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Packages that use Peptide | |
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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 |
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Methods in com.compomics.util.experiment.biology with parameters of type Peptide | |
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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 |
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Constructors in com.compomics.util.experiment.biology.ions with parameters of type Peptide | |
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PrecursorIon(Peptide peptide)
Constructor. |
Uses of Peptide in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return Peptide | |
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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 | |
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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 | |
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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 |
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Methods in com.compomics.util.experiment.identification.matches that return Peptide | |
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Peptide |
PeptideMatch.getTheoreticPeptide()
Getter for the theoretic peptide. |
Methods in com.compomics.util.experiment.identification.matches with parameters of type Peptide | |
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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 | |
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PeptideMatch(Peptide peptide)
Constructor for the peptide match. |
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PeptideMatch(Peptide peptide,
java.lang.String spectrumMatchKey)
Constructor for the peptide match. |
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ProteinMatch(Peptide peptide)
Constructor for the protein match. |
Uses of Peptide in com.compomics.util.experiment.identification.ptm |
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Methods in com.compomics.util.experiment.identification.ptm with parameters of type Peptide | |
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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 |
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Methods in com.compomics.util.experiment.identification.scoring with parameters of type Peptide | |
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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 |
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Methods in com.compomics.util.gui.spectrum with parameters of type Peptide | |
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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 | |
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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. |
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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 |
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Methods in com.compomics.util.preferences with parameters of type Peptide | |
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void |
AnnotationPreferences.setCurrentSettings(Peptide currentPeptide,
int currentPrecursorCharge,
boolean newSpectrum)
Sets the annotation settings for the current peptide and precursor charge. |
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