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

Packages that use CvTerm
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. e.g., pepties, proteins, modifications and spectra. 
com.compomics.util.pride   
com.compomics.util.pride.prideobjects   
 

Uses of CvTerm in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology that return CvTerm
abstract  CvTerm Ion.getPrideCvTerm()
          Returns the pride cv term adapted to the fragment ion. null if none corresponding.
 

Uses of CvTerm in com.compomics.util.experiment.biology.ions
 

Methods in com.compomics.util.experiment.biology.ions that return CvTerm
 CvTerm ReporterIon.getPrideCvTerm()
           
 CvTerm PrecursorIon.getPrideCvTerm()
           
 CvTerm PeptideFragmentIon.getPrideCvTerm()
           
 CvTerm ImmoniumIon.getPrideCvTerm()
           
 CvTerm Glycon.getPrideCvTerm()
           
 CvTerm ElementaryIon.getPrideCvTerm()
           
 

Uses of CvTerm in com.compomics.util.experiment.identification.matches
 

Methods in com.compomics.util.experiment.identification.matches that return CvTerm
 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
 

Methods in com.compomics.util.pride that return CvTerm
 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
 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
 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
 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
 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
 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
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
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.
 



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