Uses of Class
ambit2.base.data.study.Protocol

Packages that use Protocol

Package	Description
ambit2.base.data.study	Detailed description of experimental data, linked to substances
ambit2.core.io	Input output support.
ambit2.core.io.json
ambit2.core.io.study
ambit2.db.substance.study
ambit2.db.substance.study.facet

Uses of Protocol in ambit2.base.data.study

Fields in ambit2.base.data.study declared as Protocol

Modifier and Type	Field and Description
protected Protocol	ProtocolEffectRecord.protocol

Methods in ambit2.base.data.study that return Protocol

Modifier and Type	Method and Description
Protocol	ProtocolEffectRecord.getProtocol()
Protocol	Protocol._categories.getProtocol(String guide)

Methods in ambit2.base.data.study with parameters of type Protocol

Modifier and Type	Method and Description
void	ProtocolEffectRecord.setProtocol(Protocol protocol)

Method parameters in ambit2.base.data.study with type arguments of type Protocol

Modifier and Type	Method and Description
IStructureRecord	StructureRecordValidator.validate(SubstanceRecord record, ProtocolApplication<Protocol,IParams,String,IParams,String> papp)

Uses of Protocol in ambit2.core.io

Methods in ambit2.core.io that return types with arguments of type Protocol

Modifier and Type	Method and Description
protected ProtocolApplication<Protocol,IParams,String,IParams,String>	StringArrayHeader.getExperiment(CATEGORIES categories, SubstanceRecord record, Protocol protocol, ReliabilityParams reliability)

Methods in ambit2.core.io with parameters of type Protocol

Modifier and Type	Method and Description
protected ProtocolApplication<Protocol,IParams,String,IParams,String>	StringArrayHeader.getExperiment(CATEGORIES categories, SubstanceRecord record, Protocol protocol, ReliabilityParams reliability)

Method parameters in ambit2.core.io with type arguments of type Protocol

Modifier and Type	Method and Description
protected void	StringArrayHeader.setCitation(ProtocolApplication<Protocol,IParams,String,IParams,String> experiment)

Uses of Protocol in ambit2.core.io.json

Methods in ambit2.core.io.json that return Protocol

Modifier and Type	Method and Description
Protocol	SubstanceStudyParser.parseProtocol(com.fasterxml.jackson.databind.node.ObjectNode node)

Methods in ambit2.core.io.json with parameters of type Protocol

Modifier and Type	Method and Description
protected EffectRecord	SubstanceStudyParser.createEffectRecord(Protocol protocol)
List<EffectRecord>	SubstanceStudyParser.parseEffects(com.fasterxml.jackson.databind.node.ArrayNode node, Protocol protocol)
List<ValueAnnotated>	SubstanceStudyParser.parseValuesAnnotated(com.fasterxml.jackson.databind.node.ArrayNode node, Protocol protocol)

Uses of Protocol in ambit2.core.io.study

Method parameters in ambit2.core.io.study with type arguments of type Protocol

Modifier and Type	Method and Description
int	StudyFormatter.format(ProtocolApplication<Protocol,String,String,Object,String> pa, IStudyPrinter printer)

Uses of Protocol in ambit2.db.substance.study

Classes in ambit2.db.substance.study with type parameters of type Protocol

Modifier and Type	Class and Description
class	ReadSubstanceStudy<PA extends ProtocolApplication<Protocol,String,String,IParams,String>>

Constructors in ambit2.db.substance.study with parameters of type Protocol

Constructor and Description
SubstanceStudyFlatQuery(Protocol papp)
SubstanceStudyFlatQuery(Protocol papp, int[] idchemicals)
SubstanceStudyFlatQuery(Protocol papp, String[] search_query)
SubstanceStudyFlatQuery(SubstanceStudyFlatQuery._QUERY_TYPE querytype, Protocol papp, String[] search_query)

Constructor parameters in ambit2.db.substance.study with type arguments of type Protocol

Constructor and Description
DeleteEffectRecords(ProtocolApplication<Protocol,Params,String,Params,String> papp)
UpdateEffectRecords(String substanceUUID, ProtocolApplication<Protocol,Params,String,Params,String> papp, EffectRecord effect)
UpdateEffectRecordsBundle(SubstanceEndpointsBundle bundle, String substanceUUID, ProtocolApplication<Protocol,Params,String,Params,String> papp, EffectRecord effect)
UpdateSubstanceStudy(String substanceuuid, ProtocolApplication<Protocol,IParams,String,IParams,String> papp)
UpdateSubstanceStudyBundle(SubstanceEndpointsBundle bundle, String substanceuuid, ProtocolApplication<Protocol,IParams,String,IParams,String> papp)

Uses of Protocol in ambit2.db.substance.study.facet

Method parameters in ambit2.db.substance.study.facet with type arguments of type Protocol

Modifier and Type	Method and Description
protected void	FacetAnnotator.annotate(ProtocolApplication<Protocol,IParams,String,IParams,String> papp)