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.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 with parameters of type Peptide
 void PTMFactory.checkFixedModifications(ModificationProfile modificationProfile, Peptide peptide)
          Removes the fixed modifications of the peptide and remaps the one searched for according to the ModificationProfile.
 java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile, Peptide peptide, double modificationMass, double massTolerance)
          Returns the expected modifications based on the modification profile, the peptide found and the modification details.
 java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile, Peptide peptide, java.lang.String ptmName)
          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.
 java.util.ArrayList<Ion> IonFactory.getFragmentIons(Peptide peptide)
          This method returns the theoretic ions expected from a peptide.
static java.lang.String Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile, Peptide peptide, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> mainModificationSites, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> secondaryModificationSites, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.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 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.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
static NeutralLossesMap SpectrumAnnotator.getDefaultLosses(Peptide peptide)
          Returns the possible neutral losses expected by default for a given peptide.
 java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>> SpectrumAnnotator.getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, Peptide peptide)
          Returns the expected ions in a map indexed by the possible charges.
 java.util.ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.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 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.
 java.util.ArrayList<IonMatch> SpectrumAnnotator.matchPeak(Peptide peptide, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<java.lang.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 eValue, java.lang.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 java.lang.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, java.lang.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 java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> PTMLocationScores.getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location without accounting for neutral losses.
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> PTMLocationScores.getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location accounting for neutral losses.
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> PTMLocationScores.getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns the A-score for the best PTM location.
static java.util.HashMap<PeptideFragmentIon,java.util.ArrayList<IonMatch>> PTMLocationScores.getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Returns the ptm plot series in the jfreechart format for one psm.
static PtmtableContent PTMLocationScores.getPTMTableContent(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Get the PTM table content.
 

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, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.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, java.util.ArrayList<IonMatch> annotations, int aForwardIon, int aReverseIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags)
          Add reference areas annotating the de novo tags.
 

Constructors in com.compomics.util.gui.spectrum with parameters of type Peptide
FragmentIonTable(Peptide currentPeptide, java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations, java.util.ArrayList<java.lang.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, java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations, java.util.ArrayList<MSnSpectrum> allSpectra, java.util.ArrayList<java.lang.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.
 



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