Uses of Class
ambit2.base.data.SubstanceRecord

Packages that use SubstanceRecord

Package	Description
ambit2.base.data	Base data structures; no chemistry.
ambit2.base.data.study	Detailed description of experimental data, linked to substances
ambit2.base.relation.composition	Classes to describe chemical composition
ambit2.base.ro	Ro did not begin with attempting to rival or supplant any other language whatever, either natural or artificial, nor was it suggested by any of them.
ambit2.core.io	Input output support.
ambit2.core.io.json
ambit2.core.io.study
ambit2.db.substance
ambit2.db.substance.ids
ambit2.db.substance.processor
ambit2.db.substance.properties
ambit2.db.substance.relation
ambit2.db.substance.study
ambit2.db.substance.study.facet
ambit2.db.update.bundle.chemicals
ambit2.db.update.bundle.substance
ambit2.export.isa.json
ambit2.export.isa.v1_0
ambit2.ml.io
ambit2.rest.substance

Uses of SubstanceRecord in ambit2.base.data

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

Modifier and Type	Method and Description
static String	SubstanceRecord.getURI(String ref, SubstanceRecord item)

Uses of SubstanceRecord in ambit2.base.data.study

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

Modifier and Type	Method and Description
protected void	StructureRecordValidator.log(SubstanceRecord record, String msg)
IStructureRecord	StructureRecordValidator.validate(SubstanceRecord record)
IStructureRecord	StructureRecordValidator.validate(SubstanceRecord record, CompositionRelation rel)
IStructureRecord	StructureRecordValidator.validate(SubstanceRecord record, ProtocolApplication<Protocol,IParams,String,IParams,String> papp)

Uses of SubstanceRecord in ambit2.base.relation.composition

Constructors in ambit2.base.relation.composition with parameters of type SubstanceRecord

Constructor and Description
Additive(SubstanceRecord structure1, IStructureRecord structure2, Proportion relation)
CompositionRelation(SubstanceRecord structure1, IStructureRecord structure2, Proportion proportion)
CompositionRelation(SubstanceRecord structure1, IStructureRecord structure2, STRUCTURE_RELATION type, Proportion proportion)
Constituent(SubstanceRecord structure1, IStructureRecord structure2, Proportion relation)
Impurity(SubstanceRecord structure1, IStructureRecord structure2, Proportion relation)

Uses of SubstanceRecord in ambit2.base.ro

Methods in ambit2.base.ro that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	SubstanceRecordAnnotationProcessor.process(SubstanceRecord record)

Methods in ambit2.base.ro with parameters of type SubstanceRecord

Modifier and Type	Method and Description
String[]	SubstanceRecordAnnotationProcessor.annotateSubstance(SubstanceRecord record)
SubstanceRecord	SubstanceRecordAnnotationProcessor.process(SubstanceRecord record)

Uses of SubstanceRecord in ambit2.core.io

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

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

Uses of SubstanceRecord in ambit2.core.io.json

Fields in ambit2.core.io.json declared as SubstanceRecord

Modifier and Type	Field and Description
protected SubstanceRecord	SubstanceStudyParser.record

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

Modifier and Type	Method and Description
SubstanceRecord	SubstanceStudyParser.parseSubstance(com.fasterxml.jackson.databind.JsonNode node)
SubstanceRecord	SubstanceStudyParser.parseSubstance(Reader reader)

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

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)

Uses of SubstanceRecord in ambit2.core.io.study

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

Modifier and Type	Method and Description
static void	ProtocolEffectRecord2SubstanceProperty.addValues(SubstanceRecord master, Property key, Value value, Object oldValue)

Uses of SubstanceRecord in ambit2.db.substance

Classes in ambit2.db.substance with type parameters of type SubstanceRecord

Modifier and Type	Class and Description
class	UpdateSubstance<C extends SubstanceRecord>

Fields in ambit2.db.substance declared as SubstanceRecord

Modifier and Type	Field and Description
protected SubstanceRecord	ReadSubstances.record

