Uses of Class
ambit2.base.data.substance.SubstanceEndpointsBundle

Packages that use SubstanceEndpointsBundle

Package	Description
ambit2.base.data	Base data structures; no chemistry.
ambit2.db.reporters
ambit2.db.reporters.xlsx
ambit2.db.substance
ambit2.db.substance.processor
ambit2.db.substance.relation
ambit2.db.substance.study
ambit2.db.update.bundle
ambit2.db.update.bundle.chemicals
ambit2.db.update.bundle.effects
ambit2.db.update.bundle.endpoints
ambit2.db.update.bundle.matrix
ambit2.db.update.bundle.substance
ambit2.export.isa.json
ambit2.export.isa.v1_0

Uses of SubstanceEndpointsBundle in ambit2.base.data

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

Modifier and Type	Method and Description
static LiteratureEntry	LiteratureEntry.getBundleReference(SubstanceEndpointsBundle bundle)

Uses of SubstanceEndpointsBundle in ambit2.db.reporters

Fields in ambit2.db.reporters declared as SubstanceEndpointsBundle

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle[]	CSVReporter.bundles

Methods in ambit2.db.reporters that return SubstanceEndpointsBundle

Modifier and Type	Method and Description
SubstanceEndpointsBundle[]	CSVReporter.getBundles()

Methods in ambit2.db.reporters with parameters of type SubstanceEndpointsBundle

Modifier and Type	Method and Description
void	CSVReporter.setBundles(SubstanceEndpointsBundle[] bundles)

Constructors in ambit2.db.reporters with parameters of type SubstanceEndpointsBundle

Constructor and Description
CSVReporter(String baseRef, Template template, Profile groupedProperties, String[] folders, SubstanceEndpointsBundle[] bundles, String urlPrefix, boolean includeMol)

Uses of SubstanceEndpointsBundle in ambit2.db.reporters.xlsx

Constructors in ambit2.db.reporters.xlsx with parameters of type SubstanceEndpointsBundle

Constructor and Description
AbstractXLSXReporter(String baseRef, boolean hssf, Template template, Profile groupedProperties, SubstanceEndpointsBundle[] bundles, String urlPrefix, boolean includeMol)
StructureRecordXLSXReporter(String baseRef, boolean hssf, Template template, Profile groupedProperties, SubstanceEndpointsBundle[] bundles, String urlPrefix, boolean includeMol, String configResource)
SubstanceRecordXLSXReporter(String baseRef, boolean hssf, SubstanceEndpointsBundle[] bundles, String configResource)
SubstanceRecordXLSXReporter(String baseRef, boolean hssf, Template template, Profile groupedProperties, SubstanceEndpointsBundle[] bundles, String urlPrefix)

Uses of SubstanceEndpointsBundle in ambit2.db.substance

Fields in ambit2.db.substance declared as SubstanceEndpointsBundle

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle	QueryCountProtocolApplications.bundle

Methods in ambit2.db.substance that return SubstanceEndpointsBundle

Modifier and Type	Method and Description
SubstanceEndpointsBundle	QueryCountProtocolApplications.getBundle()

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

Modifier and Type	Method and Description
void	QueryCountProtocolApplications.setBundle(SubstanceEndpointsBundle bundle)

Uses of SubstanceEndpointsBundle in ambit2.db.substance.processor

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

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle	DBBundleStudyWriter.bundle

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

Modifier and Type	Method and Description
SubstanceEndpointsBundle	DBBundleStudyWriter.getBundle()

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

Modifier and Type	Method and Description
void	DBBundleStudyWriter.setBundle(SubstanceEndpointsBundle bundle)

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

Constructor and Description
DBBundleStudyWriter(SubstanceEndpointsBundle bundle, SourceDataset dataset, SubstanceRecord importedRecord)
DBMatrixValueMarker(SubstanceEndpointsBundle bundle)

Uses of SubstanceEndpointsBundle in ambit2.db.substance.relation

Fields in ambit2.db.substance.relation declared as SubstanceEndpointsBundle

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle	ReadSubstanceComposition.bundle

Methods in ambit2.db.substance.relation that return SubstanceEndpointsBundle

Modifier and Type	Method and Description
SubstanceEndpointsBundle	ReadSubstanceComposition.getBundle()

Methods in ambit2.db.substance.relation with parameters of type SubstanceEndpointsBundle

Modifier and Type	Method and Description
static CompositionRelation	ReadSubstanceComposition.readCompositionRelation(CompositionRelation record, ResultSet rs, SubstanceEndpointsBundle bundle)
void	ReadSubstanceComposition.setBundle(SubstanceEndpointsBundle bundle)

Uses of SubstanceEndpointsBundle in ambit2.db.substance.study

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

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle	UpdateEffectRecordsBundle.bundle
protected SubstanceEndpointsBundle	UpdateSubstanceStudyBundle.bundle

