares to peptides.
 

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

Methods in com.compomics.util.experiment.identification that return Peptide
 Peptide PeptideAssumption.getPeptide()
          get the theoretic peptide
 

Methods in com.compomics.util.experiment.identification with parameters of type Peptide
 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
 Vector<DefaultSpectrumAnnotation> SpectrumAnnotator.getSpectrumAnnotations(Peptide peptide, MSnSpectrum spectrum, double massTolerance, double intensityLimit)
          Annotates a spectrum and returns the annotations as a vector of DefaultSpectrumAnnotation that can be added to a SpectrumPanel.
 ArrayList<IonMatch> SpectrumAnnotator.matchPeak(Peptide peptide, Peak peak, double massTolerance, Charge charge)
          This method matches the potential fragment ions of a given peptide with a given peak.
 

Constructors in com.compomics.util.experiment.identification with parameters of type Peptide
PeptideAssumption(Peptide aPeptide, int rank, int advocate, double measuredMass, double eValue, String identificationFile)
          Constructor for a peptide assumption
 

Uses of Peptide in com.compomics.util.experiment.identification.matches
 

Methods in com.compomics.util.experiment.identification.matches that return Peptide
 Peptide PeptideMatch.getTheoreticPeptide()
          getter for the theoretic peptide
 

Methods in com.compomics.util.experiment.identification.matches with parameters of type Peptide
static String ProteinMatch.getProteinMatchKey(Peptide peptide)
          Convenience method which returns the protein key of a peptide
 void PeptideMatch.setTheoreticPeptide(Peptide theoreticPeptide)
          setter for the theoretic peptide
 

Constructors in com.compomics.util.experiment.identification.matches with parameters of type Peptide
PeptideMatch(Peptide peptide)
          Constructor for the peptide match
PeptideMatch(Peptide peptide, SpectrumMatch spectrumMatch)
          Constructor for the peptide match
 

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

Constructors in com.compomics.util.gui.spectrum with parameters of type Peptide
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.
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.
 



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