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Packages that use CvTerm | |
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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.matches | This package contains experiment classes releated to matches. |
com.compomics.util.pride | |
com.compomics.util.pride.prideobjects |
Uses of CvTerm in com.compomics.util.experiment.biology |
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Methods in com.compomics.util.experiment.biology that return CvTerm | |
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abstract CvTerm |
Ion.getPrideCvTerm()
Returns the pride cv term adapted to the fragment ion. |
Uses of CvTerm in com.compomics.util.experiment.biology.ions |
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Methods in com.compomics.util.experiment.biology.ions that return CvTerm | |
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CvTerm |
ReporterIon.getPrideCvTerm()
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CvTerm |
PrecursorIon.getPrideCvTerm()
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CvTerm |
PeptideFragmentIon.getPrideCvTerm()
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CvTerm |
ImmoniumIon.getPrideCvTerm()
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CvTerm |
Glycon.getPrideCvTerm()
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CvTerm |
ElementaryIon.getPrideCvTerm()
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Uses of CvTerm in com.compomics.util.experiment.identification.matches |
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Methods in com.compomics.util.experiment.identification.matches that return CvTerm | |
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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()
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 |
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Methods in com.compomics.util.pride that return CvTerm | |
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CvTerm |
PtmToPrideMap.getCVTerm(String ptmName)
Returns the cv term corresponding to the given PTM name. |
static CvTerm |
PtmToPrideMap.getDefaultCVTerm(String ptmName)
Returns the default cvTerm of a modification when it exists. |
Methods in com.compomics.util.pride with parameters of type CvTerm | |
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void |
PtmToPrideMap.putCVTerm(String modName,
CvTerm cvTerm)
Puts a new mapping in the map. |
Uses of CvTerm in com.compomics.util.pride.prideobjects |
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Methods in com.compomics.util.pride.prideobjects that return CvTerm | |
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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 | |
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ArrayList<CvTerm> |
Sample.getCvTerms()
Returns the CV terms. |
ArrayList<CvTerm> |
Protocol.getCvTerms()
Returns the CV terms. |
ArrayList<CvTerm> |
Instrument.getCvTerms()
Returns the CV terms. |
Methods in com.compomics.util.pride.prideobjects with parameters of type CvTerm | |
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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 | |
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void |
Sample.setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms. |
void |
Protocol.setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms. |
void |
Instrument.setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms. |
Constructors in com.compomics.util.pride.prideobjects with parameters of type CvTerm | |
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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 | |
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Instrument(String name,
CvTerm source,
CvTerm detector,
ArrayList<CvTerm> cvTerms)
Create a new Instrument object. |
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Protocol(String name,
ArrayList<CvTerm> cvTerms)
Create a new Protocol object. |
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Sample(String name,
ArrayList<CvTerm> cvTerms)
Create a new Sample object. |
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