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

Modifier and Type	Method and Description
SubstanceEndpointsBundle	UpdateEffectRecordsBundle.getBundle()
SubstanceEndpointsBundle	UpdateSubstanceStudyBundle.getBundle()

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

Modifier and Type	Method and Description
void	UpdateEffectRecordsBundle.setBundle(SubstanceEndpointsBundle bundle)
void	UpdateSubstanceStudyBundle.setBundle(SubstanceEndpointsBundle bundle)

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

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

Uses of SubstanceEndpointsBundle in ambit2.db.update.bundle

Methods in ambit2.db.update.bundle that return SubstanceEndpointsBundle

Modifier and Type	Method and Description
protected SubstanceEndpointsBundle	ReadBundle.createObject(String title, LiteratureEntry le, String username)
SubstanceEndpointsBundle	ReadBundle.getObject(ResultSet rs)

Constructors in ambit2.db.update.bundle with parameters of type SubstanceEndpointsBundle

Constructor and Description
CreateBundle(SubstanceEndpointsBundle dataset)
CreateBundleCopy(SubstanceEndpointsBundle bundle)
CreateBundleVersion(SubstanceEndpointsBundle bundle)
DeleteBundle(SubstanceEndpointsBundle dataset)
DeleteBundle(SubstanceEndpointsBundle dataset, int stars)
UpdateBundle(SubstanceEndpointsBundle dataset)

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

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

Constructor and Description
AddAllChemicalsperSubstanceToBundle(SubstanceEndpointsBundle bundle, SubstanceRecord dataset)
AddChemicalToBundle(SubstanceEndpointsBundle bundle, IStructureRecord dataset)
DeleteChemicalsFromBundle(SubstanceEndpointsBundle bundle, IStructureRecord record)
ReadChemicalsByBundle(SubstanceEndpointsBundle bundle)

Uses of SubstanceEndpointsBundle in ambit2.db.update.bundle.effects

Fields in ambit2.db.update.bundle.effects declared as SubstanceEndpointsBundle

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle	ReadEffectRecordByBundle.bundle

Constructors in ambit2.db.update.bundle.effects with parameters of type SubstanceEndpointsBundle

Constructor and Description
ReadEffectRecordByBundle(SubstanceEndpointsBundle bundle)

Uses of SubstanceEndpointsBundle in ambit2.db.update.bundle.endpoints

Constructors in ambit2.db.update.bundle.endpoints with parameters of type SubstanceEndpointsBundle

Constructor and Description
AddEndpointToBundle(SubstanceEndpointsBundle bundle, SubstanceProperty property)
DeleteEndpointFromBundle(SubstanceEndpointsBundle bundle, SubstanceProperty property)

Uses of SubstanceEndpointsBundle in ambit2.db.update.bundle.matrix

Fields in ambit2.db.update.bundle.matrix declared as SubstanceEndpointsBundle

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle	ReadEffectRecordByBundleMatrix.bundle

Constructors in ambit2.db.update.bundle.matrix with parameters of type SubstanceEndpointsBundle

Constructor and Description
CreateMatrixFromBundle(SubstanceEndpointsBundle bundle, boolean deleteMatrix, ReadEffectRecordByBundleMatrix._matrix matrix)
CreateMatrixFromBundle(SubstanceEndpointsBundle bundle, ReadEffectRecordByBundleMatrix._matrix matrix)
DeleteMatrixFromBundle(SubstanceEndpointsBundle bundle)
DeleteMatrixProtocolApplicationValue(SubstanceEndpointsBundle bundle, ValueAnnotated<VALUE,String> value)
DeleteMatrixValue(SubstanceEndpointsBundle bundle, ValueAnnotated<VALUE,Integer> value)
ReadEffectRecordByBundleMatrix(SubstanceEndpointsBundle bundle, ReadEffectRecordByBundleMatrix._matrix matrix)

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

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

Modifier and Type	Method and Description
void	AddCompoundAsSubstanceToBundle.setGroup(SubstanceEndpointsBundle group)

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

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

Uses of SubstanceEndpointsBundle in ambit2.export.isa.json

Methods in ambit2.export.isa.json that return SubstanceEndpointsBundle

Modifier and Type	Method and Description
SubstanceEndpointsBundle	ISAJsonExporter.getEndpointBundle()

Methods in ambit2.export.isa.json with parameters of type SubstanceEndpointsBundle

Modifier and Type	Method and Description
void	ISAJsonExporter.setEndpointBundle(SubstanceEndpointsBundle endpointBundle)

Constructors in ambit2.export.isa.json with parameters of type SubstanceEndpointsBundle

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 SubstanceEndpointsBundle in ambit2.export.isa.v1_0

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

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