Uses of Class
com.compomics.util.pride.CvTerm
Package | Description |
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com.compomics.util.experiment.biology.enzymes |
Classes related to enzymes.
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com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
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com.compomics.util.experiment.biology.ions.impl |
Ion implementations.
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com.compomics.util.experiment.biology.modifications | |
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.pride |
Objects related to mapping to PRIDE.
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com.compomics.util.pride.prideobjects |
Objects related to mapping experiment annotation to PRIDE.
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Uses of CvTerm in com.compomics.util.experiment.biology.enzymes
Methods in com.compomics.util.experiment.biology.enzymes that return CvTerm Modifier and Type Method Description CvTerm
Enzyme. getCvTerm()
Returns the CV term associated with this enzyme.Methods in com.compomics.util.experiment.biology.enzymes with parameters of type CvTerm Modifier and Type Method Description void
Enzyme. setCvTerm(CvTerm cvTerm)
Sets the CV term associated with this enzyme. -
Uses of CvTerm in com.compomics.util.experiment.biology.ions
Methods in com.compomics.util.experiment.biology.ions that return CvTerm Modifier and Type Method Description abstract CvTerm
Ion. getPrideCvTerm()
Returns the CV term adapted to the fragment ion.abstract CvTerm
Ion. getPsiMsCvTerm()
Returns the CV term adapted to the fragment ion.CvTerm
NeutralLoss. getPsiMsCvTerm()
Returns the CV term for the neutral loss. -
Uses of CvTerm in com.compomics.util.experiment.biology.ions.impl
Methods in com.compomics.util.experiment.biology.ions.impl that return CvTerm Modifier and Type Method Description CvTerm
ElementaryIon. getPrideCvTerm()
CvTerm
Glycan. getPrideCvTerm()
CvTerm
ImmoniumIon. getPrideCvTerm()
CvTerm
PeptideFragmentIon. getPrideCvTerm()
CvTerm
PrecursorIon. getPrideCvTerm()
CvTerm
RelatedIon. getPrideCvTerm()
CvTerm
ReporterIon. getPrideCvTerm()
CvTerm
TagFragmentIon. getPrideCvTerm()
CvTerm
ElementaryIon. getPsiMsCvTerm()
CvTerm
Glycan. getPsiMsCvTerm()
CvTerm
ImmoniumIon. getPsiMsCvTerm()
CvTerm
PeptideFragmentIon. getPsiMsCvTerm()
CvTerm
PrecursorIon. getPsiMsCvTerm()
CvTerm
RelatedIon. getPsiMsCvTerm()
CvTerm
ReporterIon. getPsiMsCvTerm()
CvTerm
TagFragmentIon. getPsiMsCvTerm()
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Uses of CvTerm in com.compomics.util.experiment.biology.modifications
Methods in com.compomics.util.experiment.biology.modifications that return CvTerm Modifier and Type Method Description CvTerm
Modification. getPsiModCvTerm()
Returns the PSI-MOD CV term associated with this modification.CvTerm
Modification. getUnimodCvTerm()
Returns the Unimod CV term associated with this modification.Methods in com.compomics.util.experiment.biology.modifications with parameters of type CvTerm Modifier and Type Method Description void
Modification. setPsiModCvTerm(CvTerm cvTerm)
Set the PSI-MOD CV term associated with this modification.void
Modification. setUnimodCvTerm(CvTerm cvTerm)
Set the Unimod CV term associated with this modification.Constructors in com.compomics.util.experiment.biology.modifications with parameters of type CvTerm Constructor Description Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, CvTerm unimodCvTerm, CvTerm psiModCvTerm, ModificationCategory category)
Constructor for a reference modification. -
Uses of CvTerm in com.compomics.util.experiment.identification.matches
Methods in com.compomics.util.experiment.identification.matches that return CvTerm Modifier and Type Method Description CvTerm
IonMatch. getChargePrideCvTerm()
Returns the pride CV term for the ion match charge.CvTerm
IonMatch. getIntensityPrideCvTerm()
Returns the pride CV term for the ion match intensity.CvTerm
IonMatch. getIonMassErrorPrideCvTerm(int minIsotope, int maxIsotope)
Returns the pride CV term for the ion match error.CvTerm
IonMatch. getMZPrideCvTerm()
Returns the pride CV term for the ion match m/z. -
Uses of CvTerm in com.compomics.util.pride
Methods in com.compomics.util.pride that return CvTerm Modifier and Type Method Description CvTerm
PtmToPrideMap. getCVTerm(String ptmName)
Returns the CV term corresponding to the given PTM name.static CvTerm
PtmToPrideMap. getDefaultCVTerm(String ptmName)
Deprecated.use the getCvTerm method for the PTM insteadMethods in com.compomics.util.pride with parameters of type CvTerm Modifier and Type Method Description void
PtmToPrideMap. putCVTerm(String modName, CvTerm cvTerm)
Puts a new mapping in the map. -
Uses of CvTerm in com.compomics.util.pride.prideobjects
Methods in com.compomics.util.pride.prideobjects that return CvTerm Modifier and Type Method Description CvTerm
Instrument. getDetector()
Returns the instrument detector.CvTerm
Instrument. getSource()
Returns the instrument source.Methods in com.compomics.util.pride.prideobjects that return types with arguments of type CvTerm Modifier and Type Method Description ArrayList<CvTerm>
Instrument. getCvTerms()
Returns the CV terms.ArrayList<CvTerm>
Protocol. getCvTerms()
Returns the CV terms.ArrayList<CvTerm>
Sample. getCvTerms()
Returns the CV terms.Methods in com.compomics.util.pride.prideobjects with parameters of type CvTerm Modifier and Type Method Description void
Instrument. setDetector(CvTerm detector)
Set the instrument detector.void
Instrument. setSource(CvTerm source)
Set the instrument source.Method parameters in com.compomics.util.pride.prideobjects with type arguments of type CvTerm Modifier and Type Method Description void
Instrument. setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms.void
Protocol. setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms.void
Sample. setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms.Constructors in com.compomics.util.pride.prideobjects with parameters of type CvTerm Constructor Description Instrument(String name, CvTerm source, CvTerm detector, ArrayList<CvTerm> cvTerms)
Create a new Instrument object.Constructor parameters in com.compomics.util.pride.prideobjects with type arguments of type CvTerm Constructor Description Instrument(String name, CvTerm source, CvTerm detector, ArrayList<CvTerm> cvTerms)
Create a new Instrument object.Protocol(String name, ArrayList<CvTerm> cvTerms)
Create a new Protocol object.Sample(String name, ArrayList<CvTerm> cvTerms)
Create a new Sample object.