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.biology.ions This package contains experiment classes related to ions. 
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.experiment.identification.ptm   
com.compomics.util.experiment.identification.ptm.ptmscores   
com.compomics.util.experiment.identification.scoring   
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
com.compomics.util.preferences   
 

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

Methods in com.compomics.util.experiment.biology that return Peptide
static Peptide Peptide.getNoModPeptide(Peptide peptide, ArrayList<PTM> ptms)
          Returns a version of the peptide which does not contain the inspected PTMs.
 

Methods in com.compomics.util.experiment.biology with parameters of type Peptide
 void PTMFactory.checkFixedModifications(ModificationProfile modificationProfile, Peptide peptide, ProteinMatch.MatchingType matchingType, Double massTolerance)
          Removes the fixed modifications of the peptide and remaps the one searched for according to the ModificationProfile.
 HashMap<Integer,ArrayList<String>> PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile, Peptide peptide, double modificationMass, double massTolerance, ProteinMatch.MatchingType matchingType)
          Returns the expected modifications based on the modification profile, the peptide found and the modification details.
 HashMap<Integer,ArrayList<String>> PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile, Peptide peptide, String ptmName, ProteinMatch.MatchingType matchingType, Double massTolerance)
          Returns the names of the possibly expected modification based on the name of the expected modification in a map where the PTM names are indexed by their potential site on the sequence.
 ArrayList<Ion> IonFactory.getFragmentIons(Peptide peptide)
          This method returns the theoretic ions expected from a peptide.
static Peptide Peptide.getNoModPeptide(Peptide peptide, ArrayList<PTM> ptms)
          Returns a version of the peptide which does not contain the inspected PTMs.
static String Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile, Peptide peptide, HashMap<Integer,ArrayList<String>> mainModificationSites, HashMap<Integer,ArrayList<String>> secondaryModificationSites, HashMap<Integer,ArrayList<String>> fixedModificationSites, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
          Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
 boolean Peptide.isSameAs(Peptide anotherPeptide)
          A method which compares two peptides.
 boolean Peptide.isSameModificationStatus(Peptide anotherPeptide)
          Indicates whether another peptide has the same variable modifications as this peptide.
 boolean Peptide.isSameSequence(Peptide anotherPeptide)
          Returns a boolean indicating whether another peptide has the same sequence as the given peptide
 boolean Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide)
          Indicates whether another peptide has the same sequence and modification status without accounting for modification localization.
 boolean Peptide.sameModificationsAs(Peptide anotherPeptide)
          Indicates whether another peptide has the same modifications at the same localization as this peptide.
 boolean Peptide.sameModificationsAs(Peptide anotherPeptide, ArrayList<String> ptms)
          Indicates whether another peptide has the same modifications at the same localization as this peptide.
 

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

Constructors in com.compomics.util.experiment.biology.ions with parameters of type Peptide
PrecursorIon(Peptide peptide)
          Constructor.
 

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
 HashMap<Integer,ArrayList<IonMatch>> SpectrumAnnotator.getCoveredAminoAcids(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 ion matches corresponding to fragment ions indexed by amino acid number in the sequence.
static NeutralLossesMap SpectrumAnnotator.getDefaultLosses(Peptide peptide)
          Returns the possible neutral losses expected by default for a given peptide.
 HashMap<Integer,ArrayList<Ion>> SpectrumAnnotator.getExpectedIons(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, Peptide peptide)
          Returns the expected ions in a map indexed by the possible charges.
 ArrayList<String> Identification.getProteinMatches(Peptide peptide)
          Returns the keys of the protein matches where a peptide can be found.
 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.
 boolean SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion, Peptide peptide)
          Returns a boolean indicating whether the neutral loss should be accounted for.
 boolean Identification.isUnique(Peptide peptide)
          Indicates whether a peptide is found in a single protein match.
 boolean SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon, 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, 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.
 void SpectrumAnnotator.setPeptide(Peptide peptide, int precursorCharge)
          Sets a new peptide to match.
 

Constructors in com.compomics.util.experiment.identification with parameters of type Peptide
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score)
          Constructor for a peptide assumption.
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score, 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.experiment.identification.ptm
 

Methods in com.compomics.util.experiment.identification.ptm with parameters of type Peptide
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> PtmtableContent.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.
static PtmtableContent PtmtableContent.getPTMTableContent(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)
          Get the PTM table content.
 

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

Methods in com.compomics.util.experiment.identification.ptm.ptmscores with parameters of type Peptide
static HashMap<ArrayList<Integer>,Double> AScore.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location without accounting for neutral losses.
static HashMap<ArrayList<Integer>,Double> AScore.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location accounting for neutral losses.
static HashMap<ArrayList<Integer>,Double> AScore.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns the A-score for the best PTM location.
static Double MDScore.getMDScore(SpectrumMatch spectrumMatch, Peptide peptideCandidate, ArrayList<String> ptms)
          Returns the MD score for the given peptide in a spectrum match.
static HashMap<Integer,HashMap<Integer,Double>> AScore.getPositionToScoreMap(Peptide peptide, Peptide noModPeptide, ArrayList<Integer> possibleSites, MSnSpectrum spectrum, HashMap<Integer,MSnSpectrum> spectrumMap, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap scoringLossesMap, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, SpectrumAnnotator spectrumAnnotator, PTM refPTM)
          Returns a map PTM localization -> score.
 

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

Methods in com.compomics.util.experiment.identification.scoring with parameters of type Peptide
static double PsmScores.getAScorePeptideScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns a PSM score like the peptide score calculated for the A-score.
 

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

Methods in com.compomics.util.gui.spectrum with parameters of type Peptide
 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, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
 void SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aReverseIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags, double forwardIonPercentHeight, double reverseIonPercentHeight)
          Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
 void SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aReverseIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags, double forwardIonPercentHeight, double reverseIonPercentHeight, boolean excludeFixedPtms)
          Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
 void SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aReverseIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags, double forwardIonPercentHeight, double reverseIonPercentHeight, float forwardIonAlphaLevel, float reverseIonAlphaLevel, boolean excludeFixedPtms)
          Add reference areas annotating the de novo tags.
 

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

Uses of Peptide in com.compomics.util.preferences
 

Methods in com.compomics.util.preferences with parameters of type Peptide
 void AnnotationPreferences.setCurrentSettings(Peptide currentPeptide, int currentPrecursorCharge, boolean newSpectrum)
          Sets the annotation settings for the current peptide and precursor charge.
 boolean IdFilter.validateModifications(Peptide peptide, ProteinMatch.MatchingType matchingType, Double massTolerance)
          Validates the modifications of a peptide.
 boolean IdFilter.validateProteins(Peptide peptide)
          Validates a peptide depending on its protein inference status.
 



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