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

Packages that use ProtocolApplication

Package	Description
ambit2.base.data	Base data structures; no chemistry.
ambit2.base.data.study	Detailed description of experimental data, linked to substances
ambit2.base.exceptions
ambit2.core.io	Input output support.
ambit2.core.io.json
ambit2.core.io.study
ambit2.db.substance.processor
ambit2.db.substance.study
ambit2.db.substance.study.facet
ambit2.rest.substance

Uses of ProtocolApplication in ambit2.base.data

Fields in ambit2.base.data with type parameters of type ProtocolApplication

Modifier and Type	Field and Description
protected List<ProtocolApplication>	SubstanceRecord.measurements

Methods in ambit2.base.data that return types with arguments of type ProtocolApplication

Modifier and Type	Method and Description
List<ProtocolApplication>	SubstanceRecord.getMeasurements()

Methods in ambit2.base.data with parameters of type ProtocolApplication

Modifier and Type	Method and Description
void	SubstanceRecord.addMeasurement(ProtocolApplication measurement)

Method parameters in ambit2.base.data with type arguments of type ProtocolApplication

Modifier and Type	Method and Description
void	SubstanceRecord.setMeasurements(List<ProtocolApplication> measurements)

Uses of ProtocolApplication in ambit2.base.data.study

Subclasses of ProtocolApplication in ambit2.base.data.study

Modifier and Type	Class and Description
class	ProtocolApplicationAnnotated<PROTOCOL,PARAMS,ENDPOINT,CONDITIONS,UNIT>

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

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

Uses of ProtocolApplication in ambit2.base.exceptions

Fields in ambit2.base.exceptions declared as ProtocolApplication

Modifier and Type	Field and Description
protected ProtocolApplication	NoDocumentUUIDException.papp

Methods in ambit2.base.exceptions that return ProtocolApplication

Modifier and Type	Method and Description
ProtocolApplication	NoDocumentUUIDException.getPapp()

Constructors in ambit2.base.exceptions with parameters of type ProtocolApplication

Constructor and Description
NoDocumentUUIDException(ProtocolApplication papp)

Uses of ProtocolApplication in ambit2.core.io

Methods in ambit2.core.io that return ProtocolApplication

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 ProtocolApplication

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

Uses of ProtocolApplication in ambit2.core.io.json

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

Modifier and Type	Method and Description
ProtocolApplication	SubstanceStudyParser.parseProtocolApplication(com.fasterxml.jackson.databind.node.ObjectNode node)

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

Modifier and Type	Method and Description
List<ProtocolApplication>	SubstanceStudyParser.parseProtocolApplication(Reader reader, SubstanceRecord record)
List<ProtocolApplication>	SubstanceStudyParser.parseProtocolApplications(com.fasterxml.jackson.databind.JsonNode papps, SubstanceRecord record)

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

Modifier and Type	Method and Description
protected void	SubstanceStudyParser.generateDocumentUUID(ProtocolApplication papp)
protected void	SubstanceStudyParser.parseCompany(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	SubstanceStudyParser.parseInterpretation(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	SubstanceStudyParser.parseInterpretationCriteria(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	SubstanceStudyParser.parseInterpretedResult(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	SubstanceStudyParser.parseOwner(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
protected void	SubstanceStudyParser.parseReliability(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
protected void	SubstanceStudyParser.parseStudyReference(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
protected void	SubstanceStudyParser.parseSubstance(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)

Uses of ProtocolApplication in ambit2.core.io.study

Methods in ambit2.core.io.study with parameters of type ProtocolApplication

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

Uses of ProtocolApplication in ambit2.db.substance.processor

Methods in ambit2.db.substance.processor with parameters of type ProtocolApplication

Modifier and Type	Method and Description
protected UpdateEffectRecords	DBBundleStudyWriter.createEffectRecordUpdateQuery(ProtocolApplication papp, EffectRecord effect)
protected UpdateEffectRecords	DBSubstanceWriter.createEffectRecordUpdateQuery(ProtocolApplication papp, EffectRecord effect)
protected UpdateSubstanceStudy	DBBundleStudyWriter.createSubstanceStudyUpdateQuery(ProtocolApplication papp)
protected UpdateSubstanceStudy	DBSubstanceWriter.createSubstanceStudyUpdateQuery(ProtocolApplication papp)

Uses of ProtocolApplication in ambit2.db.substance.study

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

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

Fields in ambit2.db.substance.study declared as ProtocolApplication

Modifier and Type	Field and Description
protected PA	ReadSubstanceStudy.record

Fields in ambit2.db.substance.study with type parameters of type ProtocolApplication

Modifier and Type	Field and Description
protected List<ProtocolApplication>	ReadSubstanceStudyFlat.measurements

Methods in ambit2.db.substance.study that return types with arguments of type ProtocolApplication

Modifier and Type	Method and Description
List<ProtocolApplication>	ReadSubstanceStudyFlat.getObject(ResultSet rs) protected ProtocolApplication record;
List<ProtocolApplication>	ReadSubstanceStudyFlat.getRecord()
List<ProtocolApplication>	ReadSubstanceStudyFlat.getValue()

Methods in ambit2.db.substance.study with parameters of type ProtocolApplication

Modifier and Type	Method and Description
double	ReadSubstanceStudy.calculateMetric(ProtocolApplication object)

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

Modifier and Type	Method and Description
double	ReadSubstanceStudyFlat.calculateMetric(List<ProtocolApplication> object)
protected void	SubstanceStudyDetailsProcessor.configureQuery(SubstanceRecord target, net.idea.modbcum.i.IParameterizedQuery<SubstanceRecord,List<ProtocolApplication>,net.idea.modbcum.i.IQueryCondition> query)
protected SubstanceRecord	SubstanceStudyDetailsProcessor.processDetail(SubstanceRecord target, List<ProtocolApplication> measurements)
void	ReadSubstanceStudyFlat.setRecord(List<ProtocolApplication> record)
void	ReadSubstanceStudyFlat.setValue(List<ProtocolApplication> value)

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

Constructor and Description
DeleteEffectRecords(ProtocolApplication<Protocol,Params,String,Params,String> papp)
SubstanceStudyFlatQuery(ProtocolApplication papp)
SubstanceStudyFlatQuery(ProtocolApplication papp, SubstanceStudyFlatQuery._QUERY_TYPE qtype)
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)

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

Constructor and Description
SubstanceStudyDetailsProcessor(net.idea.modbcum.i.IQueryRetrieval<List<ProtocolApplication>> query)

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

Methods in ambit2.db.substance.study.facet with parameters of type ProtocolApplication

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

Uses of ProtocolApplication in ambit2.rest.substance

Method parameters in ambit2.rest.substance with type arguments of type ProtocolApplication

Modifier and Type	Method and Description
protected void	SubstanceRecordStaxWriter.writeMeasurementgroups(String substanceURI, List<ProtocolApplication> measurements) 2015-06-13-05:00 ...