Uses of Class
com.compomics.util.pride.CvTerm

Packages that use CvTerm

Package	Description
com.compomics.util.experiment.biology.enzymes	Classes related to enzymes.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.biology.ions.impl	Ion implementations.
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.pride	Objects related to mapping to PRIDE.
com.compomics.util.pride.prideobjects	Objects related to mapping experiment annotation to PRIDE.

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()

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

Modifier	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 instead

Methods 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

Modifier	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

Modifier	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.