Methods in ambit2.db.substance that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	AbstractReadSubstance.getObject(ResultSet rs)
SubstanceRecord	ReadSubstance.getObject(ResultSet rs)
protected abstract SubstanceRecord	AbstractReadSubstance.getRecord()
protected SubstanceRecord	FacetedSearchSubstance.getRecord()
protected SubstanceRecord	ReadByReliabilityFlags.getRecord()
protected SubstanceRecord	ReadSubstance.getRecord()
protected SubstanceRecord	ReadSubstanceByExternalIDentifier.getRecord()
protected SubstanceRecord	ReadSubstanceByName.getRecord()
protected SubstanceRecord	ReadSubstanceByOwner.getRecord()
protected SubstanceRecord	ReadSubstanceByStudy.getRecord()
protected SubstanceRecord	ReadSubstanceByType.getRecord()
protected SubstanceRecord	ReadSubstances.getRecord()

Methods in ambit2.db.substance with parameters of type SubstanceRecord

Modifier and Type	Method and Description
double	AbstractReadSubstance.calculateMetric(SubstanceRecord object)
protected String	ReadSubstance.stringify(SubstanceRecord value)

Constructors in ambit2.db.substance with parameters of type SubstanceRecord

Constructor and Description
CreateSubstance(SubstanceRecord substance)
DeleteSubstance(SubstanceRecord substance)
ReadSubstance(SubstanceRecord record)

Uses of SubstanceRecord in ambit2.db.substance.ids

Classes in ambit2.db.substance.ids with type parameters of type SubstanceRecord

Modifier and Type	Class and Description
class	UpdateSubstanceIdentifiers<C extends SubstanceRecord>

Methods in ambit2.db.substance.ids that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	ReadChemIdentifiersByComposition.processDetail(SubstanceRecord target, IStructureRecord detail)

Methods in ambit2.db.substance.ids with parameters of type SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	ReadChemIdentifiersByComposition.processDetail(SubstanceRecord target, IStructureRecord detail)
void	ReadSubstanceIdentifiers.setFieldname(SubstanceRecord fieldname)

Uses of SubstanceRecord in ambit2.db.substance.processor

Fields in ambit2.db.substance.processor declared as SubstanceRecord

Modifier and Type	Field and Description
protected SubstanceRecord	DBSubstanceWriter.importedRecord

Methods in ambit2.db.substance.processor that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	DBSubstanceWriter.getImportedRecord()

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

Modifier and Type	Method and Description
protected void	DBSubstanceWriter.importBundles(SubstanceRecord substance)
protected void	DBSubstanceWriter.importSubstanceMeasurements(SubstanceRecord substance)
protected void	DBBundleStudyWriter.importSubstanceRecord(SubstanceRecord substance)
protected void	DBSubstanceWriter.importSubstanceRecord(SubstanceRecord substance)
void	DBSubstanceWriter.setImportedRecord(SubstanceRecord importedRecord)

Constructors in ambit2.db.substance.processor with parameters of type SubstanceRecord

Constructor and Description
DBBundleStudyWriter(SubstanceEndpointsBundle bundle, SourceDataset dataset, SubstanceRecord importedRecord)
DBSubstanceWriter(SourceDataset dataset, SubstanceRecord importedRecord, boolean clearMeasurements, boolean clearComposition)
DBSubstanceWriter(SourceDataset dataset, SubstanceRecord importedRecord, boolean clearMeasurements, boolean clearComposition, IStructureKey matchByKey)

Uses of SubstanceRecord in ambit2.db.substance.properties

Methods in ambit2.db.substance.properties that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	ReadChemPropertiesByComposition.processDetail(SubstanceRecord target, IStructureRecord detail) Hack for merging dataset properties with substances; This is not necessarily correct, as the substance may have many components!

Methods in ambit2.db.substance.properties with parameters of type SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	ReadChemPropertiesByComposition.processDetail(SubstanceRecord target, IStructureRecord detail) Hack for merging dataset properties with substances; This is not necessarily correct, as the substance may have many components!

