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. 
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.
 boolean Peptide.sameModificationsAs(Peptide anotherPeptide)
          Indicates whether another peptide has the same modifications at the same localization as this peptide.
 

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

Methods in com.compomics.util.experiment.identification that return Peptide
 Peptide SpectrumAnnotator.getCurrentlyLoadedPeptide()
          Returns the currently inspected peptide
 Peptide PeptideAssumption.getPeptide()
          get the theoretic peptide
 

Methods in com.compomics.util.experiment.identification with parameters of type Peptide
static HashMap<NeutralLoss,Integer> SpectrumAnnotator.getDefaultLosses(Peptide peptide)
          Returns the possible neutral losses expected by default for a given peptide.
static HashMap<NeutralLoss,Integer> SpectrumAnnotator.getDefaultLosses(Peptide peptide, ArrayList<NeutralLoss> imposedNeutralLosses)
          Returns the neutral losses map by default for a given peptide and a given list of neutral losses.
 ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, HashMap<NeutralLoss,Integer> neutralLosses, ArrayList<Integer> charges, 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(HashMap<NeutralLoss,Integer> neutralLosses, NeutralLoss neutralLoss, PeptideFragmentIon fragmentIon, Peptide peptide)
          Returns a boolean indicating whether the neutral loss should be accounted for
 boolean SpectrumAnnotator.lossesValidated(HashMap<NeutralLoss,Integer> 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, HashMap<NeutralLoss,Integer> neutralLosses, Peak peak, double massTolerance)
          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, String spectrumMatchKey)
          Constructor for the peptide match
ProteinMatch(Peptide peptide)
          Constructor for the protein 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<ArrayList<IonMatch>> 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, ArrayList<IonMatch> 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.
 



Copyright © 2011. All Rights Reserved.