Uses of Class
uk.ac.ebi.pride.utilities.data.core.Modification

Packages that use Modification

Package	Description
uk.ac.ebi.pride.utilities.data.controller.access
uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl
uk.ac.ebi.pride.utilities.data.core

Uses of Modification in uk.ac.ebi.pride.utilities.data.controller.access

Methods in uk.ac.ebi.pride.utilities.data.controller.access that return types with arguments of type Modification

Modifier and Type	Method and Description
Collection<Modification>	PeptideDataAccess.getPTMs(Comparable proteinId, Comparable peptideId) Get the ptms assigned to a peptide
Collection<Modification>	QuantDataAccess.getQuantPTMs(Comparable proteinId, Comparable peptideId) Get the ptms assigned to a peptide

Uses of Modification in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

Methods in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl that return types with arguments of type Modification

Modifier and Type	Method and Description
List<Modification>	CachedDataAccessController.getPTMs(Comparable proteinId, Comparable peptideId) Get ptms using identification id nad peptide id
List<Modification>	AbstractDataAccessController.getPTMs(Comparable proteinId, Comparable peptideId)
Collection<Modification>	AbstractDataAccessController.getQuantPTMs(Comparable proteinId, Comparable peptideId)

Uses of Modification in uk.ac.ebi.pride.utilities.data.core

Methods in uk.ac.ebi.pride.utilities.data.core that return types with arguments of type Modification

Modifier and Type	Method and Description
List<Modification>	SpectrumIdentification.getModifications()
List<Modification>	PeptideSequence.getModifications()
List<Modification>	Peptide.getModifications()

Method parameters in uk.ac.ebi.pride.utilities.data.core with type arguments of type Modification

Modifier and Type	Method and Description
void	PeptideSequence.setModifications(List<Modification> modifications)

Constructor parameters in uk.ac.ebi.pride.utilities.data.core with type arguments of type Modification

Constructor and Description
PeptideSequence(List<CvParam> cvParams, List<UserParam> userParams, String id, String name, String sequence, List<Modification> modifications)
PeptideSequence(List<CvParam> cvParams, List<UserParam> userParams, String id, String name, String sequence, List<Modification> modifications, List<SubstitutionModification> substitutionModifications)
PeptideSequence(ParamGroup params, String id, String name, String sequence, List<Modification> modifications)
PeptideSequence(ParamGroup params, String id, String name, String sequence, List<Modification> modifications, List<SubstitutionModification> substitutionModifications)
PeptideSequence(String sequence, List<Modification> modifications)
PeptideSequence(String id, String name, String sequence, List<Modification> modifications)
PeptideSequence(String id, String name, String sequence, List<Modification> modifications, List<SubstitutionModification> substitutionModifications)