Uses of SubstanceRecord in ambit2.db.substance.relation

Constructors in ambit2.db.substance.relation with parameters of type SubstanceRecord

Constructor and Description
DeleteSubstanceRelation(SubstanceRecord structure1, IStructureRecord structure2, STRUCTURE_RELATION relation)
ReadSubstanceRelation(STRUCTURE_RELATION relation, SubstanceRecord id)
ReadSubstanceRelation(SubstanceRecord structure)

Uses of SubstanceRecord in ambit2.db.substance.study

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

Modifier and Type	Field and Description
protected SubstanceRecord	ReadSubstanceStudyFlat.fieldname
protected SubstanceRecord	ReadEffectRecordBySubstance.record

Methods in ambit2.db.substance.study that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	ReadSubstanceStudyFlat.getFieldname()
protected SubstanceRecord	SubstanceStudyDetailsProcessor.processDetail(SubstanceRecord target, List<ProtocolApplication> measurements)

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

Modifier and Type	Method and Description
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.setFieldname(SubstanceRecord fieldname)

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

Modifier and Type	Method and Description
protected void	SubstanceStudyDetailsProcessor.configureQuery(SubstanceRecord target, net.idea.modbcum.i.IParameterizedQuery<SubstanceRecord,List<ProtocolApplication>,net.idea.modbcum.i.IQueryCondition> query)

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

Constructor and Description
SubstanceStudyFlatQuery(SubstanceRecord record)

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

Fields in ambit2.db.substance.study.facet declared as SubstanceRecord

Modifier and Type	Field and Description
protected SubstanceRecord	SubstanceDataAvailabilityFacet.record

Methods in ambit2.db.substance.study.facet that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	SubstanceDataAvailabilityFacet.getRecord()

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

Modifier and Type	Method and Description
void	SubstanceDataAvailabilityFacet.setRecord(SubstanceRecord record)

Uses of SubstanceRecord in ambit2.db.update.bundle.chemicals

Constructors in ambit2.db.update.bundle.chemicals with parameters of type SubstanceRecord

Constructor and Description
AddAllChemicalsperSubstanceToBundle(SubstanceEndpointsBundle bundle, SubstanceRecord dataset)
AddAllChemicalsperSubstanceToBundle(SubstanceRecord dataset)

Uses of SubstanceRecord in ambit2.db.update.bundle.substance

Methods in ambit2.db.update.bundle.substance that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	ReadSubstanceChemicalsUnionByBundle.getObject(ResultSet rs)
SubstanceRecord	ReadSubstancesByBundle.getObject(ResultSet rs)
protected SubstanceRecord	ReadSubstancesByBundle.getRecord()
protected SubstanceRecord	ReadSubstancesByBundleCompounds.getRecord()
static SubstanceRecord	AddCompoundAsSubstanceToBundle.structure2substance(IStructureRecord compound)

Methods in ambit2.db.update.bundle.substance with parameters of type SubstanceRecord

Modifier and Type	Method and Description
void	AddCompoundAsSubstanceToBundle.setObject(SubstanceRecord object)

Constructors in ambit2.db.update.bundle.substance with parameters of type SubstanceRecord

Constructor and Description
AddCompoundAsSubstanceToBundle(SubstanceEndpointsBundle bundle, SubstanceRecord record)
AddSubstanceToBundle(SubstanceEndpointsBundle bundle, SubstanceRecord dataset)
AddSubstanceToBundle(SubstanceRecord dataset)
DeleteSubstanceFromBundle(SubstanceEndpointsBundle bundle, SubstanceRecord record)
DeleteSubstanceFromBundle(SubstanceRecord record)

Uses of SubstanceRecord in ambit2.export.isa.json

Methods in ambit2.export.isa.json that return types with arguments of type SubstanceRecord

Modifier and Type	Method and Description
Iterator<SubstanceRecord>	ISAJsonExporter.getRecords()

Method parameters in ambit2.export.isa.json with type arguments of type SubstanceRecord

Modifier and Type	Method and Description
void	ISAJsonExporter.setRecords(Iterator<SubstanceRecord> records)

Constructor parameters in ambit2.export.isa.json with type arguments of type SubstanceRecord

Constructor and Description
ISAJsonExporter(ISAConst.ISAVersion isaVersion, Iterator<SubstanceRecord> records, File outputDir, File exportConfig, SubstanceEndpointsBundle endpointBundle)
ISAJsonExporter(Iterator<SubstanceRecord> records, File outputDir, File exportConfig, SubstanceEndpointsBundle endpointBundle)

Uses of SubstanceRecord in ambit2.export.isa.v1_0

Methods in ambit2.export.isa.v1_0 with parameters of type SubstanceRecord

Modifier and Type	Method and Description
Investigation	ISAJsonExporter1_0.process(SubstanceRecord record)

Method parameters in ambit2.export.isa.v1_0 with type arguments of type SubstanceRecord

Modifier and Type	Method and Description
void	ISAJsonExporter1_0.export(SubstanceEndpointsBundle endpointBundle, Iterator<SubstanceRecord> records)

Uses of SubstanceRecord in ambit2.ml.io

Fields in ambit2.ml.io declared as SubstanceRecord

Modifier and Type	Field and Description
protected SubstanceRecord	OutputARFF.item

Methods in ambit2.ml.io that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	OutputARFF.transform(org.apache.commons.csv.CSVRecord record, int columnid)
SubstanceRecord	OutputVW_LDA.transform(org.apache.commons.csv.CSVRecord record, int columnid)

Uses of SubstanceRecord in ambit2.rest.substance

Classes in ambit2.rest.substance with type parameters of type SubstanceRecord

Modifier and Type	Class and Description
class	SubstanceRDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>>
class	SubstanceURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>>

Methods in ambit2.rest.substance that return SubstanceRecord

Modifier and Type	Method and Description
SubstanceRecord	SubstanceRecordStaxWriter.process(SubstanceRecord record)

Methods in ambit2.rest.substance that return types with arguments of type SubstanceRecord

Modifier and Type	Method and Description
protected net.idea.restnet.db.QueryURIReporter<SubstanceRecord,net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>>	SubstanceBundleStAXReporter.createURIReporter(org.restlet.Request req, net.idea.restnet.c.ResourceDoc doc)
protected net.idea.restnet.db.QueryURIReporter<SubstanceRecord,net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>>	SubstanceBundleStAXReporter.createURIReporter(org.restlet.Request req, net.idea.restnet.c.ResourceDoc doc)
protected net.idea.restnet.db.QueryURIReporter<SubstanceRecord,net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>>	SubstanceRDFReporter.createURIReporter(org.restlet.Request req, net.idea.restnet.c.ResourceDoc doc)
protected net.idea.restnet.db.QueryURIReporter<SubstanceRecord,net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>>	SubstanceRDFReporter.createURIReporter(org.restlet.Request req, net.idea.restnet.c.ResourceDoc doc)

Methods in ambit2.rest.substance with parameters of type SubstanceRecord

Modifier and Type	Method and Description
String	SubstanceURIReporter.getURI(String ref, SubstanceRecord item)
SubstanceRecord	SubstanceRecordStaxWriter.process(SubstanceRecord record)
Object	SubstanceBundleStAXReporter.processItem(SubstanceRecord item)
Object	SubstanceRDFReporter.processItem(SubstanceRecord record)

Constructor parameters in ambit2.rest.substance with type arguments of type SubstanceRecord

Constructor and Description
SubstanceRecordStaxWriter(net.idea.restnet.db.QueryURIReporter<SubstanceRecord,net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>> urireporter)
SubstanceRecordStaxWriter(net.idea.restnet.db.QueryURIReporter<SubstanceRecord,net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>> urireporter)